Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics.

ABSTRACT: Cancer genomes are highly complex and heterogeneous. The standard short-read sequencing and analytical methods are unable to provide the complete and precise base-level structural variant landscape of cancer genomes. In this work, we apply high-resolution long accurate HiFi and long-range Hi-C sequencing to the melanoma COLO829 cancer line. Also, we develop an efficient graph-based approach that processes these data types for chromosome-scale haplotype-resolved reconstruction to characterise the cancer precise structural variant landscape. Our method produces high-quality phased scaffolds on the chromosome level on three healthy samples and the COLO829 cancer line in less than half a day even in the absence of trio information, outperforming existing state-of-the-art methods. In the COLO82

SUBMITTER: Garg S 

PROVIDER: S-EPMC10011606 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature