{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "## Access ClinVar Data from MyVariant.info Services" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "[ClinVar](http://www.clinvar.com/) is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. It is commonly used in genomics research and is also a very important data source included in [MyVariant.info](http://myvariant.info).\n", "\n", "[myvariant.py](https://pypi.python.org/pypi/myvariant) is an easy-to-use Python wrapper to access MyVariant.Info services. By utilizing myvariant.py, you can easily access ClinVar data with only a few lines of code. \n", "\n", "In this demo, we will show you how to use myvariant.py to query for ClinVar data by a few use cases." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Install myvariant.py\n", "Install myvariant.py is easy, as pip is your friend:\n", "\n", " pip install myvariant\n", "You can find more usage examples from [MyVariant.py PyPI page](https://pypi.python.org/pypi/myvariant). The detailed API documentation can be found at http://myvariant-py.readthedocs.org ." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now you just need to import it and instantiate **MyVariantInfo** class:" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "import myvariant\n", "mv = myvariant.MyVariantInfo()" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "### Retrieve ClinVar data of a variant or variants\n", "myvariant.py allows you to query for annotation information of a given variant or variants by calling **getvariant** or **getvariants** method. You can also customize the output by passing specific field name or names as parameters. For more information about field names available in MyVariant.info, please check [the detailed documentation](http://docs.myvariant.info/en/latest/doc/data.html#available-fields).\n", "\n", "* If you want to get available ClinVar annotation of a variant, you can pass an *hgvs id* and *'clinvar'* as the ***fields*** parameter to the **getvariant** method. Without ***fields*** parameter, you will get back all annotations available for the passed variant, including ClinVar." ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'_id': u'chr17:g.7578532A>G',\n", " u'_version': 1,\n", " u'clinvar': {u'allele_id': 27396,\n", " u'alt': u'G',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17p13.1',\n", " u'gene': {u'id': u'7157', u'symbol': u'TP53'},\n", " u'hg19': {u'end': 7578532, u'start': 7578532},\n", " u'hg38': {u'end': 7675214, u'start': 7675214},\n", " u'hgvs': {u'coding': [u'LRG_321t8:c.281T>C',\n", " u'LRG_321t5:c.2T>C',\n", " u'LRG_321t6:c.2T>C',\n", " u'LRG_321t7:c.2T>C',\n", " u'LRG_321t1:c.398T>C',\n", " u'LRG_321t2:c.398T>C',\n", " u'LRG_321t3:c.398T>C',\n", " u'LRG_321t4:c.398T>C',\n", " u'NM_001276697.1:c.-80T>C',\n", " u'NM_001126118.1:c.281T>C',\n", " u'NM_001126115.1:c.2T>C',\n", " u'NM_001126116.1:c.2T>C',\n", " u'NM_001126117.1:c.2T>C',\n", " u'NM_000546.5:c.398T>C',\n", " u'NM_001126112.2:c.398T>C',\n", " u'NM_001126113.2:c.398T>C',\n", " u'NM_001126114.2:c.398T>C'],\n", " u'genomic': [u'LRG_321:g.17337T>C',\n", " u'NG_017013.2:g.17337T>C',\n", " u'NC_000017.11:g.7675214A>G',\n", " u'NC_000017.10:g.7578532A>G']},\n", " u'omim': u'191170.0011',\n", " u'rcv': {u'accession': u'RCV000013151',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C1835398',\n", " u'omim': u'151623',\n", " u'orphanet': u'524'},\n", " u'name': u'Li-Fraumeni syndrome 1 (LFS1)'},\n", " u'last_evaluated': u'1999-01-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000546.5(TP53):c.398T>C (p.Met133Thr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'A',\n", " u'rsid': u'rs28934873',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 12357}}" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mv.getvariant('chr17:g.7578532A>G', fields = 'clinvar')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Suppose you want to retrieve the *clinvar variant id* of a variant, you can pass hgvs id and the speicific field name to the **getvariant** method." ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'_id': u'chr17:g.7578532A>G',\n", " u'_version': 1,\n", " u'clinvar': {u'variant_id': 12357}}" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mv.getvariant('chr17:g.7578532A>G', fields = 'clinvar.variant_id')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* You can also retreive annotation information of multiple fields for the same variant by calling the **getvariant** method. " ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [], "source": [ "out = mv.getvariant('chr17:g.7578532A>G', fields = ['clinvar.variant_id','clinvar.rcv.accession'])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " In this case, your output is clinvar *variant id* and *rcv accession number* of the variant." ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'_id': u'chr17:g.7578532A>G',\n", " u'_version': 1,\n", " u'clinvar': {u'rcv': {u'accession': u'RCV000013151'}, u'variant_id': 12357}}" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* One major advantage using MyVariant.info is that you can query fields from different data sources." ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true }, "outputs": [], "source": [ "out = mv.getvariant('chr6:g.26093141G>A', fields = ['clinvar.rcv.accession', 'exac.af', 'dbnsfp.sift.converted_rankscore'])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " Here, you get the *rcv accession number* from ClinVar, *allele frequency* information from EXAC and *sift converted_rankscore* from dbnsfp for your target variant as the output." ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'_id': u'chr6:g.26093141G>A',\n", " u'_version': 1,\n", " u'clinvar': {u'rcv': [{u'accession': u'RCV000000019'},\n", " {u'accession': u'RCV000000020'},\n", " {u'accession': u'RCV000000021'},\n", " {u'accession': u'RCV000000022'},\n", " {u'accession': u'RCV000000023'},\n", " {u'accession': u'RCV000000024'},\n", " {u'accession': u'RCV000000025'},\n", " {u'accession': u'RCV000117222'},\n", " {u'accession': u'RCV000178096'}]},\n", " u'dbnsfp': {u'sift': {u'converted_rankscore': 0.91219}},\n", " u'exac': {u'af': 0.032}}" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* To retrieve annotation objects for a list of hgvs ids, you can call the **getvariants** methods." ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "querying 1-2...done.\n" ] } ], "source": [ "out = mv.getvariants(['chr6:g.26093141G>A', 'chr11:g.118896012A>G'], fields = 'clinvar.gene.symbol')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " Here, your output is the *gene symbol* of both variants." ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "[{u'_id': u'chr6:g.26093141G>A',\n", " u'_score': 1.0,\n", " u'clinvar': {u'gene': {u'symbol': u'HFE'}},\n", " u'query': u'chr6:g.26093141G>A'},\n", " {u'_id': u'chr11:g.118896012A>G',\n", " u'_score': 1.0,\n", " u'clinvar': {u'gene': {u'symbol': u'SLC37A4'}},\n", " u'query': u'chr11:g.118896012A>G'}]" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Make queries based on a specific ClinVar field or fields\n", "myvariant.py also allows you to query for a specific field or fields in MyVariant.info.\n", "\n", "* You can make query based on a single RCV accession number." ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'hits': [{u'_id': u'chr17:g.7578532A>G',\n", " u'_score': 16.53367,\n", " u'cadd': {u'_license': u'http://goo.gl/bkpNhq',\n", " u'alt': u'G',\n", " u'anc': u'A',\n", " u'annotype': u'CodingTranscript',\n", " u'bstatistic': 473,\n", " u'chmm': {u'bivflnk': 0.0,\n", " u'enh': 0.008,\n", " u'enhbiv': 0.0,\n", " u'het': 0.0,\n", " u'quies': 0.008,\n", " u'reprpc': 0.0,\n", " u'reprpcwk': 0.0,\n", " u'tssa': 0.0,\n", " u'tssaflnk': 0.0,\n", " u'tssbiv': 0.0,\n", " u'tx': 0.819,\n", " u'txflnk': 0.0,\n", " u'txwk': 0.11,\n", " u'znfrpts': 0.055},\n", " u'chrom': 17,\n", " u'consdetail': u'missense',\n", " u'consequence': u'NON_SYNONYMOUS',\n", " u'consscore': 7,\n", " u'cpg': 0.07,\n", " u'dna': {u'helt': 0.01, u'mgw': 0.24, u'prot': 4.04, u'roll': 1.29},\n", " u'encode': {u'exp': 1100.13,\n", " u'h3k27ac': 6.2,\n", " u'h3k4me1': 16.04,\n", " u'h3k4me3': 3.08,\n", " u'nucleo': 1.8},\n", " u'exon': u'5/11',\n", " u'fitcons': 0.726386,\n", " u'gc': 0.58,\n", " u'gene': {u'ccds_id': u'CCDS11118.1',\n", " u'cds': {u'cdna_pos': 588,\n", " u'cds_pos': 398,\n", " u'rel_cdna_pos': 0.23,\n", " u'rel_cds_pos': 0.34},\n", " u'feature_id': u'ENST00000269305',\n", " u'gene_id': u'ENSG00000141510',\n", " u'genename': u'TP53',\n", " u'prot': {u'domain': u'ndomain', u'protpos': 133, u'rel_prot_pos': 0.34}},\n", " u'gerp': {u'n': 5.48, u'rs': 367.5, u'rs_pval': 1.53237e-26, u's': 5.48},\n", " u'grantham': 81,\n", " u'isderived': u'TRUE',\n", " u'isknownvariant': u'FALSE',\n", " u'istv': u'FALSE',\n", " u'length': 0,\n", " u'mapability': {u'20bp': 1, u'35bp': 1},\n", " u'min_dist_tse': 16,\n", " u'min_dist_tss': 95,\n", " u'mutindex': 34,\n", " u'naa': u'T',\n", " u'oaa': u'M',\n", " u'phast_cons': {u'mammalian': 0.998,\n", " u'primate': 0.809,\n", " u'vertebrate': 1.0},\n", " u'phred': 23.5,\n", " u'phylop': {u'mammalian': 2.204, u'primate': 0.53, u'vertebrate': 4.641},\n", " u'polyphen': {u'cat': u'benign', u'val': 0.237},\n", " u'pos': 7578532,\n", " u'rawscore': 3.913993,\n", " u'ref': u'A',\n", " u'segway': u'TF2',\n", " u'sift': {u'cat': u'deleterious', u'val': 0},\n", " u'type': u'SNV'},\n", " u'clinvar': {u'allele_id': 27396,\n", " u'alt': u'G',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17p13.1',\n", " u'gene': {u'id': u'7157', u'symbol': u'TP53'},\n", " u'hg19': {u'end': 7578532, u'start': 7578532},\n", " u'hg38': {u'end': 7675214, u'start': 7675214},\n", " u'hgvs': {u'coding': [u'LRG_321t8:c.281T>C',\n", " u'LRG_321t5:c.2T>C',\n", " u'LRG_321t6:c.2T>C',\n", " u'LRG_321t7:c.2T>C',\n", " u'LRG_321t1:c.398T>C',\n", " u'LRG_321t2:c.398T>C',\n", " u'LRG_321t3:c.398T>C',\n", " u'LRG_321t4:c.398T>C',\n", " u'NM_001276697.1:c.-80T>C',\n", " u'NM_001126118.1:c.281T>C',\n", " u'NM_001126115.1:c.2T>C',\n", " u'NM_001126116.1:c.2T>C',\n", " u'NM_001126117.1:c.2T>C',\n", " u'NM_000546.5:c.398T>C',\n", " u'NM_001126112.2:c.398T>C',\n", " u'NM_001126113.2:c.398T>C',\n", " u'NM_001126114.2:c.398T>C'],\n", " u'genomic': [u'LRG_321:g.17337T>C',\n", " u'NG_017013.2:g.17337T>C',\n", " u'NC_000017.11:g.7675214A>G',\n", " u'NC_000017.10:g.7578532A>G']},\n", " u'omim': u'191170.0011',\n", " u'rcv': {u'accession': u'RCV000013151',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C1835398',\n", " u'omim': u'151623',\n", " u'orphanet': u'524'},\n", " u'name': u'Li-Fraumeni syndrome 1 (LFS1)'},\n", " u'last_evaluated': u'1999-01-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000546.5(TP53):c.398T>C (p.Met133Thr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'A',\n", " u'rsid': u'rs28934873',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 12357},\n", " u'cosmic': {u'alt': u'C',\n", " u'chrom': u'17',\n", " u'cosmic_id': u'COSM43723',\n", " u'hg19': {u'end': 7578532, u'start': 7578532},\n", " u'mut_freq': 0.03,\n", " u'mut_nt': u'T>C',\n", " u'ref': u'T',\n", " u'tumor_site': u'stomach'},\n", " u'dbnsfp': {u'aa': {u'alt': u'T',\n", " u'codonpos': 2,\n", " u'pos': [u'133',\n", " u'133',\n", " u'1',\n", " u'1',\n", " u'1',\n", " u'94',\n", " u'133',\n", " u'94',\n", " u'133',\n", " u'133',\n", " u'133',\n", " u'94',\n", " u'94',\n", " u'133',\n", " u'94',\n", " u'122',\n", " u'1',\n", " u'40',\n", " u'133',\n", " u'126'],\n", " u'ref': u'M',\n", " u'refcodon': u'ATG'},\n", " u'alt': u'G',\n", " u'ancestral_allele': u'A',\n", " u'cds_strand': u'-',\n", " u'chrom': u'17',\n", " u'clinvar': {u'clinsig': 