Germline Mutation Analysis in Sporadic Breast Cancer Cases With Clinical Correlations

Sadia Ajaz; Sani-E-Zehra Zaidi; Saleema Ali; Aisha Siddiqa; Muhammad Ali Memon

doi:10.3389/fgene.2022.820610

Germline Mutation Analysis in Sporadic Breast Cancer Cases With Clinical Correlations

Front Genet. 2022 Mar 9:13:820610. doi: 10.3389/fgene.2022.820610. eCollection 2022.

Authors

Sadia Ajaz^{1

2}, Sani-E-Zehra Zaidi¹, Saleema Ali¹, Aisha Siddiqa³, Muhammad Ali Memon³

Affiliations

¹ Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan.
² Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan.
³ Atomic Energy Medical Centre (AEMC), Jinnah Postgraduate Medical Centre (JPMC), Karachi, Pakistan.

Abstract

Demographics for breast cancers vary widely among nations. The frequency of germline mutations in breast cancers, which reflects the hereditary cases, has not been investigated adequately and accurately in highly-consanguineous Pakistani population. In the present discovery case series, germ-line mutations in twenty-seven breast cancer candidate genes were investigated in eighty-four sporadic breast cancer patients along with the clinical correlations. The germ-line variants were also assessed in two healthy gender-matched controls. The clinico-pathological features were evaluated by descriptive analysis and Pearson χ² test (with significant p-value <0.05). The most frequent parameters associated with hereditary cancer cases are age and ethnicity. Therefore, the analyses were stratified on the basis of age (≤40 years vs. >40 years) and ethnicity. The breast cancer gene panel assay was carried out by BROCA, which is a genomic capture, massively parallel next generation sequencing assay on Illumina Hiseq2000 with 100bp read lengths. Copy number variations were determined by partially-mapped read algorithm. Once the mutation was identified, it was validated by Sanger sequencing. The ethnic analysis stratified on the basis of age showed that the frequency of breast cancer at young age (≤40 years) was higher in Sindhis (n = 12/19; 64%) in contrast to patients in other ethnic groups. Majority of the patients had stage III (38.1%), grade III (50%), tumor size 2-5 cm (54.8%), and invasive ductal carcinoma (81%). Overall, the analysis revealed germ-line mutations in 11.9% of the patients, which was not significantly associated with younger age or any particular ethnicity. The mutational spectrum was restricted to three genes: BRCA1, BRCA2, and TP53. The identified mutations consist of seven novel germ-line mutations, while three mutations have been reported previously. All the mutations are predicted to result in protein truncation. No mutations were identified in the remaining twenty-four candidate breast cancer genes. The present study provides the framework for the development of hereditary-based preventive and treatment strategies against breast cancers in Pakistani population.

Keywords: Pakistani population; breast cancer; candidate genes; genomics; next-generating sequencing; susceptibility.