Genome of Europe Open Dataset from Danish National Genome Database
type: Dataset
health category: HGPD
health category: HPML
health theme: HEALTH PRODUCTS
number of records: 1500
number of unique individuals: 1414
population coverage: The National Genome Database of the Danish National Genome Center comprises data from 5 generic and 17 specialised patient groups (mutually exclusive), containing patients of all ages. For patient groups covering only patients under 18 years of age, genomic analyses were also performed on at least one, and often two, adult family members (duo or trio analyses). The generic groups are: Rare diseases, Complex diseases, Fetal medicine, Cancer and Other. The specialized groups are: Hereditary heart diseases, Hereditary haematological diseases, Hereditary cholestatic and fibrotic liver diseases, Audio genetics, Endocrinological patients, Fetal medicine, Neurogenetic patients, Kidney failure, Ophthalmology, Primary immune deficiency, Psychiatry (children and young people), Severe hereditary skin diseases, Rare diseases in children and young people under 18 years, Rare diseases in adults, Cancer: Children and young people, Cancer: Haematological cancer, Cancer: Young adults (18-30 years) and adults with hereditary cancer, Cancer: Advanced and incurable cancer.
access rights: PUBLIC
language: ENG
spatial: DNK
type: HVD
creator: Danish National Genome Center
theme: HEAL
description: A subset of 1414 healthy patients from the Danish National Genomic Database. The Danish National Genomic Database consists of 38,000+ patients treated in the Danish healthcare system from 2019- (ongoing). Data includes raw sequencing data (FASTQ for all patients; CRAM and VCF files for most)
keyword: genome
keyword: genomics
keyword: whole genome sequencing
temporal: PeriodOfTime
  start date: 2019-07-01
publisher: Danish National Genome Center
  type: Agent
  type: gov-public-sector-org
  contact point: ContactPoint
    contact page: https://www.eng.ngc.dk/
contact point: Kind
  has URL: https://www.eng.ngc.dk/
distribution: Genome of Europe Open Dataset from Danish National Genome Database for Researchers
  type: Distribution
  language: ENG
  description: A distribution of a public dataset for Genome of Europe, based on data from the Danish National Genome Database. The dataset identifies the variants, populations and allele frequencies.
  applicable legislation: oj
  applicable legislation: https://www.retsinformation.dk/eli/lta/2018/728
  status: DEVELOP
  access URL: https://www.api.ngc.dk/gdi/beacon
  download URL: Table
sample: TableGroup
  table: Table
  table: Table
    name: variant
    description: Defining unique variants by chromosome, position and varant types
    keyword: variant
    keyword: chromosome
    keyword: position
    primary key: Column
    column: Column
    column: Column
      name: chromosome
      description: Chromosome label (e.g., chr1,chr22, chrX, chrY, chrMT).
      datatype: string
      length: 5
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: variant_position
      description: 1-based coordinate on the declared reference genome assembly.
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: reference_allele
      description: Reference allele.
      datatype: string
      length: 128
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: alternate_allele
      description: Alternate allele.
      datatype: string
      length: 128
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: rsid
      description: External unique, stable identifier assigned by the dbSNP database, if available.
      datatype: string
      length: 50
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: variant_type
      description: Identifies variant alterations as insertion/deletions, translocations or inversions.
      datatype: string
      length: 20
      temporal: PeriodOfTime
        start date: 2019-07-01
    temporal: PeriodOfTime
      start date: 2019-07-01
  table: Table
    name: frequency
    description: Identificator (UUID) of a single allele frequency for a specific variant and population group.
    keyword: allele
    keyword: frequency
    keyword: frequencies
    keyword: homozygous
    keyword: heterozygous
    primary key: Column
    foreign key: Column
    column: Column
    column: Column
      name: allele_count
      description: Total number of alternate alleles observed for this patient group (AC).
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: allele_number
      description: Total number of alleles for this population group (AN).
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: allele_frequency
      description: Allele frequency computed as AC/AN.
      datatype: float
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: homozygous_reference_count
      description: Count of homozygous reference genotypes.
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: heterozygous_count
      description: Count of heterozygous genotypes.
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: homozygous_alternate_count
      description: Count of homozygous alternate genotypes.
      datatype: integer
      length: 10
      temporal: PeriodOfTime
        start date: 2019-07-01
    column: Column
      name: filter_status
      description: Variant QC filter flag (e.g., PASS).
      datatype: string
      length: 50
      temporal: PeriodOfTime
        start date: 2019-07-01
    temporal: PeriodOfTime
      start date: 2019-07-01

Table
name: population
description: Population groups defined by sex and birthyear
keyword: population
keyword: population group
keyword: birthyear
keyword: age
keyword: sex
primary key: Column
column: Column
column: Column
  name: birthyear
  description: Birthyear (YYYY, ex 1995), originally inferred by the structural rules of the CPR
  datatype: integer
  length: 4
  has coding system: Standard
    has coding system: opbygning-af-cpr-nummeret
  temporal: PeriodOfTime
    start date: 2019-07-01
column: Column
  name: sex
  description: Sex (female, male), originally inferred by the structural rules of the CPR.
  datatype: string
  length: 6
  has coding system: Standard
    has coding system: opbygning-af-cpr-nummeret
  temporal: PeriodOfTime
    start date: 2019-07-01
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: id
description: Identificator (UUID) of a single population group, defining age and sex. Empty values indicate this as a overall grouping transcending sex or specific age range.
datatype: string
length: 36
has coding system: Standard
  has coding system: rfc4122
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: id
description: Identificator (UUID) of a single variant, defining chromosome, vaiant position, reference allele, alternate allele, variant type and rsid.
datatype: string
length: 36
has coding system: Standard
  has coding system: rfc4122
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: id
description: Identificator (UUID) of a single allele frequency for a specific variant and population group.
datatype: string
length: 36
has coding system: Standard
  has coding system: rfc4122
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: variant_id
description: Technical field. Foreign Key linking the tables frequency and variant together.
datatype: string
length: 36
has coding system: Standard
  has coding system: rfc4122
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: population_id
description: Technical field. Foreign Key linking the tables frequency and population together.
datatype: string
length: 36
has coding system: Standard
  has coding system: rfc4122
temporal: PeriodOfTime
  start date: 2019-07-01

Column
name: quality_score
description: Aggregated quality score / confidence metric.
datatype: float
length: 10
temporal: PeriodOfTime
  start date: 2019-07-01