Whole Genome Sequencing of Colorectal Cancers: Mapping Molecular Alterations for Precision Medicine

By: Najwa Farhah Md Yusof (najwa@siswa.ukm.edu.my)

This on-going project aims to study the sequence alterations in Malaysian colorectal cancers (CRC) via the whole genome sequencing (WGS) approach.

We are looking into somatic mutations of CRC by comparing tumour and germline DNA from Malaysian CRC patients. The samples were provided by PPUKM-UMBI Biobank, and were assessed for quality prior to sequencing. With a WGS depth of coverage of approximately 33x, each sample gave a throughput of around 700 million raw reads or 100 Gb of data.

Preliminary analysis showed the sequencing data are of good quality, with over 97% of sequencing data retained after the quality filtering process. Currently in progress is the mapping and alignment to the reference human genome (hg19). Variant calling and annotation will be carried out soon.

This project, funded by the Ministry of Higher Education (MOHE)’s Long-Term Research Grant Scheme (LRGS) and spearheaded by UMBI’s director, Prof. Datuk Dr. A Rahman A Jamal, is part of a larger research in partnership with other leading Malaysian universities. First of its kind, the goal is to obtain a comprehensive description of genomic, proteomic and metabolomic changes in CRC, which is of clinical and societal importance in Malaysia.