A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]
A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment
Module for next generation sequencing assays
Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.
HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )
A type of Information Content Entity specific to OS
Format of a file (e.g. txt, csv, fastq, bam, etc.)
CDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection Method
Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)
HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated
Short unique identifier for the sequencing library.
The Library Source specifies the type of source material that is being sequenced
Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.
This is only if you are submitting a bam file aligned against a NCBI assembly.
Please provide the name of the custom assembly fasta file used during alignment
CDS custom_assembly_fasta_file_for_alignment
Count of unique basecalls present in the data. Please count each base only once if using secondary alignments.
Count of the number of reads in the data. Please count each read only once if using secondary alignments.
Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length)
The name of the software program used to align nucleotide sequencing data.
Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase
HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)
HTAN biological entity; this can be tissue, blood, analyte and subsamples of those
HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.
HTAN Data File Identifier indicating the file(s) from which these files were derived
Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.
Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'
regex match \d+$|Not\sApplicable$|unknown$
Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'
The number or amount of metastatic neoplasms related to the confirmed presence of disease or specific microorganisms during examination of the first rounded mass of lymphatic tissue to which cancer is likely to spread from the primary tumor.
The indicator to determine extranodal involvement or extent of the disease.
A yes/no indicator to ask if intransit metastases or satellite lesions are present.
A description of the location on or within the human body where the surgical biopsy/resection procedure was performed (Not covered under HTAN Clinical Data Tier 1)
The degree to which the lesion has been cut out, or resected.
The anatomic location to which radiation treatment was administered to a patient prior to enrollment on a protocol.
The indicator that describes whether or not immunosuppressive therapy was administered.
An enumerated list of the type of concomitant medication received by the patient.
The response indicates whether the family member of the patient with a history of cancer is alive. (Extension to GDC attributes in Family History Tier 1)
The indicator that describes whether or not a COVID-19 infectious disorder occurred.
The patient's current COVID-19 status of sign or symptom events or interventions
The indicator that describes whether or not there was a COVID-19 positive test result.
Text term that demonstrates the test results of immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies to the SARS-CoV-2 virus in subject serum samples.
Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.
Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder
Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)
Number of days e-cigarettes or vaping device was used in the last 30 days
e-cig frequency of use (times per day—one “time” consists of around 15 puffs or lasts around 10 minutes)
The number of cumulative years of the patient's specific type of smoke exposure
The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.
The number of cumulative years of the patient's exposure to second-hand cigarette smoke
A yes/no/unknown indicator to identify whether there is a known genetic predisposition mutation present in the patient.
History of presence of inherited genetic predisposition syndrome that confers heightened susceptibility to cancer in the patient.
Hereditary Cancer Predisposition Syndrome
Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history
Mutational signatures identified in the patient, includes signatures linked to selected exogenous carcinogens, endogenous and enzymatic modification of DNA or defective DNA repair. Note: Include only outputs of tests that were completed clinically for the participant and only include data from a diagnostic array that was completed prior to research sequencing was done.
The text that best describes the condition or state of MMR (mismatch repair system) in the patient
Laboratory tests used to evaluate the status of mismatch repair pathways
Text term used to describe the mode of cancer detection, like standard of care screening or random detection
Highest level of education that the patient completed (direct patient-derived information)
Areas or populations designated by HRSA as having too few primary care providers, high infant mortality, high poverty or a high elderly population: Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/ - enter the zip code in the main text field and use the associated county on the right side of the result field. Go to data.hrsa.gov website and select "Query Data". Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select "View Data". Enter the name of the county (_______ county) in the first "Service Area" column, adding the state in the 5th column may help direct you to the data. If the designation type in the third column is "medically underserved area" enter "Yes" as the value. If the county generates a "No data available in table" enter "No" as the value. A value of "Unknown" indicates that sufficient data was not available to look up the value. If value is yes, complete the Medically_underserved_score data element.
Density of population in the county of residence, based on census data (updated last on 4/28/20). Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the associated county on the right side of the result field. Go to https://www2.census.gov/programs-surveys/acs/data/covid_19/Data_Profiles_for_HHS/050-County_By_State/. Select the dp02_XX.csv file where XX = the two letter abbreviation for the appropriate state. On row 166 find the total population for the appropriate county. If the total population is <2,500 enter a value of "Rural Population"; if 2,500 - 50,000 enter a value of "Urban Cluster"; or if >50,000 enter "Urban Population"
Incidence of specific cancer type in a defined area (a number between 0 and 100). The rate of incident cases per population of 100,000 persons of a specific type of cancer as designated in the "primary_diagnosis" data element in the county where the patient resides, using the most recent 2013-2017 NCI Cancer Atlas derived data. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. On the https://gis.cancer.gov/canceratlas/tableview/ website, choose "Incidence" from the Topic dropdown menu, state of interest from the Area menu, "All Races" from the Race menu, and the cancer type ("Both Sexes" when possible) from the Statistic menu. Find the county of interest and enter the numeric Age-Adjusted Rate per 100,000 as the value.
The county and state in which the patient lives and to which the cancer_incidence data correlates. Record as "County, State" as they appear in the incidence box from which the cancer_incidence data is obtained in the https://gis.cancer.gov/canceratlas/tableview/ website
Cancer related clinical data specific to SRRS
An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.
Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]
An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.
The survival state of the person registered on the protocol.
Age at the time of diagnosis expressed in number of days since birth.
Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'
Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable'
Text term that describes the last known state or condition of an individual's neoplasm.
The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.
Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).
Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.
The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).
The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).
The primary tumor site used to calculate the incidence rate using the NCI Cancer Atlas, a digital atlas which provides geographical data related to cancer utilizing the Surveillance, Epidemiology, and End Results (SEER) Program cancer incidence rates for 2013 to 2017
Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.
Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.
Numeric value (or unknown) to represent the number of years a person has been smoking.
Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable'
The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Text term that describes the kind of treatment administered.
Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.
Lung cancer specific attributes in Clinical Data Tier 3
The means, manner of procedure, or systematic course of actions performed in order to discover or identify lung cancer
Text name of a surgical or operative procedure used in a natural history protocol of a lung cancer participant.
Lung Cancer Participant Procedure History
The type of morphologic characteristics observed by microscope in the tissue next to a benign or malignant tissue growth
Anatomic location of the tumor inside the lung
Anatomic lobe and bronchial location of the tumor inside the lung
Reported lung cancer related symptoms person is currently experiencing
Lung PCA specific topography (not covered in previous tiers)
Genomic aberrations in participants with lung cancer (specific lung cancer associated gene mutations not covered in Tiers 1 and 2)
Lung Cancer Harboring Genomic Aberrations
Colorectal cancer specific attributes in Clinical Data Tier 3
The means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer
Yes/No indicator to describe if the subject had a previous history of colon polyps as noted in the history/physical or previous endoscopic report (s).
The indicator to designate if any first degree relative has a history of colorectal cancer.
A yes/no/unknown/not applicable indicator related to family medical history diagnosis of polypoid lesion that arises from the colon or rectum and protrudes into the lumen.
Family Medical History Colorectal Polyp Diagnosis
Text that describes the age at which the family member was diagnosed with endometrial or uterine cancer in relationship to their 50th birthday.
Immediate Family History Endometrial Cancer
Text that describes the age at which the family member was diagnosed with ovarian cancer in relationship to their 50th birthday.
