Refer to DNA Analysis Methods for more information.
File name: {SAMPLE_ID}_hard-filtered.gvcf.gz
The small variant genome variant call file contains information on all candidate small variants evaluated, including complex variants up to 15 bp from phased variant calling across the entire TSO 500 panel.
The variant status is determined by the FILTER column in the genome VCF as follows.
File name: {SAMPLE_ID}_DNAVariants_Annotated.json.gz
The small variants annotated file provides variant annotation information for all nonreference positions from the genome VCF including pass and nonpass variants.
The TMB trace file provides comprehensive information on how the TMB value is calculated for a given sample. All passing small variants from the small variant filtering step are included in this file. To calculate the numerator of the TmbPerMb value in the TMB JSON, set the TSV file filter to use the IncludedInTMBNumerator with a value of True.
The TMB trace file is not intended to be used for variant inspections. The filtering statuses are exclusively set for TMB calculation purposes. Setting a filter does not translate into the classification of a variant as somatic or germline.
File name: {SAMPLE_ID}.cnv.vcf
The copy number VCF file contains CNV calls for DNA libraries for 500 of the 523 genes from the TSO 500 manifest, as some genes have high homology to other genes or only have probes covering one exon region. The CNV call indicates fold change results for each gene classified as reference, deletion, or amplification. The CNV vcf reports fold change for all 500 genes while the reports only genes that have events qualifying as amplifications or deletions.
The value in the QUAL column of the VCF is a Phred transformation of the p-value where Q=-10xlog10(p-value). The p-value is derived from the t-test between the fold change of the gene against the rest of the genome. Higher Q-scores indicate higher confidence in the CNV call.
In the VCF notation, <DUP> indicates the detected fold change (FC) is greater than a predefined amplification cutoff. <DEL> indicates the detected FC is less than a predefined deletion cutoff for that gene. This cutoff can vary from gene to gene.
In analysis versions prior to v2.5, <DEL> calls in the VCF are marked as LowValidation. The LowValidation filter indicates that the calls have been validated only with in silico data sets and are provided as information only.
Each copy number variant is reported as a fold change on normalized read depth in a testing sample relative to the normalized read depth in diploid genomes. Given tumor purity, you can infer the ploidy of a gene in the sample from the reported fold change.
Given tumor purity X%, for a reported fold change Y, you can calculate the copy number n using the following equation:
For example, a tumor purity at 30% and a MET with fold change of 2.2x indicates that 10 copies of MET DNA are observed.
The GIS Score is a Proprietary Genomic Instability Score (GIS) indicating level of genomic instability in sample genome. Combination of Loss of Heterozygosity (LOH), Telomeric allelic imbalance and Large-scale State Transitions (LST) scores. The GIS scores provided by TruSight Oncology 500 HRD show good correlation (R2= 0.98) with Myriad Genetics GIS however they are not identical (Refer to TruSight Oncology 500 HRD Product Data Sheet Doc# M-GL-00748 for more details). GIS from alternative HRD assays should be not be considered equivalent to Illumina/Myriad GIS.
Within the HRD output (Logs_Intermediates/Gis/), LOH variants are not denoted in the .abcn_annotated.vcf; instead this information can be found in the abcn_genes.tsv
*The GIS algorithm within the TSO500 pipeline (which does not have a cell line mode due to the TSO500 pipeline being non-configurable) is only intended for FFPE samples. Cell line samples will not accurately report GIS results as the tumor fraction (>90%) is too high to reliably distinguish tumor vs germline variants.
Site filtered because the indel length is too long.
mapping_quality
Site filtered because median mapping quality of alt reads at this locus does not meet threshold.
multiallelic
Site filtered because more than two alt alleles pass tumor LOD.
no_reliable_supporting_read
Site filtered because no reliable supporting somatic read exists.
read_position
Site filtered because median of distances between start/end of read and this locus is below threshold.
str_contraction
Site filtered due to suspected PCR error where the alt allele is one repeat unit less than the reference.
too_few_supporting_reads
Site filtered because there are too few supporting reads in the tumor sample.
weak_evidence
Somatic variant score (SQ) does not meet threshold.
systematic_noise
Site filtered based on evidence of systematic noise in normal sample.
excluded_regions
Site overlaps with VC excluded regions bed.
