Exome sequencing of 10 biopsies from the same CRPC tumor

This dataset includes WES of 10 CRPC biopsies + control. Each ran on 4 HiSeq lanes. The dataset accompanies the paper "Inferring clonal composition from multiple tumor biopsies", Manica et al.: Without detailed accounting for CNVs the accuracy of methods that estimate mutation frequencies can be alarmingly poor even when multiple biopsies are profiled for each tumor. To help resolve this problem we propose an optimization algorithm—Chimæra: clonality inference from mutations across biopsies—that accounts for the effects of CNVs and relies on having multiple biopsies from the same tumor to estimate both mutation frequencies and copy numbers of mutated alleles. We show that Chimæra is better able to estimate mutation frequencies in unstable genomes with consistently good performance relative to other methods. When studying profiles of multiple biopsies of a high-risk prostate tumor, we show that Chimæra inferences allow for the reconstruction of subclones and their ancestral relations. The paper describes 10 biopsies. To translate these to accessions here, use the following encoding: LibraryID Biopsy JAD-1C 1 JAD-23C 2 JAD-24C 3 JAD-4C 4 JAD-5C 5 JAD-6C 6 JAD-7C 7 JAD-25C 8 JAD-9C 9 JAD-26C 10 JAD-11C Normal