The indicator for patient's personal medical history of inflammatory bowel disease (chronic, non-specific disorders of unknown etiology, including Crohn disease and ulcerative colitis).
Patient Inflammatory Bowel Disease Personal Medica History
The yes/no indicator that records if the subject has undergone a previous colonoscopy.
The description of the border configuration of a colorectal tumor at pathologic assessment.
Colorectal Cancer Tumor Border Configuration
Text term to define the status of promoter methylation for the MLH1 gene. Note: MLH1 gene is commonly associated with hereditary nonpolyposis colorectal cancer. Testing for methylation of the MLH1 promoter can help distinguish sporadic from inherited cancers.
The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.
A yes/no response to a question that asks whether any new polyps greater or equal to two millimeter were identified.
Shape of polyp identified in the participant
Type of adenoma associated with the polyp
Breast cancer specific attributes in Clinical Data Tier 3
The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.
Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.
The histologic subtype for an infiltrating lobular carcinoma of the breast.
Invasive Lobular Breast Carcinoma Histologic Category
The histologic subtype for the most common type of invasive breast carcinoma.
Invasive Ductal Breast Carcinoma Histologic Category
Text term to describe the result of the examination of the breast tissue specimen or fluid as related to the presence and nature of disease.
The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.
Text term to identify assessment tests done in participants during diagnosis
Text term that represents the name of the genomic test performed for breast cancer.
Text term that represents the risk group for breast cancer as determined by assessment of the MammaPrint test.
Text term that represents the risk group for breast cancer as determined by assessment of the Oncotype recurrence score.
Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer
Breast Carcinoma Estrogen Receptor Status
Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer
Breast Carcinoma Progesteroner Receptor Status
The numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.
Breast Cancer Allred Estrogen Receptor Score
Text term to indicate prior invasive breast condition in the participant
A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer
Breast Carcinoma ER Status Percentage Value
A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer
Breast Carcinoma PR Status Percentage Value
Result of HER2 Copy Number testing (in a participant with breast cancer), expressed as a range of values.
Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.
Breast Carcinoma Centromere 17 Copy Number
Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer
Breast Carcinoma HER2 Centromere17 Copynumber Total
HER2 chromosome 17 ratio in participants with breast cancer
Breast Carcinoma HER2 Chromosome17 Ratio
Text name of a surgical procedure performed for a person with a diagnosis of breast cancer
Breast Carcinoma Surgical Procedure Name
HER2 ratio of the participant at diagnosis
Text term to signify the result of the medical procedure that involves testing a sample of blood or tissue for HER2 in a participant with breast cancer
Did the patient receive hormonal therapy for prevention of breast cancer?
Hormone Therapy Breast Cancer Prevention Indicator
Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer
Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer
The kind of technology or method performed for screening, diagnosis, surgical procedures or therapy that aids in the visualization of the breast(s).
A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from the same clone and usually located in the same quadrant of the breast.
Multifocal Breast Carcinoma Present Indicator
A response to indicate if there is breast cancer characterized by the presence of multiple cancerous tumors that originate from different clones and usually located in different quadrants of the breast.
Multicentric Breast Carcinoma Present Indicator
The category that describes the relative amount of different tissues present in the breast on a mammogram based on the updated 2015 edition of the American College of Radiology's Breast Imaging Reporting and Data System (BI-RADS) reporting guidelines.
BIRADS Mammography Breast Density Category
Brain cancer specific attributes in Clinical Data Tier 3
Primary tumor location in the central nervous system that comprise the tissues of the central nervous system (brain and spinal cord)-not covered in Tiers 1 and 2
Evidence of active brain metastasis including leptomeningeal involvement
A description of the location on or within the CNS where radiation was administered in a partcipant with glioma
Text term to identify the molecular subgroup in a supra tentorial ependymoma
Supra Tentorial Ependymoma Molecular Subgroup
Text term to identify the molecular subgroup in a infra tentorial ependymoma
Infra Tentorial Ependymoma Molecular Subgroup
Neuroblastoma MYCN amplification or over-expression status
Neuroblastoma MYCN Gene Amplification Status
Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3
The value, in percent(%) of the medical procedure that involves testing a sample of blood for blast cells, immature (undifferentiated) cells during diagnosis
The NCI risk group assigned to a patient at initial diagnosis with Acute Lymphoblastic Leukemia.
The assay sensitivity results of a diagnostic assessment of Minimal Residual Disease in patients diagnosed with Acute Lymphoblastic Leukemia.
The status of central nervous system leukemia at the time of diagnosis.
Ovarian cancer specific attributes in Clinical Data Tier 3
Text term to describe the histological subtype of ovarian cancer in the participant
Text term that describes the kind of surgical treatment administered.
Text term to indicate the status of treatment with platinum in participant with ovarian cancer
Prostate cancer specific attributes in Clinical Data Tier 3
Location and extent of extraprostatic extension
Location Extent Extraprostatic Extension
An anatomic position identifying a side of the body where local spread of malignant neoplasm is found to infiltrate tissue in the saclike glandular diverticulum on the ductus deferens in a male.
The diagnostic subclassification of an invasive prostate carcinoma.
The response used to categorize the local extent of disease for prostate cancer.
Additional findings, uninvolved prostate
Text term that describes various morphological and cytological subtypes in protate tumors.
Prostate Cancer Cytologic Morphologic Subtypes
Sarcoma specific attributes in Clinical Data Tier 3
The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.
High level grouping to describe a diagnostic grouping or category for sarcoma, a malignant mesenchymal cell tumor most commonly arising from muscle, fat, fibrous tissue, bone, cartilage, and blood vessels.
Sarcoma Diagnosis Classification Category
The field to indicate the organs and structures to which the tumor has become adherent or has invaded.
Pancreatic cancer specific attributes in Clinical Tier Data 3
The grade of precancerous pancreatic tissue based on microscopic study of characteristic tissue abnormalities by employing various cytochemical and immunocytochemical stains.
Pancreas Precancer Histopathologic Grade
The Intraductal Papillary Mucinous Neoplasm (IPMN) epithelial cell subtype based on the gross and microscopic examination of a pancreatic neoplasm specimen
Pancreatic IPMN Pathology Epithelial Subtype
The final pathology result of the pancreatic duct communication type.
Melanoma specific attributes in Clinical Data Tier 3
Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.
Cutaneous Melanoma Tumor Infiltrating Lymphocytes
Description of the degree to which tumor cells are replaced by lymphocytic inflammation with or without dermal melanophages and fibrosis._Range; the difference between the lowest and highest numerical values.
Cutaneous Melanoma Tumor Regression Range
Definition of the Clark level or depth of involvement of a melanoma in the skin or a specimen.
Text term to indicate presence of tumor at resection margins
Diameter of lesion determined on skin examination (pre-bx), in mm
The Fitzpatrick classification of skin phototype
Patient has history of blistering sunburn
History of tanning bed use of the patient
Text that describes the age at which the family member was diagnosed with melanoma skin cancer in relationship to their 50th birthday.
Biopsy resection sites specific to melanoma (not covered in Tiers 1 and 2)
Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.
Significant pathologic finding present in addition to the cutaneous melanoma.
Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable'
The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.
Numeric value to represent the calendar year in which an individual was born.
The number of years a patient worked in a specific occupation.