5,\n", " u'rs': u'rs28934873',\n", " u'trait': u'Li-Fraumeni_syndrome_1'},\n", " u'ensembl': {u'geneid': u'ENSG00000141510',\n", " u'proteinid': [u'ENSP00000410739',\n", " u'ENSP00000352610',\n", " u'ENSP00000484409',\n", " u'ENSP00000478499',\n", " u'ENSP00000481179',\n", " u'ENSP00000478219',\n", " u'ENSP00000269305',\n", " u'ENSP00000481638',\n", " u'ENSP00000482258',\n", " u'ENSP00000398846',\n", " u'ENSP00000391127',\n", " u'ENSP00000482222',\n", " u'ENSP00000480868',\n", " u'ENSP00000391478',\n", " u'ENSP00000482537',\n", " u'ENSP00000482903',\n", " u'ENSP00000425104',\n", " u'ENSP00000423862',\n", " u'ENSP00000424104',\n", " u'ENSP00000473895'],\n", " u'transcriptid': [u'ENST00000413465',\n", " u'ENST00000359597',\n", " u'ENST00000504290',\n", " u'ENST00000510385',\n", " u'ENST00000504937',\n", " u'ENST00000610292',\n", " u'ENST00000269305',\n", " u'ENST00000620739',\n", " u'ENST00000617185',\n", " u'ENST00000455263',\n", " u'ENST00000420246',\n", " u'ENST00000622645',\n", " u'ENST00000610538',\n", " u'ENST00000445888',\n", " u'ENST00000619485',\n", " u'ENST00000615910',\n", " u'ENST00000509690',\n", " u'ENST00000514944',\n", " u'ENST00000508793',\n", " u'ENST00000604348']},\n", " u'fathmm': {u'pred': [u'D',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'D',\n", " u'D',\n", " u'.'],\n", " u'rankscore': 0.99768,\n", " u'score': [-6.7,\n", " -6.7,\n", " None,\n", " None,\n", " None,\n", " None,\n", " -6.7,\n", " None,\n", " None,\n", " -6.7,\n", " -6.7,\n", " None,\n", " None,\n", " -6.7,\n", " None,\n", " None,\n", " -6.7,\n", " -6.7,\n", " -6.7,\n", " None]},\n", " u'fathmm-mkl': {u'coding_group': u'AEFDGBHI',\n", " u'coding_pred': u'D',\n", " u'coding_rankscore': 0.99134,\n", " u'coding_score': 0.99744},\n", " u'genename': u'TP53',\n", " u'gerp++': {u'nr': 5.48, u'rs': 5.48, u'rs_rankscore': 0.80555},\n", " u'gm12878': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.74317,\n", " u'fitcons_score': 0.702456},\n", " u'h1-hesc': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.64003,\n", " u'fitcons_score': 0.697927},\n", " u'hg18': {u'end': 7519257, u'start': 7519257},\n", " u'hg19': {u'end': 7578532, u'start': 7578532},\n", " u'hg38': {u'end': 7675214, u'start': 7675214},\n", " u'huvec': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.98419,\n", " u'fitcons_score': 0.735409},\n", " u'integrated': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.85317,\n", " u'fitcons_score': 0.722319},\n", " u'interpro_domain': [u'p53, DNA-binding domain',\n", " u'p53-like transcription factor, DNA-binding',\n", " u'p53/RUNT-type transcription factor, DNA-binding domain'],\n", " u'lrt': {u'converted_rankscore': 0.55863,\n", " u'omega': 0.072317,\n", " u'pred': u'D',\n", " u'score': 3.6e-05},\n", " u'metalr': {u'pred': u'D', u'rankscore': 0.99123, u'score': 0.972},\n", " u'metasvm': {u'pred': u'D', u'rankscore': 0.99543, u'score': 1.0972},\n", " u'mutationassessor': {u'pred': u'N', u'rankscore': 0.08161, u'score': 0},\n", " u'mutationtaster': {u'AAE': u'M133T',\n", " u'converted_rankscore': 0.38995,\n", " u'model': u'simple_aae',\n", " u'pred': u'A',\n", " u'score': 0.973129},\n", " u'phastcons': {u'20way': {u'mammalian': 0.996,\n", " u'mammalian_rankscore': 0.62353},\n", " u'7way': {u'vertebrate': 0.989, u'vertebrate_rankscore': 0.5315}},\n", " u'phylo': {u'p20way': {u'mammalian': 1.199,\n", " u'mammalian_rankscore': 0.95998},\n", " u'p7way': {u'vertebrate': 1.062, u'vertebrate_rankscore': 0.92612}},\n", " u'polyphen2': {u'hdiv': {u'pred': [u'P',\n", " u'B',\n", " u'B',\n", " u'B',\n", " u'B',\n", " u'B',\n", " u'P'],\n", " u'rankscore': 0.39305,\n", " u'score': [0.551, 0.002, 0.004, 0.044, 0.001, 0.003, 0.674]},\n", " u'hvar': {u'pred': [u'P', u'B', u'B', u'P', u'B', u'B', u'P'],\n", " u'rankscore': 0.59325,\n", " u'score': [0.804, 0.11, 0.062, 0.684, 0.113, 0.176, 0.858]}},\n", " u'provean': {u'pred': [u'D',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'.',\n", " u'.',\n", " u'D',\n", " u'D',\n", " u'D',\n", " u'.'],\n", " u'rankscore': 0.62478,\n", " u'score': [-2.93,\n", " -2.92,\n", " None,\n", " None,\n", " None,\n", " None,\n", " -3.01,\n", " None,\n", " None,\n", " -2.92,\n", " -2.92,\n", " None,\n", " None,\n", " -3.01,\n", " None,\n", " None,\n", " -2.76,\n", " -2.92,\n", " -2.96,\n", " None]},\n", " u'ref': u'A',\n", " u'reliability_index': 9,\n", " u'rsid': u'rs28934873',\n", " u'sift': {u'converted_rankscore': 0.91219,\n", " u'pred': [u'D',\n", " u'D',\n", " 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u'A'}, {u'allele': u'G'}],\n", " u'alt': u'G',\n", " u'chrom': u'17',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 133,\n", " u'flags': [u'ASP',\n", " u'LSD',\n", " u'NSM',\n", " u'PM',\n", " u'PMC',\n", " u'REF',\n", " u'RV',\n", " u'S3D',\n", " u'U5'],\n", " u'gene': {u'geneid': u'7157', u'symbol': u'TP53'},\n", " u'hg19': {u'end': 7578533, u'start': 7578532},\n", " u'ref': u'A',\n", " u'rsid': u'rs28934873',\n", " u'validated': False,\n", " u'var_subtype': u'ts',\n", " u'vartype': u'snp'},\n", " u'mutdb': {u'alt': u'C',\n", " u'chrom': u'17',\n", " u'cosmic_id': u'43723',\n", " u'hg19': {u'end': 7578532, u'start': 7578532},\n", " u'mutpred_score': 0.74,\n", " u'ref': u'T',\n", " u'rsid': u'rs28934873',\n", " u'strand': u'm'},\n", " u'snpeff': {u'ann': [{u'cdna': {u'length': u'2271', u'position': u'280'},\n", " u'cds': {u'length': u'786', u'position': u'2'},\n", " u'effect': u'start_lost',\n", " u'feature_id': u'NM_001126115.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.2T>C',\n", " u'hgvs_p': u'p.Met1?',\n", " u'protein': {u'length': u'261', u'position': u'1'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'1',\n", " u'total': u'7',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2404', u'position': u'280'},\n", " u'cds': {u'length': u'630', u'position': u'2'},\n", " u'effect': u'start_lost',\n", " u'feature_id': u'NM_001126116.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.2T>C',\n", " u'hgvs_p': u'p.Met1?',\n", " u'protein': {u'length': u'209', u'position': u'1'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'1',\n", " u'total': u'8',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2331', u'position': u'280'},\n", " u'cds': {u'length': u'645', u'position': u'2'},\n", " u'effect': u'start_lost',\n", " u'feature_id': u'NM_001126117.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.2T>C',\n", " u'hgvs_p': u'p.Met1?',\n", " u'protein': {u'length': u'214', u'position': u'1'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'1',\n", " u'total': u'8',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2591', u'position': u'600'},\n", " u'cds': {u'length': u'1182', u'position': u'398'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_000546.5',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.398T>C',\n", " u'hgvs_p': u'p.Met133Thr',\n", " u'protein': {u'length': u'393', u'position': u'133'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'11',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2588', u'position': u'597'},\n", " u'cds': {u'length': u'1182', u'position': u'398'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001126112.2',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.398T>C',\n", " u'hgvs_p': u'p.Met133Thr',\n", " u'protein': {u'length': u'393', u'position': u'133'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'11',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2651', u'position': u'600'},\n", " u'cds': {u'length': u'1041', u'position': u'398'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001126113.2',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.398T>C',\n", " u'hgvs_p': u'p.Met133Thr',\n", " u'protein': {u'length': u'346', u'position': u'133'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'12',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2724', u'position': u'600'},\n", " u'cds': {u'length': u'1026', u'position': u'398'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001126114.2',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.398T>C',\n", " u'hgvs_p': u'p.Met133Thr',\n", " u'protein': {u'length': u'341', u'position': u'133'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'12',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2708', u'position': u'717'},\n", " u'cds': {u'length': u'1065', u'position': u'281'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001126118.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.281T>C',\n", " u'hgvs_p': u'p.Met94Thr',\n", " u'protein': {u'length': u'354', u'position': u'94'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'4',\n", " u'total': u'10',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2651', u'position': u'600'},\n", " u'cds': {u'length': u'924', u'position': u'281'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001276695.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.281T>C',\n", " u'hgvs_p': u'p.Met94Thr',\n", " u'protein': {u'length': u'307', u'position': u'94'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'12',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2724', u'position': u'600'},\n", " u'cds': {u'length': u'909', u'position': u'281'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001276696.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.281T>C',\n", " u'hgvs_p': u'p.Met94Thr',\n", " u'protein': {u'length': u'302', u'position': u'94'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'12',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2591', u'position': u'600'},\n", " u'cds': {u'length': u'1065', u'position': u'281'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001276760.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.281T>C',\n", " u'hgvs_p': u'p.Met94Thr',\n", " u'protein': {u'length': u'354', u'position': u'94'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'11',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2588', u'position': u'597'},\n", " u'cds': {u'length': u'1065', u'position': u'281'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_001276761.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.281T>C',\n", " u'hgvs_p': u'p.Met94Thr',\n", " u'protein': {u'length': u'354', u'position': u'94'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'5',\n", " u'total': u'11',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'80',\n", " u'effect': u'5_prime_UTR_variant',\n", " u'feature_id': u'NM_001276697.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.-80T>C',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'1',\n", " u'total': u'7',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'80',\n", " u'effect': u'5_prime_UTR_variant',\n", " u'feature_id': u'NM_001276698.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.-80T>C',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'1',\n", " u'total': u'8',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'80',\n", " u'effect': u'5_prime_UTR_variant',\n", " u'feature_id': u'NM_001276699.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'hgvs_c': u'c.-80T>C',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'1',\n", " u'total': u'8',\n", " u'transcript_biotype': u'Coding'}],\n", " u'lof': {u'gene_id': u'TP53',\n", " u'gene_name': u'TP53',\n", " u'number_of_transcripts_in_gene': u'15',\n", " u'percent_of_transcripts_affected': u'0.20'}},\n", " u'vcf': {u'alt': u'G', u'position': u'7578532', u'ref': u'A'}}],\n", " u'max_score': 16.53367,\n", " u'took': 21,\n", " u'total': 1}" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mv.query('clinvar.rcv.accession:RCV000013151')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Now, let's assume you are working on cancer genomics and BRCA1 is your target gene. If you want to get all annotation information of variants located on BRCA1 and recorded in ClinVar, you can pass *clinvar gene symbol* parameter to the **query** method." ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "out = mv.query('clinvar.gene.symbol:BRCA1')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " By default, the output lists the top 10 hits among 3532 unique variants recorded in ClinVar related to BRCA1. " ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'hits': [{u'_id': u'NM_007294.3:c.4358-?