Genomic analysis of Malaysian breast cancers unravel molecular differences from Caucasian breast cancers


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Muhammad Mamduh Ahmad Zabidi1,Jia Wern Pan1,Patsy Pei Sze Ng1,Mei Yee Meng1,Stephen-John Sammut2,Oscar Rueda2,Carlos Caldas2,Suet-Feung Chin2,Soo-Hwang Teo1
1Cancer Research Malaysia,2Cancer Research UK Cambridge Institute

Abstract

Background

Breast cancer is the leading cause of cancer death among women. In Asia, breast cancer incidence shows growth over the past decades. Several appreciable differences exist between Asian and Caucasian breast cancers, for example younger age of incidence and higher prevalence of hereditary factors, hinting at crucial differences at the molecular level.

Method

We performed whole exome sequencing (WES) on 576 Malaysian breast cancers (at median coverage 75X) and their matched normal blood (40X) to detect single nucleotide variations (SNVs) and small insertions and deletions (indels). We also performed shallow whole genome sequencing (sWGS) to detect major chromosomal aberrations.

Results

We captured known copy number changes, together with major breast cancer genes and their phenotypes, for example high frequency of SNVs in hotspot regions in PIK3CA and indels in GATA3. We additionally show that Malaysian breast cancer show higher prevalence of TP53 as compared to Caucasian breast cancer cases, consistent with previous findings in Korean breast cancer samples.

Conclusion

Together, these results underlie the molecular differences between Asian and Caucasian breast cancers.