The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.
Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.
The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.
Indicate if individual has smoking exposure
Indicate if individual has alcohol exposure
The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.
The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.
The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.
The yes/no/unknown indicator used to describe whether the patient was exposed to radon.
The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.
Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.
Presence or absennce of Barretts esophagus goblet cells.
A calculated numerical quantity that represents an individual's weight to height ratio.
The text term used to describe the suspected cause or reason for the patient disease response.
The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.
The text term used to describe the method used to diagnose the patient's comorbidity disease.
Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable'
Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable'
Text term used to describe the types of treatment used to manage diabetes.
Code assigned to describe the patient's response or outcome to the disease.
The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.
The ECOG functional performance status of the patient/participant.
Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.
Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.
The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.
The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.
The height of the patient in centimeters.
The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.
Hepatitis Sustained Virological Response
Text classification to represent the strain or type of human papillomavirus identified in an individual.
Text term used to describe the classification used of the functional capabilities of a person.
Text term used to describe the patient's menopause status.
Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).
The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.
Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.
The weight of the patient measured in kilograms.
The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.
The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.
Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.
The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.
The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.
Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable'
The text term used to describe the type of evidence used to determine whether the patient's disease recurred
The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).
Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.
The text term used to indicate whether the patient used hormonal contraceptives.
The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.
The text term used to describe the type of hysterectomy the patient had.
The text term used to describe the result of the imaging or scan performed on the patient.
The text term used to describe the type of imaging or scan performed on the patient.
The text term used to describe the type of immunosuppresive treatment the patient received.
Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).
The text term used to describe the type of pregnancy the patient had
Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria
Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.
The text term used to describe the type of tracer used during the imaging or scan of the patient.
A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.
The text term used to describe the pathologic effect a treatment(s) had on the tumor.
Text term that describes the patient's final outcome after the treatment was administered.
Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable'
The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment
Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable'
The text term used to describe the status of the patient's malignancy when the treatment began.
The text term used to describe the regimen or line of therapy.
Text identification of the individual agent(s) used as part of a treatment regimen.
Text term to identify the reason for the administration of a treatment regimen. [Manually-curated]
The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.
The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.
The text term used to describe the reason a specific treatment or regimen ended.
Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.
The numeric value used to describe the dose of an agent the patient received.
The text term used to describe the dose units of an agent the patient received.
The text term used to indicate whether the treatment had an effect on the patient.
The text term used to describe the frequency the patient received an agent or regimen.
Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.
The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).
Text term used to describe the method used to confirm the patients malignant diagnosis.
The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.
A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.
The text term used to describe the extent of metastatic disease present at diagnosis.
Text term to identify an anatomic site in which metastatic disease involvement is found.
Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.
Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable'
The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.
Text terms to describe the status of a tissue margin following surgical resection.
A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.
The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.
The text term used to describe whether the patient's disease originated in a single location or multiple locations.
Numeric value used to describe the gross pathologic tumor weight, measured in grams.
The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.
The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.
Text term that represents the type of vascular tumor invasion.
Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.
The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.
For tumors in paired organs, designates the side on which the cancer originates.
A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.
A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement
The number of lymph nodes involved with disease as determined by pathologic examination.
The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.
The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.
Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.
The best improvement achieved throughout the entire course of protocol treatment.
The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.
Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.
Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.
Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).
The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.
The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.
Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).
The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.
Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.
Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).
The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.
The text term used to describe the tertiary pattern as described by the Gleason Grading System.
Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.
Numeric value that represents the measurement of the widest portion of the tumor in centimeters.
The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.
Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).
The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.
The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).
Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).
The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.
Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).
The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).
The multiple myeloma disease stage at diagnosis.
The text term used to describe the anatomic site of lymph node involvement.
Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.
The text term used to describe the anatomic sites that were involved in the survival margins.
The text term used to describe the classification of medulloblastoma tumors based on molecular features.
Medulloblastoma Molecular Classification
The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.
Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).
The text term used to describe whether the patient had non-nodal regional disease.
The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.
The text term used to describe the physical condition of the involved ovary.
The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.
The text term used to indicate whether the patient was pregnant at the time they were diagnosed.
The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.
The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.
Text term to specify the location of the supratentorial tumor.
Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).
Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.
Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.
Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.
Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.
The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.
Numeric value used to describe the number of loci determined to be abnormal.
Numeric value used to describe the number of loci tested.
Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.
The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).
Text term used to describe the number of sets of homologous chromosomes.
The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.
The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here
Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.
The text term used to describe the type of genetic variation.
The text term used to describe the zygosity of a specific genetic variant.
This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).
Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable'
List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...
Records the method of acquisition or source for the specimen under consideration.
Text term to identify the type of fixative used to preserve a tissue specimen
The method by which a biomaterial was stored after preservation or before another protocol was used.
Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable'
Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.
Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.
Material Specimen is collected into post procedure
The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media
Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.
Text term describing who (in what role) made the histological assessments of the sample
The method of assessment used to characterize histology
Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN
Measure of Tumor-Infiltrating Lymphocytes [Number]
Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.
Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]
Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).
Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.
Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.
Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.
Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.
Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.
Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.
Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.
Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.
Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.
Numeric value that represents the percentage of infiltration by tumor cells in a sample.
Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.
Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.
Imaging specific: the method by which the tissue was sliced.
scRNA-seq specific: Type of lysis buffer used
Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]
SRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimen
Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.
Specify whether specimen experienced warm or cold ischemia.
Topography Code, indicating site within the body, based on ICD-O-3.
Topography not included in the ICD-O-3 Topography codes.
The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0
Text term that represents the method used to preserve the sample.
Metadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardized
The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)
The source of the input nucleic molecule
Indicate if library preparation was based on revived frozen cells.
The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)
The tissue dissociation method used for scRNASeq or scATAC-seq assays
Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]
Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other
The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript
An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA
A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix
A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.
Number of cells and number of nuclei input; entry format: number, number
Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable'
Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable'
Single Cell Dissociation Days from Index
Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable'
Sequencing Library Construction Days from Index
Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable'
A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch)
Alignment workflows downstream of scRNA-seq Level 1
Generic name for the workflow used to analyze a data set.
Major version of the workflow (e.g. Cell Ranger v3.1)
Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion
scRNAseq Workflow Parameters Description
Link to workflow or command. DockStore.org recommended. URL
Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39)
Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz)
Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz)
Link to file listing all possible cell barcodes. URL
SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z)
SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)
All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames
Median number of genes detected per cell. Number
Number of sequenced cells. Applies to raw counts matrix only.
Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)
Raw sequencing files for the Slide-seq assay.
Offset in sequence for spot barcode read (in bp): number
Aligned sequencing files and QC for the Slide-seq assay.
Generic name for the workflow used to analyze the Slide-seq data set. String
Parameters used to run the Slide-seq workflow. String
Slide-seq Workflow Parameter Description
SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)
SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)
Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).
A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.
Links samples to a specific local sequencer run. Can be string or 'null'
Number of sequenced beads. Applies to raw counts matrix only. Integer
The median number of UMI counts per tissue covered spot.
The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.
The type of Level 3 file submitted as part of the Slide-seq workflow.
Average cDNA length associated with the experiemtn. Integer
The platform used for micro-regional RNA sequencing (if applicable)
The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.
