Computational protocol: Mosaic mutations in blood DNA sequence are associated with solid tumor cancers

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Protocol publication

[…] Genotypes data set was created by joint variant calling of cancer cases and non-cancer controls using HaplotypeCaller (GATK-3.0)– with Broad Institute calling pipeline. For functional annotation of variants we used Variant Effect Predictor by Ensembl. PCA was performed to keep for analysis only samples of European ancestry to eliminate possible population effects. PCA was performed with EIGENSTRAT., Resulting genotype file was used to create a PLINK/SEQ (Https://atgu.mgh.harvard.edu/plinkseq/. PLINK/SEQ) project for further manipulations. […]

Pipeline specifications

Software tools GATK, VEP, PLINK/SEQ
Application GWAS
Diseases Glioblastoma, Leukemia, Lung Neoplasms, Melanoma, Neoplasms, Ovarian Neoplasms, Hereditary Breast and Ovarian Cancer Syndrome