_5277+?del',\n", " u'_score': 12.69064,\n", " u'clinvar': {u'allele_id': 94606,\n", " u'chrom': u'17',\n", " u'coding_hgvs_only': True,\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.4358-?_5277+?del',\n", " u'NM_007294.3:c.4358-?_5277+?del'],\n", " u'genomic': [u'LRG_292:g.(?_141370_160932_?)del',\n", " u'NC_000017.11:g.(?_43057052)_(43076614_?)del',\n", " u'NC_000017.10:g.(?_41209069)_(41228631_?)del']},\n", " u'rcv': [{u'accession': u'RCV000119187',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0677776'},\n", " u'name': u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer (HBOC)',\n", " u'synonyms': [u'q', u'Hereditary breast and ovarian cancer syndrome']},\n", " u'last_evaluated': u'2014-03-27',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000074593',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0346153',\n", " u'omim': u'114480'},\n", " u'name': u'Familial cancer of breast',\n", " u'synonyms': [u'CHEK2-Related Breast Cancer',\n", " u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',\n", " u'review_status': u'criteria provided, single submitter'}],\n", " u'type': u'Deletion',\n", " u'variant_id': 89063}},\n", " {u'_id': u'chr17:g.41197590_41197593del',\n", " u'_score': 12.69064,\n", " u'clinvar': {u'allele_id': 102794,\n", " u'alt': u'-',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41197593, u'start': 41197590},\n", " u'hg38': {u'end': 43045576, u'start': 43045573},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',\n", " u'NM_007294.3:c.*102_*105delCTGT'],\n", " u'genomic': [u'LRG_292:g.172408_172411delCTGT',\n", " u'NG_005905.2:g.172408_172411delCTGT',\n", " u'NC_000017.11:g.43045573_43045576delACAG',\n", " u'NC_000017.10:g.41197590_41197593delACAG']},\n", " u'rcv': {u'accession': u'RCV000083012',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C2676676',\n", " u'omim': u'604370',\n", " u'orphanet': u'145'},\n", " u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',\n", " u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'OVARIAN CANCER, SUSCEPTIBILITY TO',\n", " u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'Breast cancer, familial 1',\n", " u'hereditary breast and ovarian cancer, BROVCA1',\n", " u'Breast-ovarian cancer, familial, 1']},\n", " u'last_evaluated': u'2011-10-17',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.*102_*105delCTGT',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'ACAG',\n", " u'rsid': u'rs431825382',\n", " u'type': u'Deletion',\n", " u'variant_id': 96891},\n", " u'snpeff': {u'ann': [{u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*102_*105delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'24',\n", " u'total': u'24',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': 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u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41199702, u'start': 41199702},\n", " u'hg38': {u'end': 43047685, u'start': 43047685},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.5425G>T', u'NM_007294.3:c.5425G>T'],\n", " u'genomic': [u'LRG_292:g.170299G>T',\n", " u'NG_005905.2:g.170299G>T',\n", " u'NC_000017.11:g.43047685C>A',\n", " u'NC_000017.10:g.41199702C>A']},\n", " u'rcv': [{u'accession': u'RCV000048988',\n", " u'clinical_significance': u'not provided',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0346153',\n", " u'omim': u'114480'},\n", " u'name': u'Familial cancer of breast',\n", " u'synonyms': [u'CHEK2-Related Breast Cancer',\n", " u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},\n", " u'last_evaluated': u'2013-02-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.5425G>T (p.Val1809Phe)',\n", " u'review_status': u'no assertion provided'},\n", " {u'accession': u'RCV000112651',\n", " u'clinical_significance': u'Uncertain significance',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C2676676',\n", " u'omim': u'604370',\n", " u'orphanet': u'145'},\n", " u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',\n", " u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'OVARIAN CANCER, SUSCEPTIBILITY TO',\n", " u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'Breast cancer, familial 1',\n", " u'hereditary breast and ovarian cancer, BROVCA1',\n", " u'Breast-ovarian cancer, familial, 1']},\n", " u'last_evaluated': u'2002-05-29',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.5425G>T (p.Val1809Phe)',\n", " u'review_status': u'no assertion criteria provided'}],\n", " u'ref': u'C',\n", " u'rsid': u'rs28897698',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 55573},\n", " u'dbnsfp': 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[u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae',\n", " u'simple_aae'],\n", " u'pred': [u'D',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N',\n", " u'N'],\n", " u'score': [0.978687,\n", " 0.64294,\n", " 0.574257,\n", " 0.574257,\n", " 0.713266,\n", " 0.617361,\n", " 0.64294,\n", " 0.574257,\n", " 0.995933,\n", " 0.574257,\n", " 0.995933,\n", " 0.574257,\n", " 0.574257,\n", " 0.931237]},\n", " u'phastcons': {u'20way': {u'mammalian': 0.615,\n", " u'mammalian_rankscore': 0.2897},\n", " u'7way': {u'vertebrate': 0.244, u'vertebrate_rankscore': 0.21102}},\n", " u'phylo': {u'p20way': {u'mammalian': 0.022,\n", " u'mammalian_rankscore': 0.14435},\n", " u'p7way': {u'vertebrate': -0.621, u'vertebrate_rankscore': 0.03621}},\n", " u'polyphen2': {u'hdiv': {u'pred': u'P',\n", " u'rankscore': 0.50293,\n", " u'score': 0.935},\n", " u'hvar': {u'pred': u'P', u'rankscore': 0.45284, u'score': 0.481}},\n", " u'provean': {u'pred': u'N', u'rankscore': 0.0336, u'score': 0.42},\n", " u'ref': u'C',\n", " u'reliability_index': 9,\n", " u'rsid': u'rs28897698',\n", " u'sift': {u'converted_rankscore': 0.91219, u'pred': u'D', u'score': 0.0},\n", " u'siphy_29way': {u'logodds': 6.5492,\n", " u'logodds_rankscore': 0.21406,\n", " u'pi': {u'a': 0.0, u'c': 0.7208, u'g': 0.1826, u't': 0.0966}},\n", " u'uniprot': {u'acc': u'Q6IN79', u'pos': u'680'}},\n", " u'dbsnp': {u'allele_origin': u'unspecified',\n", " u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}],\n", " u'alt': u'A',\n", " u'chrom': u'17',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 125,\n", " u'flags': [u'ASP',\n", " u'HD',\n", " u'LSD',\n", " u'NSM',\n", " u'PM',\n", " u'REF',\n", " u'RV',\n", " u'S3D',\n", " u'SLO'],\n", " u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41199703, u'start': 41199702},\n", " u'ref': u'C',\n", " u'rsid': u'rs28897698',\n", " u'validated': False,\n", " u'var_subtype': u'tv',\n", " u'vartype': u'snp'},\n", " u'mutdb': {u'alt': u'T',\n", " u'chrom': u'17',\n", " u'hg19': {u'end': 41199702, u'start': 41199702},\n", " u'mutpred_score': 0.797,\n", " u'ref': u'G',\n", " u'rsid': u'rs28897698',\n", " u'strand': u'm'},\n", " u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5720'},\n", " u'cds': {u'length': u'5655', u'position': u'5488'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5488G>T',\n", " u'hgvs_p': u'p.Val1830Phe',\n", " u'protein': {u'length': u'1884', u'position': u'1830'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'23',\n", " u'total': u'24',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'3682', u'position': u'2132'},\n", " u'cds': {u'length': u'2280', u'position': u'2113'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.2113G>T',\n", " u'hgvs_p': u'p.Val705Phe',\n", " u'protein': {u'length': u'759', u'position': u'705'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'21',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'7115', u'position': u'5565'},\n", " u'cds': {u'length': u'5451', u'position': u'5284'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007297.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5284G>T',\n", " u'hgvs_p': u'p.Val1762Phe',\n", " u'protein': {u'length': u'1816', u'position': u'1762'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'21',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'3783', u'position': u'2233'},\n", " u'cds': {u'length': u'2100', u'position': u'2039'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007299.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.2039G>T',\n", " u'hgvs_p': u'p.Gly680Val',\n", " u'protein': {u'length': u'699', u'position': u'680'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'21',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'7207', u'position': u'5657'},\n", " u'cds': {u'length': u'5592', u'position': u'5425'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007294.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5425G>T',\n", " u'hgvs_p': u'p.Val1809Phe',\n", " u'protein': {u'length': u'1863', u'position': u'1809'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'22',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'non_coding_exon_variant',\n", " u'feature_id': u'NR_027676.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'n.5561G>T',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'22',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Noncoding'}]},\n", " u'vcf': {u'alt': u'A', u'position': u'41199702', u'ref': u'C'}}],\n", " u'max_score': 12.69064,\n", " u'took': 17,\n", " u'total': 3532}" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* You can also set the output size to numbers other than 10. " ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'hits': [{u'_id': u'NM_007294.3:c.4358-?_5277+?del',\n", " u'_score': 12.69064,\n", " u'clinvar': {u'allele_id': 94606,\n", " u'chrom': u'17',\n", " u'coding_hgvs_only': True,\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.4358-?_5277+?del',\n", " u'NM_007294.3:c.4358-?_5277+?del'],\n", " u'genomic': [u'LRG_292:g.(?_141370_160932_?)del',\n", " u'NC_000017.11:g.(?_43057052)_(43076614_?)del',\n", " u'NC_000017.10:g.(?_41209069)_(41228631_?)del']},\n", " u'rcv': [{u'accession': u'RCV000119187',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0677776'},\n", " u'name': u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer (HBOC)',\n", " u'synonyms': [u'q', u'Hereditary breast and ovarian cancer syndrome']},\n", " u'last_evaluated': u'2014-03-27',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000074593',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0346153',\n", " u'omim': u'114480'},\n", " u'name': u'Familial cancer of breast',\n", " u'synonyms': [u'CHEK2-Related Breast Cancer',\n", " u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',\n", " u'review_status': u'criteria provided, single submitter'}],\n", " u'type': u'Deletion',\n", " u'variant_id': 89063}},\n", " {u'_id': u'chr17:g.41197590_41197593del',\n", " u'_score': 12.69064,\n", " u'clinvar': {u'allele_id': 102794,\n", " u'alt': u'-',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41197593, u'start': 41197590},\n", " u'hg38': {u'end': 43045576, u'start': 43045573},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',\n", " u'NM_007294.3:c.