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Genome wide association study to identify SNPs associated with Homocysteine, Vitamin B12 and holotranscobalamin in Indian Population

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Molecular Cytogenetics20147 (Suppl 1) :P51

  • Published:


  • Single Nucleotide Polymorphism
  • Methionine
  • Healthy Individual
  • Homocysteine
  • Genome Wide Association Study


Vitamin B12, a cofactor for the enzyme methionine synthase, catalyzes the remethylation of homocysteine to methionine. About 50-60% of the Indian population are deficient in vitamin B12, a micronutrient that is only synthesized by microorganisms while mammals have evolved ways for its absorption from diet. Of the various factors involved in Vitamin B12 absorption, Transcobalamin II (TC II) is most important as vitamin B12 bound to TCII is bioavailable. Thus, the objective of our study was to identify the genetic variants that are associated with homocysteine, vitamin B12 and holotranscobalamin levels.


A total of 3024 healthy individuals of Indo-European ethnicity were included in the study. Biochemical parameters like homocysteine, vitamin B12, holotranscobalamin etc were determined for each individual. In the first phase (discovery phase) Genome wide association studies were performed using Illumina Omni express chip and 524 individuals were genotyped for 731,442 single nucleotide polymorphisms (SNPs). Statistical analysis was performed using PLINK software (v 1.07) after stringent quality control. In the second phase SNPs that were found to be significantly associated were genotyped in 2500 healthy individuals.


Several genetic variants, some of which are novel, were found to be significantly associated with homocysteine, vitamin B12 and holotranscobalamin. This is the first GWAS for holoTC which we found is a better predictor of vitamin B12 status.


Although we found several SNPs earlier reported to be significantly associated with the biochemical traits measured in our population also, many of the SNPs were previously not reported to be associated with the biochemical traits measured.

Authors’ Affiliations

CSIR-Institute of Genomics and Integrative Biology, Delhi, India
National Institute of Biomedical Genomics, Kalyani, West Bengal, India
Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India


© Tanwar et al; licensee BioMed Central Ltd. 2014

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