The length of the sequencing reads. Can be integer, null
Vendor of Library Preparation Kit. String
Version of Library Preparation Kit. String
Base sequence of the sequencing adapter. String
Flow cell barcode. Wrong or missing information may affect analysis results. String
Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer
Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number
Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer
Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number
The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer
The barcode/index sequence used. Wrong or missing information may affect analysis results. String
The targeted read depth prior to sequencing. Integer
Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number
A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number
Represents the percentage of RNA fragments that are >200 nucleotides in size. Number
State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.
Version of ASCII encoding of quality values found in the file. String
The overall %GC of all bases in all sequences. Integer
Total number of reads per sample. Integer
Generic name for the workflow used to analyze a data set. String
Bulk RNA-seq alignment protocol description
Link to workflow used for read alignment. DockStore.org recommended. String
The name (or part of a name) of a file (of any type). String
Average base quality collected from samtools. Number
Average insert size collected from samtools. Integer
Average read length collected from samtools. Integer
Fraction of reads coming from cross-sample contamination collected from GATK4. Number
Estimation error of cross-sample contamination collected from GATK4. Number
Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number
Link to method workflow (or command) used in estimating the MSI. URL
Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number
MSIsensor determination of either microsatellite stability or instability.
Pairs on different chromosomes collected from samtools. Integer
Number of reads that map to genome. Integer
Number of reads that did not map to genome. Integer
Proportion of duplicated reads collected from samtools. Number
Proportion of mapped reads collected from samtools. Number
Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number
Proportion of mismatched bases collected from samtools. Number
Number of reads that were too short. Integer
Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing
Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.
How quantities are corrected for gene length
Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.
Bulk Whole Exome Sequencing aligned files and QC
Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.
Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.
Bulk Whole Exome Sequencing called variants
Link to workflow document, e.g. Github, DockStore.org recommended
Is the sample case or control in somatic variant analysis
Link to workflow document. DockStore.org recommended. URL
Microarray Level 1 refers to the raw text table of probe level intensities
The NCBI GEO Microarray Platform ID that links to the table containing the array definition
Microarray is measuring this kind of molecule
Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).
Microarray Level 2 provides a normalized matrix of values.
scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM files
Name of the transposase, transposon sequences
Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from
Median fraction of reads in peaks (FRIP)
Median fraction of reads in annotated cis-DNA elements (FRIADE)
Median Fraction of Reads in Annotated cis DNA Elements
Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode
Contamination from mitochondrial sequences
Median Percentage of Mitochondrial Reads per Nucleus
scATAC-seq files containing aligned sequence data, as a BAM file
Processed data files containing peak information for cells
Number of chimerically mapped read-pairs
Number of read-pairs with at least one end not mapped
Number of read-pairs with <30 mapq on at least one end
Number of read-pairs mapping to mitochondria and non-nuclear contigs
Number of non-duplicate, usable read-pairs i.e. fragments
Number of fragments overlapping with TSS regions
Number of fragments overlapping with DNase sensitive regions
Number of fragments overlapping enhancer regions
Number of fragments overlapping promoter regions
Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)
Number of fragments overlapping blacklisted regions
Number of ends of fragments in peak regions
Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))
Transcription start site (TSS) enrichment score
Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm
Peak score (proportional to q-value) in MACS2
Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2
Negative log10 p-value for the peak summit in MACS2
Negative log10 q-value for the peak summit in MACS2
Position of the peak summit related to the start position in MACS2
Name of the kit used in bisulfite conversion.
Files contain scmC-seq files containing aligned sequence data, as a BAM file.
Parameters used to run the scATAC-seq workflow.
scATACseq Workflow Parameters Description
Alignment workflows downstream of scDNA-seq Level 1
Proportion of reads mapping to mitochondria.
Raw sequencing files for the multiplexed CITE-seq assay
The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910]
Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.
Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays
Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]
Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)
The method by which cells are multiplex or labeled with cell surface markers or probes
The library construction methods for the feature barcode library
Synapse ID of the folder containing the barcode lists
A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data
Alignment workflows downstream of Multiplexed CITE-seq Level 1
Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMs
A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.
Assay types normally determine genomic coverage
Overall number of reads for a given sample in digits (microgram, nanogram).
Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.
The human genome reference used in the alignment of reads
Software used for remove duplicate reads
Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.
Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.
Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR)
Methylation ratio of mostly methylated pUC19 control, as a percentage
Methylation ratio of mostly unmethylated lambda control, as a percentage
Name of software used to generate expression values. String
Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]
Pre-processing steps completed to convert level 1 raw data to a single level 2 image
Pre-processing steps required to convert level 1 raw data to a single level 2 image
Free text field (generally for QC comment)
Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details
Microscope type (manufacturer, model, etc) used for this experiment
The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units)
The numerical aperture of the lens. Floating point value > 0.
The working distance of the lens, expressed as a floating point number. Floating point > 0.
The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)
Does data file contain pyramid of images
Does data file contain a Z-stack of images
Does data file contain a time-series of images
Did all channels pass QC (if not add free text Comment)
Index of FOV (as it pertains to its sequence order). Integer >= 1
Field of view X dimension. Floating point
Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)
Field of view Y dimension. Floating point value
Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)
Number of frames averaged together (if no averaging, set to 1). Integer >= 1
Unique internal image identifier. eg "Image:0". (To be extracted from OME-XML)
The order in which the individual planes of data are interleaved.
Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.
The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um)
Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.
Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.
Number of Z-planes (not to be confused with downsampled "pyramid"). Integer >=1
Size of image: X dimension (in pixels). Integer >= 1
Size of image: Y dimension (in pixels). Integer >= 1
Size of image: Z dimension (in pixels). Integer >= 1
Data type for each pixel value. E.g. "uint16"
The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.
The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.
Specifies how the segmentation is stored
Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis
Defines the structure that the mask delineates
The number of objects (eg cells) described
Files contain raw RNA-seq data associated with spot/slide data.
10x Visium Spatial Transcriptomics - RNA-seq Level 1
Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.
Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.
For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.
To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.
Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.
Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.
10x Visium Spatial Transcriptomics - RNA-seq Level 2
Link to file listing all possible spatial barcodes. URL
Auxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.
10x Visium Spatial Transcriptomics - Auxiliary Files
The file type generated for the visium experiment.
Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.
10x Visium Spatial Transcriptomics - RNA-seq Level 3
The number of barcodes associated with a spot under tissue.
The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.
The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).
Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.
Proportion Reads Mapped to Transcriptome
Processed data files based on Spatial Transcriptomics RNA-seq Level 3.
10x Visium Spatial Transcriptomics - RNA-seq Level 4
Generic name for the workflow used to analyze the visium data set.
Length of spot barcode read (in bp): number
Start position of UMI barcode in the sequence. Values: number, 0 for start of read
Length of UMI barcode read (in bp): number
Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.
NanoString GeoMx DSP Spatial Transcriptomics Level 1
The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.
GeoMx DSP NGS Library Preparation Kit Name
GeoMx DSP Library Preparation Kit Vendor
GeoMx DSP Library Preparation Kit Version
Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.
GeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates.
NanoString GeoMx DSP ROI RCC Segment Annotation Metadata
NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
The assay type which was used for the GeoMx DSP pipeline.
Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.
NanoString GeoMx DSP Spatial Transcriptomics Level 3
Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.
Synapse ID of GeoMx DSP ROI Segment Annotation File
Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx
Generic name for the workflow used to analyze the GeoMx DSP data set.
Parameters used to run the GeoMx DSP workflow.
