Bulk RNA-seq alignment protocol description

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 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.

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.

A custom acquisition method [Text - max length 100 characters]

Records the method of acquisition or source for the specimen under consideration.

Activity or behavior of any independent integral living, organization or mechanical actor in the world

Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3

State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.

Base sequence of the sequencing adapter. String

List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...

Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.

The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.

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.

Age at the time of diagnosis expressed in number of days since birth.

For GDC submission only - this is going to be always 0 since HTAN's index is the date of birth

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.

Indicate if individual has alcohol exposure

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.

Read length used for alignment if hard trimming was applied

Generic name for the workflow used to analyze a data set.

Link to workflow used for read alignment. DockStore.org recommended. String

A molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen

The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen

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.

The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment

A subcellular location, cell type or gross anatomical part

Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))

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.

Imaging specific: information on antigen retrieval when it is used for a pathology specimen. E.g. pH 6 (Citric Acid), pH 8 (tris), or pH 10. [Text - max length 100] 

The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.

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]

The type and level of assay this metadata applies to (e.g. RPPA, Nanostring DSP, etc.)

Average base quality collected from samtools. Number

Average insert size collected from samtools. Integer

Average read length collected from samtools. Integer

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.

A calculated numerical quantity that represents an individual's weight to height ratio.

The best improvement achieved throughout the entire course of protocol treatment.

One or more causally connected executions of molecular functions

Either an individual molecular activity, or a collection of causally connected molecular activities

HTAN biological entity; this can be tissue, blood, analyte and subsamples of those

Imaging specific: text term to capture the relative position and orientation of the core location within a piece of tissue on the slide relative to the region of interest slide coordinates. use https://docs.openmicroscopy.org/ome-model/6.0.1/developers/roi.html#shape-concrete-implementations if applciable

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 upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.

Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.

Brain cancer specific attributes in Clinical Data Tier 3

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 numeric Allred score, that is cell staining percentage plus intensity, to determine estrogen receptor status.

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.

Breast cancer specific attributes in Clinical Data Tier 3

Result of Centromere 17 testing in a sample or specimen of metastatic breast carcinoma, expressed as a range of values.

The means, manner of procedure, or systematic course of actions performed in order to discover or identify breast cancer.

Text term to indicate the ER staining intensity on pathology assessment in a participant with breast cancer

A numerical quantity measured or assigned or computed which captures the estrogen receptor level measured in a participant with breast cancer

Text term to represent the overall result of Estrogen Receptor (ER) testing in a participant with breast cancer

Number of Cells Counted for HER2 & Centromere 17 Copy Numbers in a participant with breast cancer

HER2 chromosome 17 ratio in participants with breast cancer

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

Classification of the type of invasive breast carcinoma diagnosed based on histologic attributes.

Text term to indicate the PR staining intensity on pathology assessment in a participant with breast cancer

A numerical quantity measured or assigned or computed which captures the progesterone receptor level measured in a participant with breast cancer

Text term to represent the overall result of Progresterone Receptor (PR) testing in a participant with breast cancer

Text name of a surgical procedure performed for a person with a diagnosis of 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).

The breast quadrant or structure from which the breast tissue specimen was removed for microscopic examination.

The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.

Bulk Whole Exome Sequencing aligned files and QC

Bulk Whole Exome Sequencing called variants

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.

Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase

Offset in sequence for cDNA read (in bp): number

Highly-multiplexed plate-based single-cell RNA-Seq assay

The status of central nervous system leukemia at the time of diagnosis.

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

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.

Indicator that describes if cancer treatment was modified for the patient due to COVID-19 infectious disorder

Text term that retrospectively indicates the worst complications during COVID-19 infectious disorder in the patient.

The patient's current COVID-19 status of sign or symptom events or interventions

The indicator that describes whether or not a COVID-19 infectious disorder occurred.

The indicator that describes whether or not there was a COVID-19 positive test result.

Type of inherited germline or other gene mutations that confers heightened susceptibility to cancer identified in patient history

An individual organism that has a patient role in some clinical context.

