基于 MassARRAY 的印度北部人群乳腺癌单核苷酸多态性分析。
MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population.
机构信息
School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India.
Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, India.
出版信息
BMC Cancer. 2020 Sep 7;20(1):861. doi: 10.1186/s12885-020-07361-8.
BACKGROUND
Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis.
METHODS
SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study.
RESULTS
The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123-0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings.
CONCLUSION
It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.
背景
乳腺癌（BC）与遗传基因突变有关。对 BC 样本进行高通量基因分型导致了对用于诊断 BC 的生物标志物的鉴定和特征描述。研究中最常见的遗传变体是 SNP（单核苷酸多态性），它们决定了对一系列疾病的易感性，因此可作为识别乳腺癌发生潜在原因的潜在工具。
方法
采用 Agena MassARRAY 的 SNP 基因分型提供了一种强大、敏感、具有成本效益的方法，可同时评估多个 SNP 和样本。在本研究中，我们分析了 550 个样本（150 例病例和 400 例对照）中的 14 个基因的 15 个 SNP。我们鉴定了基因 TCF21、SLC19A1、DCC 和 ERCC1 的四个 SNP，它们在研究人群中与 BC 具有显著相关性。
结果
这些 SNP 是 rs12190287（TCF21），其 OR 为 1.713（95%CI 为 1.08-2.716），p 值为 0.022（显性），rs1051266（SLC19A1），其 OR 为 3.461（95%CI 为 2.136-5.609），p 值为 0.000000466（显性），rs2229080（DCC），其 OR 为 0.6867（95%CI 为 0.5123-0.9205），p 值为 0.0116（等位基因）和 rs2298881（ERCC1），其 OR 为 0.669（95%CI 为 0.46-0.973），p 值为 0.035（加性）。进一步使用计算机分析来加强上述发现。
结论
进一步预计应在其他人群中评估这些变体，这可能有助于了解遗传复杂性并弥合缺失的遗传率。
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