*102_*105delCTGT'],\n", " u'genomic': [u'LRG_292:g.172408_172411delCTGT',\n", " u'NG_005905.2:g.172408_172411delCTGT',\n", " u'NC_000017.11:g.43045573_43045576delACAG',\n", " u'NC_000017.10:g.41197590_41197593delACAG']},\n", " u'rcv': {u'accession': u'RCV000083012',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C2676676',\n", " u'omim': u'604370',\n", " u'orphanet': u'145'},\n", " u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',\n", " u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'OVARIAN CANCER, SUSCEPTIBILITY TO',\n", " u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'Breast cancer, familial 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{u'pred': [u'N', u'N', u'.', u'.', u'.', u'N', u'N', u'N'],\n", " u'rankscore': 0.53216,\n", " u'score': [-0.55, -2.43, None, None, None, -0.54, -0.49, -2.43]},\n", " u'ref': u'C',\n", " u'reliability_index': 10,\n", " u'rsid': u'rs80357268',\n", " u'sift': {u'converted_rankscore': 0.91219,\n", " u'pred': [u'D', u'D', u'.', u'.', u'.', u'D', u'D', u'D'],\n", " u'score': [0.0, 0.001, None, None, None, 0.0, 0.002, 0.001]},\n", " u'siphy_29way': {u'logodds': 14.3724,\n", " u'logodds_rankscore': 0.66207,\n", " u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}},\n", " u'uniprot': [{u'acc': u'B4DES0', u'pos': u'682'},\n", " {u'acc': u'C6YB45', u'pos': u'143'},\n", " {u'acc': u'E7ETR2', u'pos': u'728'},\n", " {u'acc': u'E9PFC7', u'pos': u'1855'},\n", " {u'acc': u'P38398', u'pos': u'1833'},\n", " {u'acc': u'P38398-2', u'pos': u'1833'}]},\n", " u'dbsnp': {u'allele_origin': u'unspecified',\n", " u'alleles': [{u'allele': u'C'}, {u'allele': u'T'}],\n", " u'alt': u'T',\n", " u'chrom': u'17',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 132,\n", " u'flags': [u'ASP',\n", " u'LSD',\n", " u'NSM',\n", " u'PM',\n", " u'REF',\n", " u'RV',\n", " u'S3D',\n", " u'SLO',\n", " u'U3'],\n", " u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41197791, u'start': 41197790},\n", " u'ref': u'C',\n", " u'rsid': u'rs80357268',\n", " u'validated': False,\n", " u'var_subtype': u'ts',\n", " u'vartype': u'snp'},\n", " u'mutdb': {u'alt': u'A',\n", " u'chrom': u'17',\n", " u'hg19': {u'end': 41197790, u'start': 41197790},\n", " u'mutpred_score': 0.585,\n", " u'ref': u'G',\n", " u'rsid': u'rs80357268',\n", " u'strand': u'm'},\n", " u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5792'},\n", " u'cds': {u'length': u'5655', u'position': u'5560'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5560G>A',\n", " u'hgvs_p': u'p.Val1854Met',\n", " u'protein': {u'length': u'1884', u'position': u'1854'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'24',\n", " u'total': u'24',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'3682', u'position': u'2204'},\n", " u'cds': {u'length': u'2280', u'position': u'2185'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.2185G>A',\n", " u'hgvs_p': u'p.Val729Met',\n", " u'protein': {u'length': u'759', u'position': u'729'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'7115', u'position': u'5637'},\n", " u'cds': {u'length': u'5451', u'position': u'5356'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007297.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5356G>A',\n", " u'hgvs_p': u'p.Val1786Met',\n", " u'protein': {u'length': u'1816', u'position': u'1786'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'7207', u'position': u'5729'},\n", " u'cds': {u'length': u'5592', u'position': u'5497'},\n", " u'effect': u'missense_variant',\n", " u'feature_id': u'NM_007294.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5497G>A',\n", " u'hgvs_p': u'p.Val1833Met',\n", " u'protein': {u'length': u'1863', u'position': u'1833'},\n", " u'putative_impact': u'MODERATE',\n", " u'rank': u'23',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'11',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007299.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*11G>A',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'non_coding_exon_variant',\n", " u'feature_id': u'NR_027676.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'n.5633G>A',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'23',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Noncoding'}]},\n", " u'vcf': {u'alt': u'T', u'position': u'41197790', u'ref': u'C'}}],\n", " u'max_score': 12.69064,\n", " u'took': 4,\n", " u'total': 3532}" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mv.query('clinvar.gene.symbol:BRCA1', size=5)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* Otherwise, you can also choose to return a [generator](https://docs.python.org/3.5/library/stdtypes.html#generator-types) to retrieve all the query results." ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mv.query('clinvar.gene.symbol:BRCA1',fetch_all=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* If you want to filter for all BRCA1 related variants that are defined as pathogenic in ClinVar, you can pass *gene symbol* and *clinical significance* parameters to the **query** method. " ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true }, "outputs": [], "source": [ "out = mv.query('clinvar.gene.symbol:BRCA1 AND clinvar.rcv.clinical_significance:pathogenic')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " Now, only 1126 variants are left matching these two criteria." ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "{u'hits': [{u'_id': u'chr17:g.41197590_41197593del',\n", " u'_score': 15.629933,\n", " u'clinvar': {u'allele_id': 102794,\n", " u'alt': u'-',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41197593, u'start': 41197590},\n", " u'hg38': {u'end': 43045576, u'start': 43045573},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',\n", " u'NM_007294.3:c.*102_*105delCTGT'],\n", " u'genomic': [u'LRG_292:g.172408_172411delCTGT',\n", " u'NG_005905.2:g.172408_172411delCTGT',\n", " u'NC_000017.11:g.43045573_43045576delACAG',\n", " u'NC_000017.10:g.41197590_41197593delACAG']},\n", " u'rcv': {u'accession': u'RCV000083012',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C2676676',\n", " u'omim': u'604370',\n", " u'orphanet': u'145'},\n", " u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',\n", " u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'OVARIAN CANCER, SUSCEPTIBILITY TO',\n", " u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'Breast cancer, familial 1',\n", " u'hereditary breast and ovarian cancer, BROVCA1',\n", " u'Breast-ovarian cancer, familial, 1']},\n", " u'last_evaluated': u'2011-10-17',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.*102_*105delCTGT',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'ACAG',\n", " u'rsid': u'rs431825382',\n", " u'type': u'Deletion',\n", " u'variant_id': 96891},\n", " u'snpeff': {u'ann': [{u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*102_*105delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'24',\n", " u'total': u'24',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*102_*105delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007297.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*102_*105delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'208',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007299.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*208_*211delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'22',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'},\n", " {u'distance_to_feature': u'102',\n", " u'effect': u'3_prime_UTR_variant',\n", " u'feature_id': u'NM_007294.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.*102_*105delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'23',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'non_coding_exon_variant',\n", " u'feature_id': u'NR_027676.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'n.5830_5833delCTGT',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'23',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Noncoding'}]},\n", " u'vcf': {u'alt': u'G', u'position': u'41197589', u'ref': u'GACAG'}},\n", " {u'_id': u'chr17:g.41203078A>C',\n", " u'_score': 15.629933,\n", " u'clinvar': {u'allele_id': 180821,\n", " u'alt': u'C',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41203078, u'start': 41203078},\n", " u'hg38': {u'end': 43051061, u'start': 43051061},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.5332+2T>G',\n", " u'NM_007294.3:c.5332+2T>G'],\n", " u'genomic': [u'LRG_292:g.166923T>G',\n", " u'NG_005905.2:g.166923T>G',\n", " u'NC_000017.11:g.43051061A>C',\n", " u'NC_000017.10:g.41203078A>C']},\n", " u'rcv': {u'accession': u'RCV000160004',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0346153',\n", " u'omim': u'114480'},\n", " u'name': u'Familial cancer of breast',\n", " u'synonyms': [u'CHEK2-Related Breast Cancer',\n", " u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},\n", " u'last_evaluated': u'2014-08-20',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.5332+2T>G',\n", " u'review_status': u'criteria provided, single submitter'},\n", " u'ref': u'A',\n", " u'rsid': u'rs80358182',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 182168},\n", " u'dbnsfp': {u'aa': {u'pos': -1},\n", " u'alt': u'C',\n", " u'ancestral_allele': u'A',\n", " u'cds_strand': u'-',\n", " u'chrom': u'17',\n", " u'clinvar': {u'clinsig': 5,\n", " u'rs': u'rs80358182',\n", " u'trait': u'Familial_cancer_of_breast'},\n", " u'ensembl': {u'geneid': u'ENSG00000012048',\n", " u'proteinid': [u'ENSP00000350283',\n", " u'ENSP00000312236',\n", " u'ENSP00000417148',\n", " u'ENSP00000465818',\n", " u'ENSP00000467329',\n", " u'ENSP00000418775',\n", " u'ENSP00000418960',\n", " u'ENSP00000420705'],\n", " u'transcriptid': [u'ENST00000357654',\n", " u'ENST00000352993',\n", " u'ENST00000468300',\n", " u'ENST00000586385',\n", " u'ENST00000591534',\n", " u'ENST00000493795',\n", " u'ENST00000471181',\n", " u'ENST00000491747']},\n", " u'fathmm-mkl': {u'coding_group': u'AEFBI',\n", " u'coding_pred': u'D',\n", " u'coding_rankscore': 0.72135,\n", " u'coding_score': 0.97037},\n", " u'genename': u'BRCA1',\n", " u'gerp++': {u'nr': 5.21, u'rs': 5.21, u'rs_rankscore': 0.71834},\n", " u'gm12878': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.04603,\n", " u'fitcons_score': 0.30413},\n", " u'h1-hesc': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.03107,\n", " u'fitcons_score': 0.137589},\n", " u'hg18': {u'end': 38456604, u'start': 38456604},\n", " u'hg19': {u'end': 41203078, u'start': 41203078},\n", " u'hg38': {u'end': 43051061, u'start': 43051061},\n", " u'huvec': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.02674,\n", " u'fitcons_score': 0.109871},\n", " u'integrated': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.0442,\n", " u'fitcons_score': 0.295142},\n", " u'mutationtaster': {u'converted_rankscore': 0.81033,\n", " u'model': u'without_aae',\n", " u'pred': u'D',\n", " u'score': 1},\n", " u'phastcons': {u'20way': {u'mammalian': 0.989,\n", " u'mammalian_rankscore': 0.53465},\n", " u'7way': {u'vertebrate': 0.996, u'vertebrate_rankscore': 0.63571}},\n", " u'phylo': {u'p20way': {u'mammalian': 1.199,\n", " u'mammalian_rankscore': 0.95998},\n", " u'p7way': {u'vertebrate': 1.062, u'vertebrate_rankscore': 0.92612}},\n", " u'ref': u'A',\n", " u'siphy_29way': {u'logodds': 11.6541,\n", " u'logodds_rankscore': 0.50308,\n", " u'pi': {u'a': 1.0, u'c': 0.0, u'g': 0.0, u't': 0.0}}},\n", " u'dbsnp': {u'allele_origin': u'unspecified',\n", " u'alleles': [{u'allele': u'A'}, {u'allele': u'C'}, {u'allele': u'T'}],\n", " u'alt': u'C',\n", " u'chrom': u'17',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 132,\n", " u'flags': [u'ASP', u'DSS', u'LSD', u'PM', u'RV', u'SLO'],\n", " u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41203079, u'start': 41203078},\n", " u'ref': u'A',\n", " u'rsid': u'rs80358182',\n", " u'validated': False,\n", " u'var_subtype': u'unknown',\n", " u'vartype': u'snp'},\n", " u'snpeff': {u'ann': [{u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5395+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'21',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.2020+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'19',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NR_027676.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'n.5468+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'20',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Noncoding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007297.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5191+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'19',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007299.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.2020+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'20',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007294.