Cohorts Data in ICA Base

ICA Cohorts data can be viewed in an ICA Project Base instance as a shared database. A shared database in ICA Base operates as a database view. To use this feature, enable Base for your project prior to starting any ICA Cohorts ingestions. See Base for more information on enabling this feature in your ICA Project.

ICA Cohorts Base Tables

After ingesting data into your project, select Phenotypic and Molecular data are available to view in Base. See Cohorts Import for instruction on importing data sets into Cohorts.

1. Post ingestion, data will be represented in Base.

2. Select BASE from the ICA left-navigation and click Query.

3. Under the New Query window, a list of tables is displayed. Expand the Shared Database for Project \<your project name\> .

4. Cohorts tables will be displayed.

5. To preview the table and fields click each view listed.

6. Clicking any of these views then selecting PREVIEW on the right-hand side will show you a preview of the data in the tables.

Note: If your ingestion includes Somatic variants, there will be two molecular tables: ANNOTATED_SOMATIC_MUTATIONS and ANNOTATED_VARIANTS. All ingestions will include a PHENOTYPE table.

Note: The PHENOTYPE table includes a harmonized set that is collected across all data ingestions and is not representative of all data ingested for the Subject or Sample. Sample information is also displayed in this table, if applicable. Sample information drives the annotation process if molecular data is included in the ingestion. That data is stored in the PHENOTYPE table.

Phenotype Data

Field Name	Type	Description
SAMPLE_BARCODE	STRING	Sample Identifier
SUBJECTID	STRING	Identifer for Subject entity
STUDY	STRING	Study designation
AGE	NUMERIC	Age in years
SEX	STRING	Sex field to drive annotation
POPULATION	STRING	Population Designation for 1000 Genomes Project
SUPERPOPULATION	STRING	Superpopulation Designation from 1000 Genomes Project
RACE	STRING	Race according to NIH standard
CONDITION_ONTOLOGIES	VARIANT	Diagnosis Ontology Source
CONDITION_IDS	VARIANT	Diagnosis Concept Ids
CONDITIONS	VARIANT	Diagnosis Names
HARMONIZED_CONDITIONS	VARIANT	Diagnosis High-level concept to drive UI
LIBRARYTYPE	STRING	Seqencing technology
ANALYTE	STRING	Substance sequenced
TISSUE	STRING	Tissue source
TUMOR_OR_NORMAL	STRING	Tumor designation for somatic
GENOMEBUILD	STRING	Genome Build to drive annotations - hg38 only
SAMPLE_BARCODE_VCF	STRING	Sample ID from VCF
AFFECTED_STATUS	NUMERIC	Affected, Unaffected, or Unknown for Family Based Analysis
FAMILY_RELATIONSHIP	STRING	Relationship designation for Family Based Analysis

Annotated Variants

This table will be available for all projects with ingested molecular data

Field Name	Type	Description
SAMPLE_BARCODE	STRING	Original sample barcode used in VCF column
STUDY	STRING	Study designation
GENOMEBUILD	STRING	Only hg38 is supported
CHROMOSOME	STRING	Chromosome without 'chr' prefix
CHROMOSOMEID	NUMERIC	Chromosome ID: 1..22, 23=X, 24=Y, 25=Mt
DBSNP	STRING	dbSNP Identifiers
VARIANT_KEY	STRING	Variant ID in the form "1:12345678:12345678:C"
NIRVANA_VID	STRING	Broad Institute VID: "1-12345678-A-C"
VARIANT_TYPE	STRING	Description of Variant Type (e.g. SNV, Deletion, Insertion)
VARIANT_CALL	NUMERIC	1=germline, 2=somatic
DENOVO	BOOLEAN	true / false
GENOTYPE	STRING	"G|T"
READ_DEPTH	NUMERIC	Sequencing read depth
ALLELE_COUNT	NUMERIC	Counts of each alternate allele for each site across all samples
ALLELE_DEPTH	STRING	Unfiltered count of reads that support a given allele for an individual sample
FILTERS	STRING	Filter field from VCF. If all filters pass, field is PASS
ZYGOSITY	NUMERIC	0 = hom ref, 1 = het ref/alt, 2 = hom alt, 4 = hemi alt
GENEMODEL	NUMERIC	1=Ensembl, 2=RefSeq
GENE_HGNC	STRING	HUGO/HGNC gene symbol
GENE_ID	STRING	Ensembl gene ID ("ENSG00001234")
GID	NUMERIC	NCBI Entrez Gene ID (RefSeq) or numerical part of Ensembl ENSG ID
TRANSCRIPT_ID	STRING	Ensembl ENST or RefSeq NM_
CANONICAL	STRING	Transcript designated 'canonical' by source
CONSEQUENCE	STRING	missense, stop gained, intronic, etc.
HGVSC	STRING	The HGVS coding sequence name
HGVSP	STRING	The HGVS protein sequence name

Annotated Somatic Mutations

This table will only be available for data sets with ingested Somatic molecular data.

