Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Lines. Homo sapiens

We developed HiCNAtra tool to identify high-resolution CNVs (copy number variations) from 3C-seq/Hi-C data of cancer cell lines with abnormal karyotype and to correct the chromatin contact matrices from all systematic biases including CNV-induced bias. In this study, we have generated genome-wide chromatin interaction maps of K562 (chronic myelogenous leukemia) and H69AR (small cell lung carcinoma) cell lines using high-throughput chromosome conformation capture- sequencing (3C-seq) technique.