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.5332+2T>G',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'20',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'}],\n", " u'lof': {u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'number_of_transcripts_in_gene': u'6',\n", " u'percent_of_transcripts_affected': u'0.83'}},\n", " u'vcf': {u'alt': u'C', u'position': u'41203078', u'ref': u'A'}},\n", " {u'_id': u'chr17:g.41226347C>A',\n", " u'_score': 15.629933,\n", " u'clinvar': {u'allele_id': 184911,\n", " u'alt': u'A',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41226347, u'start': 41226347},\n", " u'hg38': {u'end': 43074330, u'start': 43074330},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.4675+1G>T',\n", " u'NM_007294.3:c.4675+1G>T'],\n", " u'genomic': [u'LRG_292:g.143654G>T',\n", " u'NG_005905.2:g.143654G>T',\n", " u'NC_000017.11:g.43074330C>A',\n", " u'NC_000017.10:g.41226347C>A']},\n", " u'rcv': {u'accession': u'RCV000164823',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'identifiers': {u'medgen': u'C0027672'},\n", " u'name': u'Hereditary cancer-predisposing syndrome',\n", " u'synonyms': u'Neoplastic Syndromes, Hereditary'},\n", " u'last_evaluated': u'2014-06-12',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.4675+1G>T',\n", " u'review_status': u'criteria provided, single 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u'n.1120_1121insC',\n", " u'putative_impact': u'MODIFIER',\n", " u'rank': u'10',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Noncoding'}],\n", " u'lof': {u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'number_of_transcripts_in_gene': u'6',\n", " u'percent_of_transcripts_affected': u'0.50'}},\n", " u'vcf': {u'alt': u'TG', u'position': u'41246563', u'ref': u'T'}},\n", " {u'_id': u'chr17:g.41251791C>T',\n", " u'_score': 15.629933,\n", " u'clinvar': {u'allele_id': 131419,\n", " u'alt': u'T',\n", " u'chrom': u'17',\n", " u'cytogenic': u'17q21.31',\n", " u'gene': {u'id': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41251791, u'start': 41251791},\n", " u'hg38': {u'end': 43099774, u'start': 43099774},\n", " u'hgvs': {u'coding': [u'LRG_292t1:c.547+1G>A', u'NM_007294.3:c.547+1G>A'],\n", " u'genomic': [u'LRG_292:g.118210G>A',\n", " u'NG_005905.2:g.118210G>A',\n", " u'NC_000017.11:g.43099774C>T',\n", " u'NC_000017.10:g.41251791C>T']},\n", " u'rcv': {u'accession': u'RCV000112729',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'All ages',\n", " u'identifiers': {u'medgen': u'C2676676',\n", " u'omim': u'604370',\n", " u'orphanet': u'145'},\n", " u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',\n", " u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'OVARIAN CANCER, SUSCEPTIBILITY TO',\n", " u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',\n", " u'Breast cancer, familial 1',\n", " u'hereditary breast and ovarian cancer, BROVCA1',\n", " u'Breast-ovarian cancer, familial, 1']},\n", " u'last_evaluated': u'2003-12-23',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_007294.3(BRCA1):c.547+1G>A',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'C',\n", " u'rsid': u'rs80358030',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 125881},\n", " u'dbnsfp': {u'aa': {u'pos': -1},\n", " u'alt': u'T',\n", " u'ancestral_allele': u'C',\n", " u'cds_strand': u'-',\n", " u'chrom': u'17',\n", " u'clinvar': {u'clinsig': 5,\n", " u'rs': u'rs80358030',\n", " u'trait': u'Breast-ovarian_cancer\\\\x2c_familial_1'},\n", " u'ensembl': {u'geneid': u'ENSG00000012048',\n", " u'proteinid': [u'ENSP00000350283',\n", " u'ENSP00000312236',\n", " u'ENSP00000417148',\n", " u'ENSP00000418775',\n", " u'ENSP00000418960',\n", " u'ENSP00000420705',\n", " u'ENSP00000419481',\n", " u'ENSP00000420412',\n", " u'ENSP00000418819',\n", " u'ENSP00000418212',\n", " u'ENSP00000326002',\n", " u'ENSP00000419274',\n", " u'ENSP00000419988',\n", " u'ENSP00000419103',\n", " u'ENSP00000417554'],\n", " u'transcriptid': [u'ENST00000357654',\n", " u'ENST00000352993',\n", " u'ENST00000468300',\n", " u'ENST00000493795',\n", " u'ENST00000471181',\n", " u'ENST00000491747',\n", " u'ENST00000484087',\n", " u'ENST00000478531',\n", " u'ENST00000493919',\n", " u'ENST00000487825',\n", " u'ENST00000354071',\n", " u'ENST00000470026',\n", " u'ENST00000477152',\n", " u'ENST00000494123',\n", " u'ENST00000476777']},\n", " u'fathmm-mkl': {u'coding_group': u'AEFBI',\n", " u'coding_pred': u'D',\n", " u'coding_rankscore': 0.45601,\n", " u'coding_score': 0.86583},\n", " u'genename': u'BRCA1',\n", " u'gerp++': {u'nr': 5.16, u'rs': 5.16, u'rs_rankscore': 0.70385},\n", " u'gm12878': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.02865,\n", " u'fitcons_score': 0.156173},\n", " u'h1-hesc': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.02788,\n", " u'fitcons_score': 0.125526},\n", " u'hg18': {u'end': 38505317, u'start': 38505317},\n", " u'hg19': {u'end': 41251791, u'start': 41251791},\n", " u'hg38': {u'end': 43099774, u'start': 43099774},\n", " u'huvec': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.02238,\n", " u'fitcons_score': 0.092715},\n", " u'integrated': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.02649,\n", " u'fitcons_score': 0.156188},\n", " u'mutationtaster': {u'converted_rankscore': 0.81033,\n", " u'model': u'without_aae',\n", " u'pred': u'D',\n", " u'score': 1},\n", " u'phastcons': {u'20way': {u'mammalian': 0.898,\n", " u'mammalian_rankscore': 0.37771},\n", " u'7way': {u'vertebrate': 0.559, u'vertebrate_rankscore': 0.26867}},\n", " u'phylo': {u'p20way': {u'mammalian': 0.892,\n", " u'mammalian_rankscore': 0.4006},\n", " u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},\n", " u'ref': u'C',\n", " u'rsid': u'rs80358030',\n", " u'siphy_29way': {u'logodds': 14.3275,\n", " u'logodds_rankscore': 0.6588,\n", " u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}}},\n", " u'dbsnp': {u'allele_origin': u'unspecified',\n", " u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}, {u'allele': u'T'}],\n", " u'alt': u'T',\n", " u'chrom': u'17',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 132,\n", " u'flags': [u'ASP', u'DSS', u'LSD', u'PM', u'RV', u'SLO'],\n", " u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},\n", " u'hg19': {u'end': 41251792, u'start': 41251791},\n", " u'ref': u'C',\n", " u'rsid': u'rs80358030',\n", " u'validated': False,\n", " u'var_subtype': u'unknown',\n", " u'vartype': u'snp'},\n", " u'snpeff': {u'ann': [{u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007300.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.547+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'7',\n", " u'total': u'23',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007298.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.547+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'6',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NR_027676.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'n.683+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'7',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Noncoding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007297.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.406+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'6',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007299.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.547+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'7',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'},\n", " {u'effect': u'splice_donor_variant&intron_variant',\n", " u'feature_id': u'NM_007294.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'hgvs_c': u'c.547+1G>A',\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'7',\n", " u'total': u'22',\n", " u'transcript_biotype': u'Coding'}],\n", " u'lof': {u'gene_id': u'BRCA1',\n", " u'gene_name': u'BRCA1',\n", " u'number_of_transcripts_in_gene': u'6',\n", " u'percent_of_transcripts_affected': u'0.83'}},\n", " u'vcf': {u'alt': u'T', u'position': u'41251791', u'ref': u'C'}}],\n", " u'max_score': 15.629933,\n", " u'took': 72,\n", " u'total': 1126}" ] }, "execution_count": 16, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* You can also query for multiple terms. For example, if you want to query for annotation data related to multiple RCV accession numbers, you can do so by calling the **querymany** method." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " Here is a list of *RCV accession numbers* you might want to query." ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "xli = ['RCV000059118',\n", " 'RCV000059119',\n", " 'RCV000057234',\n", " 'RCV000037456',\n", " 'RCV000000019',\n", " 'RCV000000134']" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "querying 1-6...done.\n", "Finished.\n" ] } ], "source": [ "out = mv.querymany(xli, scopes='clinvar.rcv.accession')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ " Here is the output of all annotation records related to these *RCV accession numbers* in xli in MyVariant.info." ] }, { "cell_type": "code", "execution_count": 19, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/plain": [ "[{u'_id': u'chr11:g.118895925C>T',\n", " u'_score': 10.333494,\n", " u'cadd': {u'_license': u'http://goo.gl/bkpNhq',\n", " u'alt': u'T',\n", " u'anc': u'C',\n", " u'annotype': [u'CodingTranscript', u'Intergenic'],\n", " u'bstatistic': 476,\n", " u'chmm': {u'bivflnk': 0.0,\n", " u'enh': 0.197,\n", " u'enhbiv': 0.0,\n", " u'het': 0.0,\n", " u'quies': 0.0,\n", " u'reprpc': 0.0,\n", " u'reprpcwk': 0.0,\n", " u'tssa': 0.0,\n", " u'tssaflnk': 0.0,\n", " u'tssbiv': 0.0,\n", " u'tx': 0.622,\n", " u'txflnk': 0.055,\n", " u'txwk': 0.11,\n", " u'znfrpts': 0.0},\n", " u'chrom': 11,\n", " u'consdetail': [u'missense', u'downstream'],\n", " u'consequence': [u'NON_SYNONYMOUS', u'DOWNSTREAM'],\n", " u'consscore': [7, 1],\n", " u'cpg': 0.04,\n", " u'dna': {u'helt': 2.03, u'mgw': 0.26, u'prot': -2.64, u'roll': -0.64},\n", " u'encode': {u'exp': 136.25,\n", " u'h3k27ac': 13.84,\n", " u'h3k4me1': 33.84,\n", " u'h3k4me3': 6.4,\n", " u'nucleo': 2.7,\n", " u'occ': 2,\n", " u'p_val': {u'comb': 0.95,\n", " u'ctcf': 0.0,\n", " u'dnas': 1.62,\n", " u'faire': 0.0,\n", " u'mycp': 0.0,\n", " u'polii': 0.0},\n", " u'sig': {u'ctcf': 0.03,\n", " u'dnase': 0.04,\n", " u'faire': 0.01,\n", " u'myc': 0.0,\n", " u'polii': 0.0}},\n", " u'exon': u'11/12',\n", " u'fitcons': 0.2838,\n", " u'gc': 0.55,\n", " u'gene': [{u'cds': {u'cdna_pos': 1606,\n", " u'cds_pos': 1165,\n", " u'rel_cdna_pos': 0.68,\n", " u'rel_cds_pos': 0.86},\n", " u'feature_id': u'ENST00000357590',\n", " u'gene_id': u'ENSG00000137700',\n", " u'genename': u'SLC37A4',\n", " u'prot': {u'domain': u'tmhmm', u'protpos': 389, u'rel_prot_pos': 0.86}},\n", " {u'ccds_id': u'CCDS8407.1',\n", " u'feature_id': u'ENST00000533632',\n", " u'gene_id': u'ENSG00000196655',\n", " u'genename': u'TRAPPC4'}],\n", " u'gerp': {u'n': 5.12, u'rs': 2485.2, u'rs_pval': 2.73146e-114, u's': 5.12},\n", " u'grantham': 58,\n", " u'isderived': u'TRUE',\n", " u'isknownvariant': u'FALSE',\n", " u'istv': u'FALSE',\n", " u'length': 0,\n", " u'mapability': {u'20bp': 1, u'35bp': 1},\n", " u'min_dist_tse': 63,\n", " u'min_dist_tss': 3820,\n", " u'mutindex': 109,\n", " u'naa': u'T',\n", " u'oaa': u'A',\n", " u'phast_cons': {u'mammalian': 0.999, u'primate': 0.987, u'vertebrate': 1.0},\n", " u'phred': 34,\n", " u'phylop': {u'mammalian': 2.677, u'primate': 0.557, u'vertebrate': 5.851},\n", " u'polyphen': {u'cat': u'possibly_damaging', u'val': 0.861},\n", " u'pos': 118895925,\n", " u'rawscore': 7.48625,\n", " u'ref': u'C',\n", " u'segway': u'GM1',\n", " u'sift': {u'cat': u'deleterious', u'val': 0.04},\n", " u'tf': {u'bs': 1, u'bs_peaks': 1, u'bs_peaks_max': 28.018},\n", " u'type': u'SNV'},\n", " u'clinvar': {u'allele_id': 34150,\n", " u'alt': u'T',\n", " u'chrom': u'11',\n", " u'cytogenic': u'11q23.3',\n", " u'gene': {u'id': u'2542', u'symbol': u'SLC37A4'},\n", " u'hg19': {u'end': 