Field Name	Type	Description
SAMPLE_BARCODE	STRING	Original sample barcode, used in VCF column
SUBJECTID	STRING	Identifier for Subject entity
STUDY	STRING	Study designation
GENOMEBUILD	STRING	Only hg38 is supported
CHROMOSOME	STRING	Chromosome without 'chr' prefix
DBSNP	NUMERIC	dbSNP Identifiers
VARIANT_KEY	STRING	Variant ID in the form "1:12345678:12345678:C"
MUTATION_TYPE	NUMERIC	Rank of consequences by expected impact: 0 = Protein Truncating to 40 = Intergenic Variant
VARIANT_CALL	NUMERIC	1=germline, 2=somatic
GENOTYPE	STRING	"G|T"
REF_ALLELE	STRING	Reference allele
ALLELE1	STRING	First allele call in the tumor sample
ALLELE2	STRING	Second allele call in the tumor sample
GENEMODEL	NUMERIC	1=Ensembl, 2=RefSeq
GENE_HGNC	STRING	HUGO/HGNC gene symbol
GENE_ID	STRING	Ensembl gene ID ("ENSG00001234")
TRANSCRIPT_ID	STRING	Ensembl ENST or RefSeq NM_
CANONICAL	BOOLEAN	Transcript designated 'canonical' by source
CONSEQUENCE	STRING	missense, stop gained, intronic, etc.
HGVSP	STRING	HGVS nomenclature for AA change: p.Pro72Ala

Annotated Copy Number Variants

This table will only be available for data sets with ingested CNV molecular data.

Field Name	Type	Description
SAMPLE_BARCODE	STRING	Sample barcode used in the original VCF
GENOMEBUILD	STRING	Genome build, always 'hg38'
NIRVANA_VID	STRING	Variant ID of the form 'chr-pos-ref-alt'
CHRID	STRING	Chromosome without 'chr' prefix
CID	NUMERIC	Numerical representation of the chromosome, X=23, Y=24, Mt=25
GENE_ID	STRING	NCBI or Ensembl gene identifier
GID	NUMERIC	Numerical part of the gene ID; for Ensembl, we remove the 'ENSG000..' prefix
START_POS	NUMERIC	First affected position on the chromosome
STOP_POS	NUMERIC	Last affected position on the chromosome
VARIANT_TYPE	NUMERIC	1 = copy number gain, -1 = copy number loss
COPY_NUMBER	NUMERIC	Observed copy number
COPY_NUMBER_CHANGE	NUMERIC	Fold-chang of copy number, assuming 2 for diploid and 1 for haploid as the baseline
SEGMENT_VALUE	NUMERIC	Average FC for the identified chromosomal segment
PROBE_COUNT	NUMERIC	Probes confirming the CNV (arrays only)
REFERENCE	NUMERIC	Baseline taken from normal samples (1) or averaged disease tissue (2)
GENE_HGNC	STRING	HUGO/HGNC gene symbol

Annotated Structural Variants

This table will only be available for data sets with ingested SV molecular data. Note that ICA Cohorts stores copy number variants in a separate table.

