Qingyao - Institute Progress Report
IMLS Progress Report¶
Towards understanding population effect on cancer¶
With a combination of ~50,000 curated oncogenomic array data from the arrayMap database and ~20,000 profiles from TCGA project depository, we perform a meta- analysis to investigate influence of genetic background on the CNV patterns in cancer. From sequencing data of 26 world-wide populations from 1000 Genomes project, we extract the SNP markers and use them for subsequent sample analysis. First, we show that using admixture analysis, the population classification is accurate even from low- resolution arrays (10k markers). This appends genome-derived population information to the database, as an additional layer to the geographic location of each sample. Next, we will perform haplotype phasing and linkage mapping to propose potential population-specific cancer-predisposing variants.