Pathogenic germline variants in 10,389 adult cancers

Video presentation for “Pathogenic germline variants in 10,389 adult cancers” (Huang et al., Cell 2018)
By Kuan Huang, check us out at:
https://ComputationalOmicsLab.org

Pathogenic Germline Variants in 10,389 Adult Cancers
The TCGA PanCanAtlas germline analysis working group is investigating germline variants in the largest sequencing cohort of cancer to date: 10,389 cases in 33 cancer types.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. PMID: 29625052
Data Access
De-identified variant-level data for prioritized VUS and pathogenic variants: Table S2 of the publication.

The protected variants+sample ID and the full callset (Authorized User only):

GDC link: https://gdc.cancer.gov/about-data/publications/PanCanAtlas-Germline-AWG

Compressed VCF file of the combined, filtered variant calls using GATK, VarScan2, and Pindel on WES data of the 10,389 final passed-QC samples. – PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf.gz

Tabix file of the compressed VCF file of the combined, filtered variant calls using GATK, VarScan2, and Pindel on WES data of the 10,389 final passed-QC samples. – PCA.r1.TCGAbarcode.merge.tnSwapCorrected.10389.vcf.gz.tbi

Prioritized, cancer related variants discovered in 10,389 cases. Please use “Overall_Classification” column to distinguish between Pathogenic, Likely Pathogenic and Priortizied VUSs. – PCA_pathVar_integrated_filtered_adjusted.tsv

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