The text term used to describe the source used to determine the patient's cause of death.

The text term used to describe the suspected cause or reason for the patient disease response.

Length of cell barcode read (in bp): number

Offset in sequence for cell barcode read (in bp): number

SAM tag for cell barcode field; please provide a valid cell barcode tag

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.

Median number of genes detected per cell. Number

Number of sequenced  cells. Applies to raw counts matrix only.

This must match the corresponding field in the OME-XML / TIFF header. (eg "Channel:0:1")

Full path of uploaded companion CSV file containing channel-level metadata details

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.

May be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex material with multiple chemical entities as part

The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.

The quantity of daily use of tobacco, in the form of a plug, usually flavored, for chewing rather than smoking.

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 average number of cigarettes smoked per day.

Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.

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.

Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities

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.

The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.

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).

Number of days from the research participant's index date that the biospecimen was obtained.

Material Specimen is collected into post procedure

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 means, manner of procedure, or systematic course of actions performed in order to discover or identify colorectal cancer

The yes/no/not applicable indicator that describes if patient has diagnosis of colorectal cancer with known KRAS.

Colorectal cancer specific attributes in Clinical Data Tier 3

The description of the border configuration of a colorectal tumor at pathologic assessment.

Type of adenoma associated with the polyp

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

Free text field (generally for QC comment)

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.

Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.

An enumerated list of the type of concomitant medication received by the patient.

Fraction of reads coming from cross-sample contamination collected from GATK4. Number

Estimation error of cross-sample contamination collected from GATK4. Number

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.

Indicate if library preparation was based on revived frozen cells.

Reported lung cancer related symptoms person is currently experiencing

Significant pathologic finding present in addition to the cutaneous melanoma.

Text term to indicate presence of tumor at resection margins

Description of degree of lymphocytic infiltration surrounding and disrupting tumor cells of the vertical growth phase in a cutaneous melanoma.

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.

Description of extent of disruption to the surface of the skin caused by the cutaneous melanoma.

The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles)

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.

The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.

Represents the percentage of RNA fragments that are >200 nucleotides in size. Number

Number of days between the date used for index and the date of the patient's adverse event.

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.

Number of days between the date used for index and the date the patient was diagnosed with a comorbidity.

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.

Number of days between the date used for index and the date the patient was diagnosed with the malignant disease.

Number of days between the date used for index and the date of the patient's last follow-up appointment or contact.

Number of days between the date used for index and the date the imaging or scan was performed on the patient.

Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.

Number of days between the date used for index and the date the patient's disease progressed.

Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free.

Number of days between the date used for index and the date the patient's disease recurred.

Number of days between the date used for index and the date the treatment ended.

Number of days between the date used for index and the date the treatment started.

This indicates the participant is dead and defines further required metadata

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.

Individual biomedical demographics attributes

A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment"

Text term used to describe the types of treatment used to manage diabetes.

The order in which the individual planes of data are interleaved.

Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.

Code assigned to describe the patient's response or outcome to the disease.

The tissue dissociation method used for scRNASeq or scATAC-seq assays

A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease

A drug exposure is an intake of a particular chemical substance

Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5]

The ECOG functional performance status of the patient/participant.

The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization

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)

Use of non-traditional cigarette nicotine delivery device (electronic cigarette, ENDS - electronic nicotine delivery system)

Center/peak of the emission spectrum (nm)

Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.

Version of ASCII encoding of quality values found in the file. String

The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript

A feature of the environment of an organism that influences one or more phenotypic features of that organism, potentially mediated by genes

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.

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.

Class of evidence that supports an association

The text term used to describe the type of evidence used to determine whether the patient's disease recurred

Nominal width of excitation spectrum (nm)

Center/peak of the excitation spectrum (nm)

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.

How quantities are corrected for gene length

The degree to which the lesion has been cut out, or resected.

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.

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

Level Number	Definition	Example Data
1	Unaligned reads	FASTQ
2	Aligned reads	BAM
3	Gene level expression, unnormalized	Gene & isoform expression-level data (.csv)

HTAN Bulk RNA Sequencing Data Standard