118895925, u'start': 118895925},\n", " u'hg38': {u'end': 119025215, u'start': 119025215},\n", " u'hgvs': {u'coding': [u'LRG_187t1:c.1099G>A',\n", " u'NM_001164277.1:c.1099G>A',\n", " u'NM_001467.5:c.1099G>A'],\n", " u'genomic': [u'LRG_187:g.10691G>A',\n", " u'NG_013331.1:g.10691G>A',\n", " u'NC_000011.10:g.119025215C>T',\n", " u'NC_000011.9:g.118895925C>T']},\n", " u'rcv': [{u'accession': u'RCV000020461',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'Neonatal',\n", " u'identifiers': {u'medgen': u'C0268146',\n", " u'omim': u'232220',\n", " u'orphanet': u'79259'},\n", " u'name': u'Glucose-6-phosphate transport defect (GSD1B)',\n", " u'synonyms': [u'GLYCOGEN STORAGE DISEASE Ib', u'GSD Ib']},\n", " u'last_evaluated': u'2010-12-23',\n", " u'number_submitters': 1,\n", " u'origin': u'not provided',\n", " u'preferred_name': u'NM_001164277.1(SLC37A4):c.1099G>A (p.Ala367Thr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000059118',\n", " u'clinical_significance': u'not provided',\n", " u'conditions': {u'identifiers': {u'medgen': u'CN221809'},\n", " u'name': u'not provided'},\n", " u'number_submitters': 1,\n", " u'origin': u'not provided',\n", " u'preferred_name': u'NM_001164277.1(SLC37A4):c.1099G>A (p.Ala367Thr)',\n", " u'review_status': u'no assertion provided'}],\n", " u'ref': u'C',\n", " u'rsid': u'rs80356492',\n", " u'type': u'single nucleotide variant',\n", " u'uniprot': u'VAR_025602',\n", " u'variant_id': 21298},\n", " u'dbnsfp': {u'aa': {u'alt': u'T',\n", " u'codonpos': 1,\n", " u'pos': [u'389', u'294', u'367', u'367'],\n", " u'ref': u'A',\n", " u'refcodon': u'GCC'},\n", " u'alspac': {u'ac': 2, u'af': 0.0005189413596263622},\n", " u'alt': u'T',\n", " u'ancestral_allele': u'C',\n", " u'cds_strand': u'-',\n", " u'chrom': u'11',\n", " u'clinvar': {u'clinsig': 5,\n", " u'rs': u'rs80356492',\n", " u'trait': u'Glucose-6-phosphate_transport_defect'},\n", " u'ensembl': {u'geneid': u'ENSG00000137700',\n", " u'proteinid': [u'ENSP00000476176',\n", " u'ENSP00000475991',\n", " u'ENSP00000475241',\n", " u'ENSP00000476242'],\n", " u'transcriptid': [u'ENST00000357590',\n", " u'ENST00000538950',\n", " u'ENST00000545985',\n", " u'ENST00000330775']},\n", " u'exac': {u'ac': 6,\n", " u'adj_ac': 6,\n", " u'adj_af': 5.226e-05,\n", " u'af': 4.961e-05,\n", " u'afr_ac': 0,\n", " u'afr_af': 0,\n", " u'amr_ac': 0,\n", " u'amr_af': 0,\n", " u'eas_ac': 0,\n", " u'eas_af': 0,\n", " u'fin_ac': 0,\n", " u'fin_af': 0,\n", " u'nfe_ac': 4,\n", " u'nfe_af': 6.276e-05,\n", " u'sas_ac': 2,\n", " u'sas_af': 0.0001281},\n", " u'fathmm-mkl': {u'coding_group': u'AEFDBCIJ',\n", " u'coding_pred': u'D',\n", " u'coding_rankscore': 0.73687,\n", " u'coding_score': 0.97297},\n", " u'genename': u'SLC37A4',\n", " u'gerp++': {u'nr': 5.12, u'rs': 5.12, u'rs_rankscore': 0.69274},\n", " u'gm12878': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.04325,\n", " u'fitcons_score': 0.278934},\n", " u'h1-hesc': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.04794,\n", " u'fitcons_score': 0.299256},\n", " u'hg18': {u'end': 118401135, u'start': 118401135},\n", " u'hg19': {u'end': 118895925, u'start': 118895925},\n", " u'hg38': {u'end': 119025215, u'start': 119025215},\n", " u'huvec': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.03188,\n", " u'fitcons_score': 0.119812},\n", " u'integrated': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.04139,\n", " u'fitcons_score': 0.283894},\n", " u'interpro_domain': u'Major facilitator superfamily domain',\n", " u'mutationassessor': {u'pred': u'M', u'rankscore': 0.79762, u'score': 2.47},\n", " u'mutationtaster': {u'converted_rankscore': 0.81033,\n", " u'model': u'without_aae',\n", " u'pred': u'A',\n", " u'score': 1},\n", " u'phastcons': {u'20way': {u'mammalian': 0.971,\n", " u'mammalian_rankscore': 0.46156},\n", " u'7way': {u'vertebrate': 0.996, u'vertebrate_rankscore': 0.63571}},\n", " u'phylo': {u'p20way': {u'mammalian': 0.935,\n", " u'mammalian_rankscore': 0.48811},\n", " u'p7way': 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u'origin': u'germline',\n", " u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000000021',\n", " u'clinical_significance': u'risk factor',\n", " u'conditions': {u'name': u'Porphyria variegata, susceptibility to'},\n", " u'last_evaluated': u'2009-01-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000000022',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'name': u'Hemochromatosis, juvenile, digenic'},\n", " u'last_evaluated': u'2009-01-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000000023',\n", " u'clinical_significance': 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u'Microvascular complications of diabetes 7 (MVCD7)',\n", " u'synonyms': [u'MICROVASCULAR COMPLICATIONS OF DIABETES, SUSCEPTIBILITY TO, 7',\n", " u'NEPHROPATHY, DIABETIC, SUSCEPTIBILITY TO',\n", " u'NONPROLIFERATIVE RETINOPATHY, DIABETIC, SUSCEPTIBILITY TO',\n", " u'PROLIFERATIVE RETINOPATHY, DIABETIC, SUSCEPTIBILITY TO']},\n", " u'last_evaluated': u'2009-01-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',\n", " u'review_status': u'no assertion criteria provided'},\n", " {u'accession': u'RCV000117222',\n", " u'clinical_significance': u'Benign',\n", " u'conditions': {u'identifiers': {u'medgen': u'CN169374'},\n", " u'name': u'not specified',\n", " u'synonyms': u'AllHighlyPenetrant'},\n", " u'last_evaluated': u'2013-11-04',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',\n", " u'review_status': u'criteria provided, single 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u'journal': u'Am J Hum Genet',\n", " u'location_within_paper': u'Table S4',\n", " u'p_value': 1.09e-10,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],\n", " u'phenotype': u'Serum transferrin',\n", " u'pmid': 19084217,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 1.4e-23,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red and white blood cells'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 19820697,\n", " u'snpid': u'rs1800562',\n", " u'title': u'A genome-wide meta-analysis identifies 22 loci associated 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4.3e-22,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red and white blood cells'],\n", " u'phenotype': u'Mean corpuscular hemoglobin (MCH) (pg)',\n", " u'pmid': 19820697,\n", " u'snpid': u'rs1800562',\n", " u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 1.5e-08,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 2.2e-53,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Transferrin',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 0.00034,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Ferritin (log10)',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 5.1e-07,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Blood hemoglobin',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 8.2e-19,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Iron',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 1',\n", " u'p_value': 8.5e-50,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],\n", " u'phenotype': u'Transferrin saturation with iron',\n", " u'pmid': 19820699,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 1.01e-46,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 19862010,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 5.74e-19,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Hemoglobin (Hb)',\n", " u'pmid': 19862010,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 7.2e-10,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Hematocrit (Hct)',\n", " u'pmid': 19862010,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table S3',\n", " u'p_value': 9.9e-16,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Mean corpuscular hemoglobin (MCH)',\n", " u'pmid': 19862010,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},\n", " {u'date_pub': u'10/11/2009',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Table S5A',\n", " u'p_value': 0.0274,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Diastolic blood pressure (DBP)',\n", " u'pmid': 19862010,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},\n", " {u'date_pub': u'4/11/2010',\n", " u'journal': u'Nat Genet',\n", " u'location_within_paper': u'Full Scan',\n", " u'p_value': 0.0063,\n", " u'paper_phenotype_categories': u'Renal;Chronic kidney disease;Quantitative trait(s)',\n", " u'paper_phenotype_description': u'Chronic kidney disease (CKD) and renal traits',\n", " u'phenotype': u'Serum creatinine',\n", " u'pmid': 20383146,\n", " u'snpid': u'rs1800562',\n", " u'title': u'New loci associated with kidney function and chronic kidney disease.'},\n", " {u'date_pub': u'8/5/2010',\n", " u'journal': u'Nature',\n", " u'location_within_paper': u'Table S19',\n", " u'p_value': 1.1e-08,\n", " u'paper_phenotype_categories': u'CVD risk factor (CVD RF);Lipids',\n", " u'paper_phenotype_description': u'Lipid level measurements',\n", " u'phenotype': u'Total cholesterol',\n", " u'pmid': 20686565,\n", " u'snpid': u'rs1800562',\n", " u'title': [u'Biological',\n", " u' clinical and population relevance of 95 loci for blood lipids.']},\n", " {u'date_pub': u'8/5/2010',\n", " u'journal': u'Nature',\n", " u'location_within_paper': u'Table S19',\n", " u'p_value': 2.7e-10,\n", " u'paper_phenotype_categories': u'CVD risk factor (CVD RF);Lipids',\n", " u'paper_phenotype_description': u'Lipid level measurements',\n", " u'phenotype': u'LDL cholesterol',\n", " u'pmid': 20686565,\n", " u'snpid': u'rs1800562',\n", " u'title': [u'Biological',\n", " u' clinical and population relevance of 95 loci for blood lipids.']},\n", " {u'date_pub': u'9/21/2010',\n", " u'journal': u'Diabetes',\n", " u'location_within_paper': u'Table 2',\n", " u'p_value': 2.59e-20,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Hemoglobin (HbA1c',\n", " u' glycated hemoglobin levels)'],\n", " u'phenotype': u'Glycated Hemoglobin (HbA1c)',\n", " u'pmid': 20858683,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants at 10 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[u'Hemoglobin (HbA1c',\n", " u' glycated hemoglobin levels)'],\n", " u'phenotype': u'Mean corpuscular hemoglobin (MCH)',\n", " u'pmid': 20858683,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants at 10 genomic loci influence hemoglobin A\\xe2??(C) levels via glycemic and nonglycemic pathways.'},\n", " {u'date_pub': u'9/21/2010',\n", " u'journal': u'Diabetes',\n", " u'location_within_paper': u'Table S3',\n", " u'p_value': 3.5e-15,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Hemoglobin (HbA1c',\n", " u' glycated hemoglobin levels)'],\n", " u'phenotype': u'Transferrin',\n", " u'pmid': 20858683,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Common variants at 10 genomic loci influence hemoglobin A\\xe2??(C) levels via glycemic and nonglycemic pathways.'},\n", " {u'date_pub': u'9/29/2010',\n", " u'journal': u'Nature',\n", " u'location_within_paper': u'Full Data',\n", " u'p_value': 0.00947,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Height',\n", " u'paper_phenotype_description': u'Height',\n", " u'phenotype': u'Height',\n", " u'pmid': 20881960,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Hundreds of variants clustered in genomic loci and biological pathways affect human height.'},\n", " {u'date_pub': u'9/28/2010',\n", " u'journal': u'PLoS One',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 2.76e-09,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Mean corpuscular hemoglobin (MCH)',\n", " u'pmid': 20927387,\n", " u'snpid': u'rs1800562',\n", " u'title': u'A genome-wide association study of red blood cell traits using the electronic medical record.'},\n", " {u'date_pub': u'9/28/2010',\n", " u'journal': u'PLoS One',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 5.84e-07,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red blood cells'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 20927387,\n", " u'snpid': u'rs1800562',\n", " u'title': u'A genome-wide association study of red blood cell traits using the electronic medical record.'