GeoMx DSP Workflow Parameter Description
GeoMx Scan name (as appears in Segment Summary)
ROI name (application generated). For Xenium this is referred to as the “region name”
Name given to segment at time of generation
Unique descriptor of a variable group (ie. MAPK+)
ROI quality control flag as reported by the application
The binding density as reported by the application
The Positive Control Normalization factor calculated using pos-hyb controls
Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area
Number of nuclei detected in the segment (if applicable)
e.g. CD45 or PanCK (if masking was performed)
Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).
Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.
Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads
Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.
Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.
Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.
Is the median count from all probes except the negative control probes. A measure of signal to background for each segment
Enzymes and treatment length/temperature for genome digestion
Detergent and treatment condition for nuclei permeabilization and crosslinking softening
Name of ligase and condition for proximity ligation
Whether biotin is used for enriching ligation product
Amount of DNA for library construction, in nanograms.
Read length used for alignment if hard trimming was applied
Were any software or computational tools generated for this content
Binning size used for generating contact matrix, in basepair.
Tool used for identifying architectural stripe-forming, interaction hotspots.
Binning size used for calling significant dot interactions (loops)
Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.
Tool used for identifying loop interactions
Derived imaging data: Object-by-feature array
The number of features (eg channels) described
Function used to summarize object/feature intensity
SRRS-specific HTAN raw and pre-processed image data
All data pertaining to the 10X Genomics Xenium In-Situ Hybridization experiment
A comma separated list of filenames within the Xenium bundle zip file
The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))
The total number of cells analyzed on the flow cell
Refers to the target of an assay. Can be genes/transcripts or probes
A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)
Mean or Median transcript count per cell analyzed on the flow cell or slide
The percentage of transcripts assigned to assayed cells
In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).
The HTAN Data File ID of a Imaging Level 2 file
Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.
A table containing antibody level metadata for RPPA
HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.
The comma separated list of gene symbols targeted by the antibody.
The comma separated list of UNIPROT IDs targeted by the antibody.
A flag the denotes if an antibody targets a phosphoprotein.
The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442)
Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC)
Notes on antibodies replacements and antibody recognition observations.
Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.
Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.
Method that was used to batch correct Level 3 data
RNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)
A comma separated list of filenames within the CosMx bundle zip file
The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay
The total number of FOVs recorded for the sample on a single flow cell
The total unique genes detected above background
Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 1
Batch ID indicating a set of samples that were run together.
Analytes are the target molecules being measured with the assay.
The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.
An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.
The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)
The polarity of the mass analysis (positive or negative ion modes)
The low value of the scanned mass range for MS1 in m/z.
The high value of the scanned mass range for MS1 in m/z.
Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.
Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)
Indicates whether samples were labeled prior to MS analysis (e.g., TMT)
The manufacturer of the instrument used for LC.
The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'
Details of the resin used for lc, including vendor, particle size, pore size
The program dictates the mobile phase solvent composition over the course of the chromatographic run.
Additional file containing instrument metadata details. Use either synapse_path or entity_Id
Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 2
Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).
Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 3
Mass Spectrometry derived data that includes proteomics, metabolomics, and lipidomics, level 4
HTAN ID for this channel metadata table (same for all rows)
This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1')
This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin')
Identify stains that did not pass QC but are included in the dataset.
The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)
"Is this antibody acting as a primary or secondary antibody"
Short descriptive name (abbreviation) for this target (antigen)
Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))
Research Resource Identifier (eg “RRID: AB_394606”)
Fluorescent dye label (eg Alexa Fluor 488)
Center/peak of the excitation spectrum (nm)
Center/peak of the emission spectrum (nm)
Nominal width of excitation spectrum (nm)
Free text description of object class [string]
Offset in sequence for cDNA read (in bp): number
Offset in sequence for cell barcode read (in bp): number
Length of cell barcode read (in bp): number
Highly-multiplexed plate-based single-cell RNA-Seq assay
A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc]
The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization
Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes
Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes
Custom Large Construct Capture TARGET-OS Panel - 8 Genes
Custom Myeloid GENIE-VICC Panel - 37 Genes
Custom Personalis ACEcp VAREPOP-APOLLO Panel v2
Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes
Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes
Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1
Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2
Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb
Custom Solid Tumor GENIE-VICC Panel - 34 Genes
Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb
Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb
Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb
Custom SureSelect GENIE-UHN Panel - 555 Genes
Custom SureSelect Human All Exon v1.1 Plus 3 Boosters
Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb
Custom Twist Broad PanCancer Panel - 396 Genes
Foundation Medicine T5a Panel - 322 Genes
Foundation Medicine T7 Panel - 429 Genes
xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn
25 rxn xGen Universal Blocking Oligo – TS HT-i7
Specify the name of a custom alignment workflow
Specify the name of a custom workflow name
Specify fusion gene detected, if not in list
A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen
The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)
A description of the charge on the glass slide.
Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).
Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable'
Text descriptor of the shipping environment of a biospecimen.
For tumors in paired organs, designates the side on which the specimen was obtained.
Numeric value that represents the sample portion weight, measured in milligrams.
Numeric value for the total amount of sample or specimen
Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints)
First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE
Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE
Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the "dimensions_unit" CDE
Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)
A custom acquisition method [Text - max length 100 characters]
Cryopreservation in liquid nitrogen - dead tissue
Cryopreservation in dry ice - dead tissue
Cryopreservation in liquid nitrogen - live cells
Fresh dissociated and single cell sorted into plates in NP40 buffer
Fresh dissociated and single cell sorted
Fresh dissociated and single cell sorted into plates
Methacarn fixed paraffin embedded - MFPE
Unit of measurement used for the total amount of sample or specimen
Melanoma in situ - superficial spreading
Melanoma in situ - arising in a giant congenital nevus
Melanoma in situ - not otherwise classified
Invasive melanoma - superficial spreading
Normal or basal cell hyperplasia or metaplasia
Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)
native hawaiian or other pacific islander
This indicates the participant is alive and defines further required metadata
This indicates the participant is dead and defines further required metadata
Numeric value to represent the year of the death of an individual.
The text term used to describe the source used to determine the patient's cause of death.
Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. If not applicable please enter 'Not Applicable'
Saint Helena Ascension and Tristan da Cunha
High school graduate (including equivalency)
Patient's zip code is in a medically underserved area
Patient's zip code is not in a medically underserved area
Insufficient data to look up the Medically Underserved Area value
Index of Medical Underservice (IMU) score, a number between 0 and 100, where 0 represents completely underserved and 100 represents best served or least underserved. Use patient zip code to find the county the patient lives in by going to https://www.unitedstateszipcodes.org/. Enter the zip code in the main text field and use the asociated county on the right side of the result field. Go to data.hrsa.gov website and select Query Data. Pick the Medically Underserved Areas/Populations (MUA/P) data source in the step 1 menu and select View Data. Enter the name of the county (______ county) in the first "Service Area" column, adding the state in the 5th column may help direct you to the data. Enter the Index of Medical Underservice Score in the fourth column to one decimal place as the value.
The text term used to describe the gender of the patient's relative with a history of cancer.
The age (in years) when the patient's relative was first diagnosed.
The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.
The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.
Individual has a relative with cancer history
The number of relatives the patient has with a known history of cancer.
Individual has been exposed to smoke; requires additional metadata
The average number of cigarettes smoked per day.