Field Name	Type	Description
SAMPLE_BARCODE	STRING	Sample barcode used in the original VCF
GENOMEBUILD	STRING	Genome build, always 'hg38'
NIRVANA_VID	STRING	Variant ID of the form 'chr-pos-ref-alt'
CHRID	STRING	Chromosome without 'chr' prefix
CID	NUMERIC	Numerical representation of the chromosome, X=23, Y=24, Mt=25
BEGIN	NUMERIC	First affected position on the chromosome
END	NUMERIC	Last affected position on the chromosome
BAND	STRING	Chromosomal band
QUALIITY	NUMERIC	Quality from the original VCF
FILTERS	ARRAY	Filters from the original VCF
VARIANT_TYPE	STRING	Insertion, deletion, indel, tandem_duplication, translocation_breakend, inversion ("INV"), short tandem repeat ("STR2")
VARIANT_TYPE_ID	NUMERIC	21=insertion, 22=deletion, 23=indel, 24=tandem_duplication, 25=translocation_breakend, 26=inversion ("INV"), 27=short tandem repeat ("STR2")
CIPOS	ARRAY	Confidence interval around first position
CIEND	ARRAY	Confidence interval around last position
SVLENGTH	NUMERIC	Overall size of the structural variant
BONDCHR	STRING	For translocations, the other affected chromosome
BONDCID	NUMERIC	For translocations, the other affected chromosome as a numeric value, X=23, Y=24, Mt=25
BONDPOS	STRING	For translocations, positions on the other affected chromosome
BONDORDER	NUMERIC	3 or 5: Whether this fragment (the current variant/VID) "receives" the other chromosome's fragment on it's 3' end, or attaches to the 5' of the other chromosome fragment
GENOTYPE	STRING	Called genotype from the VCF
GENOTYPE_QUALITY	NUMERIC	Genotype call quality
READCOUNTSSPLIT	ARRAY	Read counts
READCOUNTSPAIRED	ARRAY	Read counts, paired end
REGULATORYREGIONID	STRING	Ensembl ID for the affected regulatory region
REGULATORYREGIONTYPE	STRING	Type of the regulatory region
CONSEQUENCE	ARRAY	Variant consequence according to SequenceOntology
TRANSCRIPTID	STRING	Ensembl of RefSeq transcript identifier
TRANSCRIPTBIOTYPE	STRING	Biotype of the transcript
INTRONS	STRING	Count of impacted introns out of the total number of introns, specified as "M/N"
GENEID	STRING	Ensembl or RefSeq gene identifier
GENEHGNC	STRING	HUGO/HGNC gene symbol
ISCANONICAL	BOOLEAN	Is the transcript ID the canonical one according to Ensembl?
PROTEINID	STRING	RefSeq or Ensembl protein ID
SOURCEID	NUMERICAL	Gene model: 1=Ensembl, 2=RefSeq

Raw RNAseq data tables for genes and transcripts

These tables will only be available for data sets with ingested RNAseq molecular data.

Table for gene quantification results:

Field Name	Type	Description
GENOMEBUILD	STRING	Genome build, always 'hg38'
STUDY_NAME	STRING	Study designation
SAMPLE_BARCODE	STRING	Sample barcode used in the original VCF
LABEL	STRING	Group label specified during import: Case or Control, Tumor or Normal, etc.
GENE_ID	STRING	Ensembl or RefSeq gene identifier
GID	NUMERIC	Numerical part of the gene ID; for Ensembl, we remove the 'ENSG000..' prefix
GENE_HGNC	STRING	HUGO/HGNC gene symbol
SOURCE	STRING	Gene model: 1=Ensembl, 2=RefSeq
TPM	NUMERICAL	Transcripts per million
LENGTH	NUMERICAL	The length of the gene in base pairs.
EFFECTIVE_LENGTH	NUMERICAL	The length as accessible to RNA-seq, accounting for insert-size and edge effects.
NUM_READS	NUMERICAL	The estimated number of reads from the gene. The values are not normalized.

The corresponding transcript table uses TRANSCRIPT_ID instead of GENE_ID and GENE_HGNC.

Differential expression tables for genes and transcripts

These tables will only be available for data sets with ingested RNAseq molecular data.

Table for differential gene expression results:

Field Name	Type	Description
GENOMEBUILD	STRING	Genome build, always 'hg38'
STUDY_NAME	STRING	Study designation
SAMPLE_BARCODE	STRING	Sample barcode used in the original VCF
CASE_LABEL	STRING	Study designation
GENE_ID	STRING	Ensembl or RefSeq gene identifier
GID	NUMERIC	Numerical part of the gene ID; for Ensembl, we remove the 'ENSG000..' prefix
GENE_HGNC	STRING	HUGO/HGNC gene symbol
SOURCE	STRING	Gene model: 1=Ensembl, 2=RefSeq
BASEMEAN	NUMERICAL
FC	NUMERICAL	Fold-change
LFC	NUMERICAL	Log of the fold-change
LFCSE	NUMERICAL	Standard error for log fold-change
PVALUE	NUMERICAL	P-value
CONTROL_SAMPLECOUNT	NUMERICAL	Number of samples used as control
CONTROL_LABEL	NUMERICAL	Label used for controls

The corresponding transcript table uses TRANSCRIPT_ID instead of GENE_ID and GENE_HGNC.