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gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

Published on: October 6, 2014

Sequencing of Chromosomal Locus 6q25.1 Revealed Two Significant SNPs rs2046210 and rs2046211 Associated with Breast

Marwa H Saied¹, Mohamed M Rizk¹, Nedaa Awad Abdelkader El Sayed¹

¹Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt.

Asian Pacific Journal of Cancer Prevention : APJCP

|April 29, 2022

Abstract

Background:

Breast cancer (BC) is one of the major health problems affecting females in Egypt. Certain chromosomal loci abnormalities were proved to be associated with BC in different populations. One of them is chromosomal locus 6q25.1, that affects estrogen receptor gene (ESR) which controls ER receptor expression. Therefore, the aim of this study was to investigate locus 6q25.1 among group of Egyptian female BC patients and compare the results to healthy matched age controls.

Methods:

Formalin fixed paraffin embedded (FFPE) samples of sixty newly diagnosed BC patients were sequenced for locus 6q25.1 using genetic analyzer with capillary electrophoresis (3500 GA). The identified single nucleotide polymorphisms (SNPs) were compared to blood samples of forty controls. Realtime PCR using TaqMan probes was used for validation.

Results:

Two SNPs rs2046210 and rs2046211 were significantly associated with BC. Frequency of rs2046210-A minor allele was 30% in controls, while the frequency of rs2046211-G minor allele was 15%. Rs2046210-A allele was associated with increased risk of BC (P=0.0001), while rs2046211-G allele was associated with reduced risk of BC (P=0.021). Combined analysis of both SNPs showed that haplotype A/C was associated with increased risk of BC (P = 0.042). No significant correlation was found between rs2046210-A allele and ER status, while positive association was observed between rs204621-C allele and ER status (p= 0.005).

Conclusion:

Our data confirmed the important association between locus 6q25.1 and risk of BC in other populations. The frequencies of minor alleles of both significant SNPs will pave the way for a wider large-scale genome study and to be investigated with other BC risk factors.

Keywords:

Single nucleotide polymorphism breast cancer chromosomal locus risk

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