The text term used to generally decribe how often the patient smokes.
The text term used to describe the patient's specific type of smoke exposure.
The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.
The year in which the participant began smoking.
The year in which the participant quit smoking.
Category describing current smoking status and smoking history as self-reported by a patient
The text term used to describe the specific type of tobacco used by the patient.
The text term used to indicate whether the patient was exposed to secondhand smoke as a child.
Text term used to describe the length of time the patient was exposed to an environmental factor.
Numeric value that represents the number of times the patient uses tobacco each day.
Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.
Numeric value used to describe the average number of alcoholic beverages a person consumes per day.
A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.
Category to describe the patient's current level of alcohol use as self-reported by the patient.
Indoor coal burning stove or fireplace smoke
Indoor wood burning stove or fireplace smoke
Workrelated smoke artificial smoke machines
Numeric value that represents the number of times the patient uses marijuana each day.
Current Reformed Smoker for < or = 15 yrs
Activated Partial Thromboplastin Time Prolonged
Blood and Lymphatic System Disorders Other
Carbon Monoxide Diffusing Capacity Decreased
Electrocardiogram QT Corrected Interval Prolonged
General Disorders and Administration Site Conditions Other
Poisoning and Procedural Complications Other
Intraoperative Reproductive Tract Injury
Joint Range of Motion Decreased Cervical Spine
Joint Range of Motion Decreased Lumbar Spine
Leukemia Secondary to Oncology Chemotherapy
Metabolism and Nutrition Disorders Other
Musculoskeletal and Connective Tissue Disorders Other
Malignant and Unspecified (Incl Cysts and Polyps) Other
Palmar-Plantar Erythrodysesthesia Syndrome
Postoperative Thoracic Procedure Complication
Puerperium and Perinatal Conditions Other
Radiation Recall Reaction (Dermatologic)
Reproductive System and Breast Disorders Other
Thoracic and Mediastinal Disorders Other
Reversible Posterior Leukoencephalopathy Syndrome
Skin and Subcutaneous Tissue Disorders Other
Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable'
Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable'
Progressive Multifocal Leukoencephalopathy
The patient has had a new tumor event after initial treatment
The text term used to describe the type of progressive or recurrent disease or relapsed disease.
Bones of skull and face and associated joints
Connective subcutaneous and other soft tissues of abdomen
Connective subcutaneous and other soft tissues of head face and neck
Connective subcutaneous and other soft tissues of lower limb and hip
Connective subcutaneous and other soft tissues of pelvis
Connective subcutaneous and other soft tissues of thorax
Connective subcutaneous and other soft tissues of trunk NOS
Connective subcutaneous and other soft tissues of upper limb and shoulder
Connective subcutaneous and other soft tissues NOS
Hypopharyngeal aspect of aryepiglottic fold
Ill-defined sites within respiratory system
Long bones of lower limb and associated joints
Long bones of upper limb scapula and associated joints
Other specified parts of female genital organs
Other specified parts of male genital organs
Overlapping lesion of bones joints and articular cartilage
Overlapping lesion of bones joints and articular cartilage of limbs
Overlapping lesion of brain and central nervous system
Overlapping lesion of connective subcutaneous and other soft tissues
Overlapping lesion of endocrine glands and related structures
Overlapping lesion of female genital organs
Overlapping lesion of heart mediastinum and pleura
Overlapping lesion of lip oral cavity and pharynx
Overlapping lesion of major salivary glands
Overlapping lesion of male genital organs
Overlapping lesion of other and unspecified parts of mouth
Overlapping lesion of peripheral nerves and autonomic nervous system
Overlapping lesion of rectum anus and anal canal
Overlapping lesion of respiratory system and intrathoracic organs
Overlapping lesion of retroperitoneum and peritoneum
Pelvic bones sacrum coccyx and associated joints
Peripheral nerves and autonomic nervous system of abdomen
Peripheral nerves and autonomic nervous system of head face and neck
Peripheral nerves and autonomic nervous system of lower limb and hip
Peripheral nerves and autonomic nervous system of pelvis
Peripheral nerves and autonomic nervous system of thorax
Peripheral nerves and autonomic nervous system of trunk NOS
Peripheral nerves and autonomic nervous system of upper limb and shoulder
Rib sternum clavicle and associated joints
Short bones of lower limb and associated joints
Short bones of upper limb and associated joints
Skin of other and unspecified parts of face
Common variable immune deficiency (CVID)
Helicobacter Pylori-Associated Gastritis
Serous tubal intraepithelial carcinoma (STIC)
Incomplete Necrosis (Viable Tumor Present)
Radiation Intensity-Modulated Radiotherapy
Stem Cell Transplantation Double Autologous
Stem Cell Transplantation Non-Myeloablative
Stem Cell Transplantation Haploidentical
Pancreatic Intraductal Papillary-Mucinous Neoplasm
Melanoma in situ arising in a giant congenital nevus
Melanoma in situ not otherwise classified
Prostate Seminal Vesicles and Lymph Nodes
Antidepressants-Moderate CYP2D6 inhibitors
Antidepressants-Strong CYP2D6 inhibitors
Antidepressants-weak CYP2D2 inhibitors or non-inhibitors
Bisphosphonates for treatment/prevention of bone loss
Non-prescription supplements for relief of hot flashes
Prescription medications for relief of hot flashes
Patient had symptoms but now is fully recovered
Patient never had any symptoms of COVID-19
Status unknown due to general COVID-19 related travel restrictions
Status unknown due to lack of disease/tumor assessment due to COVID-19 diagnosis
Attenuated familial adenomatous polyposis
Constitutional mismatch repair deficiency
Hereditary breast–ovarian cancer syndrome
Hereditary leiomyoma-renal cell carcinoma
Hereditary papillary renal cell carcinoma
Hereditary paraganglioma–pheochromocytoma syndrome
Rhabdoid tumor predisposition syndrome type I
Rhabdoid tumor predisposition syndrome type II
Alkylating Agents (Temozolomide) induced mutations
microsatellite instability (additions and deletions)
methylated CpG sequences mutagenesis(deamination of 5-methyl-cytosine)
Activation Induced Deaminases (AID) associated mutations
altered activity of the error-prone polymerase POLε (POLE)
localized substitution hypermutation (kataegis)
IHC staining for mismatch repair proteins
PCR to evaluate microsatellite instability
Clinical Examination of unrelated cancer symptoms
Biochemical evidence of disease without structural correlate
Acute lymphoblastic leukemia-lymphoma NOS
Acute lymphoblastic leukemia mature B-cell type
Acute lymphoblastic leukemia precursor cell type
Acute myeloid leukemia minimal differentiation
Adenocarcinoma combined with other types of carcinoma
Adenocarcinoma in situ in adenomatous polyp
Adenocarcinoma in situ in tubular adenoma
B lymphoblastic leukemia/lymphoma with hyperdiploidy
B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)