},\n", " {u'date_pub': u'12/10/2010',\n", " u'journal': u'Hum Mol Genet',\n", " u'location_within_paper': u'Table S4',\n", " u'p_value': 1.17e-09,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Ferritin and soluble transferrin receptor levels',\n", " u' in serum'],\n", " u'phenotype': u'Soluble transferrin receptor',\n", " u'pmid': 21149283,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels.'},\n", " {u'date_pub': u'12/10/2010',\n", " u'journal': u'Hum Mol Genet',\n", " u'location_within_paper': u'Table S5',\n", " u'p_value': 3.02e-09,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Ferritin and soluble transferrin receptor levels',\n", " u' in serum'],\n", " u'phenotype': u'Serum ferritin',\n", " u'pmid': 21149283,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels.'},\n", " {u'date_pub': u'12/12/2010',\n", " u'journal': u'Hum Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 1.4e-15,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red and white blood cells'],\n", " u'phenotype': u'Hemoglobin (Hb)',\n", " u'pmid': 21153663,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genetic association analysis highlights new loci that modulate hematological'},\n", " {u'date_pub': u'12/12/2010',\n", " u'journal': u'Hum Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 2.5e-10,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red and white blood cells'],\n", " u'phenotype': u'Hematocrit (Hct)',\n", " u'pmid': 21153663,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genetic association analysis highlights new loci that modulate hematological'},\n", " {u'date_pub': u'12/12/2010',\n", " u'journal': u'Hum Genet',\n", " u'location_within_paper': u'Table 3',\n", " u'p_value': 6.8e-16,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',\n", " u'paper_phenotype_description': [u'Blood cell counts and traits',\n", " u' in red and white blood cells'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 21153663,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genetic association analysis highlights new loci that modulate hematological'},\n", " {u'date_pub': u'3/12/2011',\n", " u'journal': u'Aging Cell',\n", " u'location_within_paper': u'Table S4',\n", " u'p_value': 0.022,\n", " u'paper_phenotype_categories': u'Aging;Mortality',\n", " u'paper_phenotype_description': u'Longevity',\n", " u'phenotype': u'Longevity',\n", " u'pmid': 21418511,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide association study identifies a single major locus contributing to'},\n", " {u'date_pub': u'3/31/2011',\n", " u'journal': u'PLoS One',\n", " u'location_within_paper': u'Table 2',\n", " u'p_value': 0.00016,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': u'Iron deficiency',\n", " u'phenotype': u'Iron deficiency (transferrin saturation)',\n", " u'pmid': 21483845,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide association study identifies genetic loci associated with iron'},\n", " {u'date_pub': u'3/31/2011',\n", " u'journal': u'PLoS One',\n", " u'location_within_paper': u'Table 2',\n", " u'p_value': 1.93e-05,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': u'Iron deficiency',\n", " u'phenotype': u'Iron deficiency (Serum iron)',\n", " u'pmid': 21483845,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide association study identifies genetic loci associated with iron'},\n", " {u'date_pub': u'3/31/2011',\n", " u'journal': u'PLoS One',\n", " u'location_within_paper': u'Table 2',\n", " u'p_value': 0.022,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',\n", " u'paper_phenotype_description': u'Iron deficiency',\n", " u'phenotype': u'Iron deficiency (Body iron)',\n", " u'pmid': 21483845,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide 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identifies genetic loci associated with iron'},\n", " {u'date_pub': u'6/10/2011',\n", " u'journal': u'Hum Mol Genet',\n", " u'location_within_paper': u'Table 2',\n", " u'p_value': 2.13e-32,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Transferrin glycosylation',\n", " u' in serum'],\n", " u'phenotype': u'Transferrin',\n", " u'pmid': 21665994,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'Table3',\n", " u'p_value': 1.64e-10,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Ferritin (log10)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'Table3',\n", " u'p_value': 0.000636,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Log10(hepcidin/ferritin)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 0.00113,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Mean corpuscular hemoglobin concentration (MCHC)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 0.0145,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Mean corpuscular volume (MCV)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 1.7e-05,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Mean corpuscular hemoglobin (MCH)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 2.64e-15,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Transferrin saturation',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 3.95e-09,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Iron',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 0.0428,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Hemoglobin (Hb)',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'7/25/2011',\n", " u'journal': u'J Med Genet',\n", " u'location_within_paper': u'TableS5',\n", " u'p_value': 4.95e-11,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Hepcidin', u' in serum'],\n", " u'phenotype': u'Transferrin',\n", " u'pmid': 21785125,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},\n", " {u'date_pub': u'8/4/2011',\n", " u'journal': u'PLoS Genet',\n", " u'location_within_paper': u'TableS7',\n", " u'p_value': 2.9e-07,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',\n", " u'paper_phenotype_description': u'Gene expression in blood cells',\n", " u'phenotype': u'Gene expression of ALAS2 in blood',\n", " u'pmid': 21829388,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},\n", " {u'date_pub': u'8/4/2011',\n", " u'journal': u'PLoS Genet',\n", " u'location_within_paper': u'TableS7',\n", " u'p_value': 4.4e-06,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',\n", " u'paper_phenotype_description': u'Gene expression in blood cells',\n", " u'phenotype': u'Gene expression of [probe 2940446 centered at chr20:36199875] in blood',\n", " u'pmid': 21829388,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},\n", " {u'date_pub': u'8/4/2011',\n", " u'journal': u'PLoS Genet',\n", " u'location_within_paper': u'TableS7',\n", " u'p_value': 8.6e-06,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',\n", " u'paper_phenotype_description': u'Gene expression in blood cells',\n", " u'phenotype': u'Gene expression of ADHFE1 in blood',\n", " u'pmid': 21829388,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},\n", " {u'date_pub': u'9/11/2011',\n", " u'journal': u'Nature',\n", " u'location_within_paper': u'TableS4',\n", " u'p_value': 0.01592528,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood pressure;CVD risk factor (CVD RF)',\n", " u'paper_phenotype_description': u'Blood pressure',\n", " u'phenotype': u'Systolic blood pressure (SBP)',\n", " u'pmid': 21909115,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.'},\n", " {u'date_pub': u'9/11/2011',\n", " u'journal': u'Nature',\n", " u'location_within_paper': u'TableS4',\n", " u'p_value': 7.26329e-07,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood pressure;CVD risk factor (CVD RF)',\n", " u'paper_phenotype_description': u'Blood pressure',\n", " u'phenotype': u'Diastolic blood pressure (DBP)',\n", " u'pmid': 21909115,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.'},\n", " {u'date_pub': u'9/24/2011',\n", " u'journal': u'BMC Med Genet',\n", " u'location_within_paper': u'Table S4',\n", " u'p_value': 4.7e-12,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);CVD risk factor (CVD RF);Lipids;Weight;Body mass index;Hepatic;Blood-related;C-reactive protein (CRP)',\n", " u'paper_phenotype_description': [u'Biomarkers (liver function',\n", " u' butrylycholinesterase',\n", " u' CRP',\n", " u' ferritin',\n", " u' glucose',\n", " u' HDL cholesterol',\n", " u' insulin',\n", " u' LDL cholesterol',\n", " u' triglycerides',\n", " u' uric acid)',\n", " u' body mass index (BMI)'],\n", " u'phenotype': u'Ferritin',\n", " u'pmid': 21943158,\n", " u'snpid': u'rs1800562',\n", " u'title': [u'Genetic variants in LPL',\n", " u' OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.']},\n", " {u'date_pub': u'9/24/2011',\n", " u'journal': u'BMC Med Genet',\n", " u'location_within_paper': u'Table S4',\n", " u'p_value': 0.008,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);CVD risk factor (CVD RF);Lipids;Weight;Body mass index;Hepatic;Blood-related;C-reactive protein (CRP)',\n", " u'paper_phenotype_description': [u'Biomarkers (liver function',\n", " u' butrylycholinesterase',\n", " u' CRP',\n", " u' ferritin',\n", " u' glucose',\n", " u' HDL cholesterol',\n", " u' insulin',\n", " u' LDL cholesterol',\n", " u' triglycerides',\n", " u' uric acid)',\n", " u' body mass index (BMI)'],\n", " u'phenotype': u'LDL cholesterol',\n", " u'pmid': 21943158,\n", " u'snpid': u'rs1800562',\n", " u'title': [u'Genetic variants in LPL',\n", " u' OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.']},\n", " {u'date_pub': u'11/5/2011',\n", " u'journal': u'Psychiatr Genet',\n", " u'location_within_paper': u'TableS1',\n", " u'p_value': 0.02562,\n", " u'paper_phenotype_categories': u'Neuro;Behavioral;Depression;Alcohol;Addiction',\n", " u'paper_phenotype_description': u'Comorbid depressive syndrome and alcohol dependence',\n", " u'phenotype': u'Comorbid depressive syndrome and alcohol dependence',\n", " u'pmid': 22064162,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Genome-wide association study of comorbid depressive syndrome and alcohol dependence.'},\n", " {u'date_pub': u'11/16/2011',\n", " u'journal': u'Hepatology',\n", " u'location_within_paper': u'Table 6',\n", " u'p_value': 0.033,\n", " u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',\n", " u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],\n", " u'phenotype': u'Serum ferritin levels in HCV-infected individuals',\n", " u'pmid': 22095909,\n", " u'snpid': u'rs1800562',\n", " u'title': u'Serum ferritin levels are associated with a distinct phenotype of chronic hepatitis C poorly responding to pegylated interferon-alpha and ribavirin therapy.'