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DNA mismatch repair MSH2 gene-based SNP associated with different populations

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Abstract

We screened for the major essential single-nucleotide polymorphism (SNP) variant that might be associated with the MSH2 gene based on the data available from three types of human tissue samples [156 lymphoblastoid cell variations (LCL), 160 epidermis, 166 fat]. An association analysis confirmed that the KCNK12 SNP variant (rs748780) was highly associated (p value 9 × 10−4) with the MSH2 gene for all three samples. Using SNP identification, we further found that the recognized SNP was also relevant among Hapmap populations. Techniques that display specific SNPs associated with the gene of interest or nearby genes provide more reliable genetic associations than techniques that rely on data from individual SNPs. We investigated the MSH2 gene regional linkage association with the determined SNP (rs748780), KCNK12 variant (Allele T>C) in the intronic region, in HapMap3 full dataset populations, Yoruba in Ibadan, Nigeria (YRI), Utah residents with ancestry from northern Europe (CEU), Han Chinese in Beijing, China (CHB), and a population of Mexican ancestry in Los Angeles, California (MEX). A gene-based SNP association analysis analyzes the combined impact of every variant within the gene while creating referrals to linkage disequilibrium or connections between markers. Our results indicated that among the four populations studied, this association was highest in the MEX population based on the r 2 value; a similar pattern was also observed in the other three populations. The relevant SNP rs748780 in KCNK12 is related to a superfamily of potassium channel pore-forming P-domain proteins as well as to other non-pore-forming proteins and has been shown to be relevant to neurological disorder predisposition in MEX as well as in other populations.

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Acknowledgments

The authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding this work through the research group project No. RGP-VPP-200.

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Authors and Affiliations

  1. Department of Medical Genetics, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia

    Zainularifeen Abduljaleel, Faisal A. Al-Allaf, Mohammad Athar & Mohiuddin M. Taher

  2. Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdul Aziz University for Health Sciences, Riyadh, 11426, Saudi Arabia

    Wajahatullah Khan

  3. Genome Research Chair Unit, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia

    Mohammed Alanazi, Mohamed Elrobh & Narasimha P. Reddy

  4. Department of Pharmacology and Toxicology, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia

    Naiyer Shahzad

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  1. Zainularifeen Abduljaleel
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Correspondence to Zainularifeen Abduljaleel.

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Abduljaleel, Z., Al-Allaf, F.A., Khan, W. et al. DNA mismatch repair MSH2 gene-based SNP associated with different populations. Mol Genet Genomics 289, 469–487 (2014). https://doi.org/10.1007/s00438-014-0826-4

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