B-cell lymphocytic leukemia/small lymphocytic lymphoma
Bronchial-associated lymphoid tissue lymphoma
Bronchio-alveolar carcinoma mixed mucinous and non-mucinous
Bronchiolo-alveolar carcinoma Clara cell
Bronchiolo-alveolar carcinoma Clara cell and goblet cell type
Bronchiolo-alveolar carcinoma goblet cell type
Bronchiolo-alveolar carcinoma indeterminate type
Bronchiolo-alveolar carcinoma non-mucinous
Burkitt lymphoma NOS (Includes all variants)
Cervical intraepithelial neoplasia grade III
Cervical intraepithelial neoplasia low grade
Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive
Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)
Chronic myelogenous leukemia BCR-ABL positive
Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive
Chronic myelomonocytic leukemia in transformation
Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis
Classical Hodgkin lymphoma lymphocyte depletion NOS
Classical Hodgkin lymphoma lymphocyte depletion reticular
Classical Hodgkin lymphoma lymphocyte-rich
Classical Hodgkin lymphoma mixed cellularity NOS
Classical Hodgkin lymphoma nodular sclerosis cellular phase
Classical Hodgkin lymphoma nodular sclerosis grade 1
Classical Hodgkin lymphoma nodular sclerosis grade 2
Classical Hodgkin lymphoma nodular sclerosis NOS
Combined hepatocellular carcinoma and cholangiocarcinoma
Combined large cell neuroendocrine carcinoma
Combined small cell-squamous cell carcinoma
Combined/mixed carcinoid and adenocarcinoma
Composite Hodgkin and non-Hodgkin lymphoma
Esophageal glandular dysplasia (intraepithelial neoplasia) high grade
Esophageal glandular dysplasia (intraepithelial neoplasia) low grade
Esophageal intraepithelial neoplasia high grade
Esophageal squamous intraepithelial neoplasia (dysplasia) high grade
Esophageal squamous intraepithelial neoplasia (dysplasia) low grade
Gastrointestinal stromal tumor malignant
Infiltrating duct and cribriform carcinoma
Intraductal adenocarcinoma noninfiltrating NOS
Intraductal carcinoma and lobular carcinoma in situ
Intraductal carcinoma noninfiltrating NOS
Intraductal papillary adenocarcinoma with invasion
Intraductal papillary adenocarcinoma NOS
Intraductal tubular-papillary neoplasm high grade
Intraductal tubular-papillary neoplasm low grade
Intraepidermal squamous cell carcinoma Bowen type
Malignant lymphoma large B-cell diffuse NOS
Malignant lymphoma lymphocytic diffuse NOS
Malignant lymphoma lymphocytic nodular NOS
Malignant lymphoma mixed cell type diffuse
Malignant lymphoma mixed cell type follicular
Malignant lymphoma mixed cell type nodular
Malignant lymphoma small B lymphocytic NOS
Malignant melanoma in congenital melanocytic nevus
Malignant melanoma in giant pigmented nevus
Malignant melanoma in Hutchinson melanotic freckle
Malignant melanoma in precancerous melanosis
Mixed adenocarcinoma and epidermoid carcinoma
Mixed adenocarcinoma and squamous cell carcinoma
Mixed pancreatic endocrine and exocrine tumor malignant
Mixed squamous cell and glandular papilloma
Mucosal-associated lymphoid tissue lymphoma
Neoplasm malignant uncertain whether primary or metastatic
Neoplasm uncertain whether benign or malignant
Paget disease and infiltrating duct carcinoma of breast
Paget disease and intraductal carcinoma of breast
Pancreatic endocrine tumor nonfunctioning
Papillary adenocarcinoma follicular variant
Papillary squamous cell carcinoma in situ
Precursor cell lymphoblastic leukemia NOS
Prostatic intraepithelial neoplasia grade III
Rhabdomyosarcoma with ganglionic differentiation
Splenic B-cell lymphoma/leukemia unclassifiable
Splenic diffuse red pulp small B-cell lymphoma
Splenic lymphoma with villous lymphocytes
T-cell large granular lymphocytic leukemia
Tubular androblastoma with lipid storage
Tumor cells uncertain whether benign or malignant
Unclassified tumor borderline malignancy
Unclassified tumor malignant uncertain whether primary or metastatic
Unclassified tumor uncertain whether benign or malignant
Undifferentiated high-grade pleomorphic sarcoma
Indicates venous invasion was detected by surgery or presence in a tumor specimen
Carcinoid tumor and lung atypical carcinoid tumor
hoarseness/laryngitis/vocal cord inflammation
air entry decreased/fair/poor/diminished
clear lungs to auscultation or percussion
cold symptoms/flu/sinus/nasal congestion
oxygen supplemental-portable O2 at night or continuous
prolonged expiration-long/forced expiratory phase
MC-Carina between right and left lungs (main carina)
TR -Trachea (airway wall between tracheo-esophageal bifurcation and main carina)
Carina NOS (Carina not otherwise specified)
LUDB-Carina between the lingula and upper division left upper lobe
Carina between LUDB orifice and lingula orifice
LUDB-orifice airway wall between LUDB and LB3(LB1+2 carinae)
Lingula orifice airway wall between LUDB and LB4/5 carinae
RMB-Right mainstem bronchus(airway wall between MC & RUL carina)
LMB-Left mainstem bronchus(airway wall between MC & LUL carina)
RL NOS (Right lung not otherwise specified)
RB1/2 - Carina between apical and posterior segments right upper lobe (Carina between RB1 orifice and RB2 orifice)
RB6A/B - Carina between apical and lateral subsegments superior segment RLL
RB6A/C - Carina between apical and medial subsegments superior segment RLL
RB6B/C - Carina between medial and lateral subsegments superior segment RLL
RB7A/B - Carina between medial and lateral subsegments medial basal segment RLL
RB8/9 - Carina between anterior and lateral segments RLL (Carina between RB8 orifice and RB9 orifice)
RB8A/B - Carina between medial and lateral subsegments anterior segment RLL
RB9/10 - Carina between lateral and posterior segments RLL
RB9A/B - Carina between medial and lateral subsegments lateral segment RLL
RB10A/B - Carina between medial and lateral subsegments posterior segment RLL
RB10A/C - Carina between medial and apical subsegments posterior segment RLL
RB1A/B - Carina between medial and lateral subsegments apical segment RUL
RB10B/C - Carina between medial and lateral subsegments posterior segment RLL
RB6 - Carina of superior segment RLL (Carina between RB6 orifice and lower portion of RLL orifice)
RB6 orifice Airway wall between RB6 and RB6A/B/C carinae
Bronchus Intermedius Bronchus (airway wall) between right upper and right middle lobes
RB1/3 - Carina between apical and anterior segments RUL (Carina between RB1 orifice and RB3 orifice)
RB2/3 - Carina between anterior and posterior segments RUL (Carina between RB2 orifice and RB3 orifice)
RB2A/B - Carina between the medial and lateral subsegments of the posterior segment (RUL)
RB3A/B - Carina between the medial and lateral subsegments of the anterior segment RUL
RB4/5 - Carina between the lateral and medial segments right middle lobe (Carina between RB4 orifice and RB5 orifice)
RB4A/B - Carina between the medial and lateral subsegments of the lateral segment of the right middle lobe
RB5A/B - Carina between the medial and lateral subsegments of the medial segment of the right middle lobe
RUL Carinae between RUL orifice and bronchus intermedius
RUL orifice Airway wall between RUL and RB1/RB2/RB3
RB1 orifice Apical segment - right upper lobe(airway wall between RB1 and RB1A/B carinae)
RB2 orifice Posterior segment - right upper lobe(airway wall between RB2 and RB2A/B carinae)
RB3 orifice Anterior segment - right upper lobe(airway wall between RB3 and RB3A/B carinae)
RML - Carina between RML orifice and RLL orifice