}],\n", " u'replication': [{u'european': 20623, u'total_samples': 20623},\n", " {u'european': 9316, u'total_samples': 9316},\n", " {u'european': 9316, u'total_samples': 9316},\n", " {u'european': 9316, u'total_samples': 9316},\n", " {u'european': 9316, u'total_samples': 9316},\n", " {u'european': 9316, u'total_samples': 9316},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 3470, u'total_samples': 3470},\n", " {u'european': 9456, u'total_samples': 9456},\n", " {u'european': 9456, u'total_samples': 9456},\n", " {u'european': 9456, u'total_samples': 9456},\n", " {u'european': 9456, u'total_samples': 9456},\n", " {u'european': 9456, u'total_samples': 9456},\n", " {u'european': 22982, u'total_samples': 22982},\n", " {u'african': 8061,\n", " u'east_asian': 15046,\n", " u'european': 7063,\n", " u'indian_south_asian': 9705,\n", " u'total_samples': 39875},\n", " {u'african': 8061,\n", " u'east_asian': 15046,\n", " u'european': 7063,\n", " u'indian_south_asian': 9705,\n", " u'total_samples': 39875},\n", " {u'european': 50074, u'total_samples': 50074},\n", " {u'european': 11731, u'total_samples': 11731},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 232, u'total_samples': 232},\n", " {u'european': 2284, u'total_samples': 2284},\n", " {u'european': 1786, u'total_samples': 1786},\n", " {u'european': 1786, 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" [u'9705 South Asians',\n", " u' 15046 East Asians',\n", " u' 8061 African Americans',\n", " u' 7063 Europeans'],\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'50074 EA individuals',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " [u'4149 EA (specified or presumed) nonagenarian cases', u' 7582 controls'],\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'71 EA cases and 161 EA controls',\n", " u'2284 Australian individuals',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " [u'1490 European ancestry blood samples',\n", " u' 74 Dutch liver samples',\n", " u' 62 Dutch muscle samples',\n", " u' 83 Dutch subcutaneous adipose samples',\n", " u' 77 visceral adipose samples'],\n", " [u'1490 European ancestry blood samples',\n", " u' 74 Dutch liver samples',\n", " u' 62 Dutch muscle samples',\n", " u' 83 Dutch subcutaneous adipose samples',\n", " u' 77 visceral adipose samples'],\n", " [u'1490 European ancestry blood samples',\n", " u' 74 Dutch liver samples',\n", " u' 62 Dutch muscle samples',\n", " u' 83 Dutch subcutaneous adipose samples',\n", " u' 77 visceral adipose samples'],\n", " u'133661 EA individuals',\n", " u'133661 EA individuals',\n", " u'NR',\n", " u'NR',\n", " u'NR',\n", " u'NR'],\n", " u'sift': u'C282Y:(C>Y);(1.00>0.00);(TOLERATED>DELETERIOUS)',\n", " u'srsid': 1800562,\n", " u'uniprot': u'(HFE;TOPO_DOM;23-306;Extracellular (Potential).);(HFE;DOMAIN;207-298;Ig-like C1-type.);(HFE;REGION;206-297;Alpha-3.);(HFE;DISULFID;225-282;26200948);(HFE;VARIANT;282-282;C -> Y (in HH; the frequency of the Tyr- 282 mutation is higher in patients with type 2 diabetes than it is in the general 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0.0,\n", " u'tssbiv': 0.0,\n", " u'tx': 0.748,\n", " u'txflnk': 0.0,\n", " u'txwk': 0.228,\n", " u'znfrpts': 0.0},\n", " u'chrom': 14,\n", " u'consdetail': u'stop_gained',\n", " u'consequence': u'STOP_GAINED',\n", " u'consscore': 8,\n", " u'cpg': 0.04,\n", " u'dna': {u'helt': -2.68, u'mgw': 0.17, u'prot': 1.79, u'roll': -1.14},\n", " u'encode': {u'exp': 95.92,\n", " u'h3k27ac': 10.28,\n", " u'h3k4me1': 4.32,\n", " u'h3k4me3': 4.0,\n", " u'nucleo': 1.2},\n", " u'exon': u'13/20',\n", " u'fitcons': 0.701516,\n", " u'gc': 0.42,\n", " u'gene': {u'ccds_id': u'CCDS9862.1',\n", " u'cds': {u'cdna_pos': 1382,\n", " u'cds_pos': 871,\n", " u'rel_cdna_pos': 0.47,\n", " u'rel_cds_pos': 0.59},\n", " u'feature_id': u'ENST00000553888',\n", " u'gene_id': u'ENSG00000151445',\n", " u'genename': u'VIPAS39',\n", " u'prot': {u'domain': u'ndomain', u'protpos': 291, u'rel_prot_pos': 0.59}},\n", " u'gerp': {u'n': 5.17, u'rs': 359.5, u'rs_pval': 1.2817e-55, u's': 4.26},\n", " u'isderived': u'TRUE',\n", " u'isknownvariant': u'FALSE',\n", " u'istv': u'FALSE',\n", " u'length': 0,\n", " u'mapability': {u'20bp': 1, u'35bp': 1},\n", " u'min_dist_tse': 714,\n", " u'min_dist_tss': 7277,\n", " u'mutindex': 46,\n", " u'naa': u'*',\n", " u'oaa': u'Q',\n", " u'phast_cons': {u'mammalian': 0.966,\n", " u'primate': 0.986,\n", " u'vertebrate': 0.999},\n", " u'phred': 39,\n", " u'phylop': {u'mammalian': 1.275, u'primate': 0.645, u'vertebrate': 3.95},\n", " u'pos': 77902228,\n", " u'rawscore': 12.441084,\n", " u'ref': u'G',\n", " u'segway': u'R1',\n", " u'type': u'SNV'},\n", " u'clinvar': {u'allele_id': 15153,\n", " u'alt': u'A',\n", " u'chrom': u'14',\n", " u'cytogenic': u'14q24.3',\n", " u'gene': {u'id': u'63894', u'symbol': u'VIPAS39'},\n", " u'hg19': {u'end': 77902228, u'start': 77902228},\n", " u'hg38': {u'end': 77435885, u'start': 77435885},\n", " u'hgvs': {u'coding': [u'NM_001193315.1:c.871C>T', u'NM_022067.3:c.871C>T'],\n", " u'genomic': [u'NG_023421.1:g.26756C>T',\n", " u'NC_000014.9:g.77435885G>A',\n", " u'NC_000014.8:g.77902228G>A']},\n", " u'omim': u'613401.0004',\n", " u'rcv': {u'accession': u'RCV000000134',\n", " u'clinical_significance': u'Pathogenic',\n", " u'conditions': {u'age_of_onset': u'Neonatal',\n", " u'identifiers': {u'medgen': u'C3150672',\n", " u'omim': u'613404',\n", " u'orphanet': u'2697'},\n", " u'name': u'Arthrogryposis, renal dysfunction, and cholestasis 2 (ARCS2)'},\n", " u'last_evaluated': u'2010-04-01',\n", " u'number_submitters': 1,\n", " u'origin': u'germline',\n", " u'preferred_name': u'NM_022067.3(VIPAS39):c.871C>T (p.Gln291Ter)',\n", " u'review_status': u'no assertion criteria provided'},\n", " u'ref': u'G',\n", " u'rsid': u'rs267607171',\n", " u'type': u'single nucleotide variant',\n", " u'variant_id': 114},\n", " u'dbnsfp': {u'aa': {u'alt': u'X',\n", " u'codonpos': 1,\n", " u'pos': [u'291', u'291', u'242', u'291', u'242', u'317'],\n", " u'ref': u'Q',\n", " u'refcodon': u'CAG'},\n", " u'alt': u'A',\n", " u'ancestral_allele': u'G',\n", " u'cds_strand': u'-',\n", " u'chrom': u'14',\n", " u'clinvar': {u'clinsig': 5,\n", " u'rs': u'rs267607171',\n", " u'trait': u'Arthrogryposis\\\\x2c_renal_dysfunction\\\\x2c_and_cholestasis_2'},\n", " u'ensembl': {u'geneid': u'ENSG00000151445',\n", " u'proteinid': [u'ENSP00000339122',\n", " u'ENSP00000452181',\n", " u'ENSP00000313098',\n", " u'ENSP00000452191',\n", " u'ENSP00000404815',\n", " u'ENSP00000451857'],\n", " u'transcriptid': [u'ENST00000343765',\n", " u'ENST00000553888',\n", " u'ENST00000327028',\n", " u'ENST00000557658',\n", " u'ENST00000448935',\n", " u'ENST00000556412']},\n", " u'fathmm-mkl': {u'coding_group': u'AEFGBI',\n", " u'coding_pred': u'D',\n", " u'coding_rankscore': 0.7169,\n", " u'coding_score': 0.96959},\n", " u'genename': u'VIPAS39',\n", " u'gerp++': {u'nr': 5.17, u'rs': 4.26, u'rs_rankscore': 0.49573},\n", " u'gm12878': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.89268,\n", " u'fitcons_score': 0.724815},\n", " u'h1-hesc': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.93697,\n", " u'fitcons_score': 0.732669},\n", " u'hg18': {u'end': 76971981, u'start': 76971981},\n", " u'hg19': {u'end': 77902228, u'start': 77902228},\n", " u'hg38': {u'end': 77435885, u'start': 77435885},\n", " u'huvec': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.83205,\n", " u'fitcons_score': 0.714379},\n", " u'integrated': {u'confidence_value': 0,\n", " u'fitcons_rankscore': 0.97429,\n", " u'fitcons_score': 0.736574},\n", " u'lrt': {u'converted_rankscore': 0.62918,\n", " u'omega': 0.150383,\n", " u'pred': u'D',\n", " u'score': 9e-06},\n", " u'mutationtaster': {u'AAE': [u'Q278*',\n", " u'Q317*',\n", " u'Q242*',\n", " u'Q291*',\n", " u'Q291*',\n", " u'Q291*'],\n", " u'converted_rankscore': 0.81033,\n", " u'model': [u'complex_aae',\n", " u'complex_aae',\n", " u'complex_aae',\n", " u'complex_aae',\n", " u'complex_aae',\n", " u'complex_aae'],\n", " u'pred': [u'A', u'A', u'A', u'A', u'A', u'A'],\n", " u'score': [1, 1, 1, 1, 1, 1]},\n", " u'phastcons': {u'20way': {u'mammalian': 0.998,\n", " u'mammalian_rankscore': 0.69624},\n", " u'7way': {u'vertebrate': 0.972, u'vertebrate_rankscore': 0.45462}},\n", " u'phylo': {u'p20way': {u'mammalian': 1.048,\n", " u'mammalian_rankscore': 0.71188},\n", " u'p7way': {u'vertebrate': 0.83, u'vertebrate_rankscore': 0.35896}},\n", " u'ref': u'G',\n", " u'rsid': u'rs267607171',\n", " u'siphy_29way': {u'logodds': 14.8639,\n", " u'logodds_rankscore': 0.69849,\n", " u'pi': {u'a': 0.0, u'c': 0.0, u'g': 0.855, u't': 0.145}}},\n", " u'dbsnp': {u'allele_origin': u'unspecified',\n", " u'alleles': [{u'allele': u'G'}, {u'allele': u'A'}],\n", " u'alt': u'A',\n", " u'chrom': u'14',\n", " u'class': u'SNV',\n", " u'dbsnp_build': 137,\n", " u'flags': [u'ASP', u'LSD', u'NSN', u'PM', u'REF', u'RV'],\n", " u'gene': {u'geneid': u'63894', u'symbol': u'VIPAS39'},\n", " u'hg19': {u'end': 77902229, u'start': 77902228},\n", " u'ref': u'G',\n", " u'rsid': u'rs267607171',\n", " u'validated': False,\n", " u'var_subtype': u'ts',\n", " u'vartype': u'snp'},\n", " u'query': u'RCV000000134',\n", " u'snpeff': {u'ann': [{u'cdna': {u'length': u'2969', u'position': u'1417'},\n", " u'cds': {u'length': u'1482', u'position': u'871'},\n", " u'effect': u'stop_gained',\n", " u'feature_id': u'NM_001193314.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'hgvs_c': u'c.871C>T',\n", " u'hgvs_p': u'p.Gln291*',\n", " u'protein': {u'length': u'493', u'position': u'291'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'13',\n", " u'total': u'20',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2569', u'position': u'1017'},\n", " u'cds': {u'length': u'1482', u'position': u'871'},\n", " u'effect': u'stop_gained',\n", " u'feature_id': u'NM_001193315.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'hgvs_c': u'c.871C>T',\n", " u'hgvs_p': u'p.Gln291*',\n", " u'protein': {u'length': u'493', u'position': u'291'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'13',\n", " u'total': u'20',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2422', u'position': u'870'},\n", " u'cds': {u'length': u'1335', u'position': u'724'},\n", " u'effect': u'stop_gained',\n", " u'feature_id': u'NM_001193316.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'hgvs_c': u'c.724C>T',\n", " u'hgvs_p': u'p.Gln242*',\n", " u'protein': {u'length': u'444', u'position': u'242'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'12',\n", " u'total': u'19',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2746', u'position': u'1194'},\n", " u'cds': {u'length': u'1482', u'position': u'871'},\n", " u'effect': u'stop_gained',\n", " u'feature_id': u'NM_001193317.1',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'hgvs_c': u'c.871C>T',\n", " u'hgvs_p': u'p.Gln291*',\n", " u'protein': {u'length': u'493', u'position': u'291'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'13',\n", " u'total': u'20',\n", " u'transcript_biotype': u'Coding'},\n", " {u'cdna': {u'length': u'2840', u'position': u'1288'},\n", " u'cds': {u'length': u'1482', u'position': u'871'},\n", " u'effect': u'stop_gained',\n", " u'feature_id': u'NM_022067.3',\n", " u'feature_type': u'transcript',\n", " u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'hgvs_c': u'c.871C>T',\n", " u'hgvs_p': u'p.Gln291*',\n", " u'protein': {u'length': u'493', u'position': u'291'},\n", " u'putative_impact': u'HIGH',\n", " u'rank': u'14',\n", " u'total': u'21',\n", " u'transcript_biotype': u'Coding'}],\n", " u'lof': {u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'number_of_transcripts_in_gene': u'5',\n", " u'percent_of_transcripts_affected': u'1.00'},\n", " u'nmd': {u'gene_id': u'VIPAS39',\n", " u'gene_name': u'VIPAS39',\n", " u'number_of_transcripts_in_gene': u'5',\n", " u'percent_of_transcripts_affected': u'1.00'}},\n", " u'vcf': {u'alt': u'A', u'position': u'77902228', u'ref': u'G'}}]" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "out" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Can I convert a very large list of ids?\n", "\n", "Yes, you can. If you pass an id list (i.e., xli above) larger than 1000 ids, we will do the id mapping in-batch with 1000 ids at a time, and then concatenate the results all together for you. So, from the user-end, it's exactly the same as passing a shorter list. You don't need to worry about saturating our backend servers." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### To read more\n", "\n", "* [MyVariant.info](http://myvariant.info)\n", "* [MyVariant.info Documentation](http://docs.myvariant.info/en/latest/index.html)\n", " * [available fields](http://docs.myvariant.info/en/latest/doc/data.html#available-fields)\n", " * [data sources](http://docs.myvariant.info/en/latest/doc/data.html#data-sources)\n", "* [MyVariant.py's Documentation](http://myvariant-py.readthedocs.org/en/latest/)\n", "* [MyVaraint.py's PyPI page](https://pypi.python.org/pypi/myvariant)" ] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.10" } }, "nbformat": 4, "nbformat_minor": 0 }