CytoBand
Cytoband of variant
GeneName
Name of gene if applicable. A semicolon delimited list is used for multiple genes.
VariantType
Type of the variant: SNV, insertion, deletion, MNV
CosmicIDs
Cosmic IDs, if multiple concatenated by “;”
MaxCosmicCount
Maximum Cosmic study count
AlleleCountsGnomadExome
Variant allele count in gnomAD exome database
AlleleCountsGnomadGenome
Variant allele count in gnomAD genome database
AlleleCounts1000Genomes
Variant allele count in 1000 genomes database
MaxDatabaseAlleleCounts
Maximum variant allele count over the three databases
GermlineFilterDatabase
TRUE if variant was filtered by the database filter
GermlineFilterProxi
TRUE if variant was filtered by the proxi filter
CodingVariant
TRUE if variant is in the coding region
Nonsynonymous
TRUE if variant has any transcript annotations with nonsynonymous consequences
IncludedinTMBNumerator
TRUE if variant is used in the TMB calculation
PASS
PASS variants.
base_quality
Site filtered because median base quality of alt reads at this locus does not meet threshold.
filtered_reads
Site filtered because the fraction of reads is too large.
fragment_length
Site filtered because absolute difference between the median fragment length of alt reads and median fragment length of ref reads at this locus exceeds threshold.
low_depth
Site filtered because the read depth is too low.
low_frac_info_reads
Site filtered because the fraction of informative reads is below threshold.
Chromosome
Chromosome
Position
Position of variant
RefCall
Reference base
AltCall
Alternate base
VAF
Variant allele frequency
Depth
Coverage of position
long_indel
The Illumina DRAGEN TruSight Oncology 500 Analysis Software allows for analysis of sequencing data generated from the TruSight Oncology 500 HRD assay. When HRD samples are analyzed new results and metrics are included in the CombinedVariantOutput and MetricsOutput files respectively. The following tables detail how these scores and QC metrics are derived.
Genomic Instability Score (GIS)
Proprietary Genomic Instability Score (GIS) indicating level of genomic instability in sample genome. Combination of Loss of Heterozygosity (LOH), Telomeric allelic imbalance and Large-scale State Transitions (LST) scores. The GIS scores provided by TruSight Oncology 500 HRD show good correlation (R2= 0.98) with Myriad Genetics GIS however they are not identical (Refer to TruSight Oncology 500 HRD Product Data Sheet Doc# M-GL-00748 for more details). GIS from alternative HRD assays should be not be considered equivalent to Illumina/Myriad GIS.
The GIS algorithm within the TSO500 pipeline (which does not have a cell line mode due to the TSO500 pipeline being non-configurable) is only intended for FFPE samples. Cell line samples will not accurately report GIS results as the tumor fraction (>90%) is too high to reliably distinguish tumor vs germline variants.
PCT_TARGET_HRD_50X
Percent of HRD probe SNP panel covered by at least 50X coverage
DNA Library QC Metrics for GIS
EXCESSIVE_TF
EXCESSIVE TF indicates if there is excessive tumor content in sample. Troubleshooting: Samples with pure tumor fraction >90% are outside the design for GIS estimation (this includes pure tumor cell lines)
DNA Library QC Metrics for GIS
ALLELE_DOSAGE_RATIO
Proprietary Myriad Genetics estimate of b-allele dosage based on b-allele noise/signal ratio. B-Allele noise is correlated with coverage; lower coverage samples will have higher noise. B-allele signal is also correlated with tumor fraction; a higher tumor fraction produces a higher signal for b-allele sites. Samples with lower tumor fraction and higher amount of noise (or lower coverage) will have higher Allele Dosage Ratio. The upper limit of the score is 50, therefore any sample with 50 Allele Dosage Ratio can be assumed to have tumor fraction close to zero and typically has a GIS = 0.
DNA Expanded Metrics
MEDIAN_TARGET_HRD_COVERAGE
Median target fragment coverage across all target positions in the genome. Coverage is the total number of non-duplicate pair alignments that overlap.
DNA Expanded Metrics