RML orifice Airway wall between RML and RB4/5
RB4 orifice Lateral segment right middle lobe (airway wall between RB4 and RB4A/B carinae)
RB5 orifice Medial segment right middle lobe (airway wall between RB5 and RB5A/B carinae)
RLL orifice Airway wall between RML and RB6-10 carinae
RB7 Medial basal segment right lower lobe (Carina at RB7 orifice takeoff from RLL orifice)
RB7 orifice Airway wall between RB7 and RB7A/B carinae
RB8 orifice Anterior segment right lower lobe(airway wall between RB8 and RB8A/B carinae)
RB9 orifice Lateral segment right lower lobe(airway wall between RB9 and RB9A/B carinae)
RB10 Posterior segment right lower lobe (Carina at RB10 orifice takeoff from RLL orifice)
RB10 orifice Airway wall between RB10 and RB10A/B carinae
LL NOS (Left lung not otherwise specified)
LB1/2 Carina between apical and posterior segment left upper lobe (Carina between LB1 orifice and LB2 orifice)
LB4/5 Carina between superior and inferior segment lingula (Carina between LB4 orifice and LB5 orifice)
LB4A/B Carina between medial and lateral subsegments superior segment lingula
LB5A/B Carina between the medial and lateral subsegments inferior segment lingula
LB6A/B Carina between the superior and lateral subsegments superior segment LLL
LB6A/C Carina between the superior and medial subsegments of superior segment LLL
LB6B/C Carina between the medial and lateral subsegments of the superior segment LLL
LB8/9 Carina between the anterior and lateral segments LLL (Carina between LB8 orifice and LB9 orifice)
LB8A/B Carina between the medial and lateral subsegments of the anterior segment LLL
LB9/10 Carina between the lateral and posterior segments LLL (Carina between LB9 orifice and LB10 orifice)
LB9A/B Carina between the medial and lateral subsegments of the lateral segment LLL
LB1A/B Carina between the lateral and medial subsegments of the apical segment of the LUL
LB10A/B Carina between the apical and lateral subsegments of the posterior segment of the LLL
LB10A/C Carina between the apical and medial segments of the posterior segment of the LLL
LB10B/C Carina between the medial and lateral subsegments of the posterior segment of the LLL
LB1+2 orifice The apico-posterior segment of the left upper lobe (airway wall between LB1+2/3 carina and LB1 or LB2)
LB6 The superior segment of the left lower lobe (Carina between LB6 orifice and lower portion of LLL orifice)
LB6 orifice Airway wall between LB6 and LB6A/B carinae
LB1A/C Carina between the apical and lateral subsegments of the apical segment left upper lobe
LB1B/C Carina between the medial and lateral subsegments of the apical segment of the left upper lobe
LB2A/B Carina between the apical and lateral subsegments of the posterior segment of the left upper lobe
LB2A/C Carina between the apical and medial subsegments of the posterior segment of the left upper lobe
LB2B/C Carina between the medial and lateral subsegments of the posterior segment left upper lobe
LB1+2/3 Carina between the apico-posterior and anterior segments of the left upper lobe (Carina between LB1+2 orifice and LB3 orifice)
LB3A/B Carina between the apical and lateral subsegments of the anterior segment of the left upper lobe
LUL Carina between the LUL orifice and LLL orifice (airways)
LUL orifice Airway wall between LUL and LUDB
LB3 orifice Anterior segment left upper lobe(airway wall between LB3 and LB3A/B carinae)
LB4 orifice Superior segment lingula(airway wall between LB4 and LB4A/B carinae)
LB5 orifice Inferior segment lingula(airway wall between LB5 and LB5A/B carinae)
LLL orifice Airway wall between LUL carina and LB6-10 carinae
LB9 orifice Lateral segment left lower lobe(airway wall between LB9 and LB9A/B carinae)
LB8 orifice Anterior segment left lower lobe(airway wall between LB8 and LB8A/B carinae)
LB10 orifice Posterior segment left lower lobe(airway wall between LB10 and LB10A/B carinae)
Invasive mixed ductal and lobular carcinoma
Invasive carcinoma-type cannot be determined
Invasive breast cancer (unrelated to the current cancer)
Left Positive in an area of extraprostatic extension (EPE)
Left Positive in an area of intraprostatic incision (II)
Left Positive where it is difficult to distinguish EPE vs II
Right Positive in an area of extraprostatic extension (EPE)
Right Positive in an area of intraprostatic incision (II)
Right Positive where it is difficult to distinguish EPE vs II
Prostatic adenocarcinoma (conventional NOS)
Acinar prostate mucinous (colloid) adenocarcinoma
Acinar prostate adenocarcinoma-signet-ring variant
Acinar prostate adenocarcinoma-sarcomatoid variant
High-grade prostatic intraepithelial neoplasia (PIN)
prostatic clear cell cribiform hyperplasia
prostatic atypical adenomatous hyperplasia (adenosis or AAH)
Low grade prostatic intraepithelial neoplasia (PIN)/(PIN I)
High grade prostatic intraepithelial neoplasia (HGPIN)/ (PIN II & PIN III)
Leiomyosarcoma (uterine or extra-uterine)
Other Synovial Sarcoma Or Malignant Peripheral Nerve Sheath Tumor Sarcoma
undifferentiated pleomorphic sarcoma or malignant fibrous histiosarcoma
An empty parent attribute for publications
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Types of data associated with the content. Fill out Other Data Type Specified, if not on the list.
Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL
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NanoString GeoMx DSP Spatial Transcriptomics
Other types of data associated with the content.
Name of a dataset (e.g. a Synapse folder)
Synapse ID of folder containing accessory files
Free text field containing description of accessory file(s)
HTAN Data File Identifier(s) of the files associated with the accessory content. Should be comma-separated lists.
Accessory-associated HTAN Parent Data File ID
If manifest is lowest level require HTAN Parent Biospecimen ID
Assay for analyzing specific mutations in a given sample
Assay that uses beads to target a specific locus on the genome.
Raw electron microscopy data as one TIFF file per plane for a 3D image stack or per tile for a 2D large area montage
How the electron microscopy signal is generated from the sample
Make and model of the EM instrument used
Duration in microseconds (µs) of electron beam data collection per pixel or frame
Accelerating voltage in kiloelectronvolts (keV)
Physical stage tilt in degrees with respect to the electron beam
Does the image use standard SEM contrast or TEM contrast
Processed electron microscopy data as one OME-TIFF image per plane or montage
Percentage of image overlap to allow tile stitching in x direction
Segmented electron microscopy data as .am or .tiff formats
Movies or other derived files from electron microscopy data
Biolegend Total seq B Human Universal cocktail V1.0
Biolegend Total seq C Human Universal cocktail V1.0
Yes/No indicator to designate the participant for whom precancerous lesion(s) was identified (premalignancy only).
Number of days between the date used for index and the reference date for designation of vital status
Indicates that the participant is a precancer case
Number of days between the date used for index and the reference date for designation of precancer status.
World Health Organization Classification of Tumour cytopathology-based coding system, includes 'precursor lesion' designations for precancers. ICD-O-3 morphology axis format eg 1234/1