Population allele frequencies of disease associated SNPs in India: a paradigm shift from HapMap
1
POSTER PRESENTATION Open Access Population allele frequencies of disease associated SNPs in India: a paradigm shift from HapMap Pankaj Mankad, Srisanth Balan * , Saleem Mohammed From International Conference on Human Genetics and 39th Annual Meeting of the Indian Society of Human Genetics (ISHG) Ahmadabad, India. 23-25 January 2013 Background One of the challenges facing us in India, translating recent discoveries of chronic disease associated SNPs into clinical domain for prevention, is the lack of knowledge about the frequency of the polymorphism in our population. Hence, using available HapMap data has become a norm. How- ever, it is anticipated that population genomics in India could be different from the HapMap Caucasian popula- tion. Relative disease risk prediction based on relevant SNPs, both for personalized medicine and for population genetics, has little value without accurate information of population allele frequencies. We report allele frequency of 384 SNPs directly related to chronic disease risk and metabolic traits in the Indian population. Materials and methods We report the allele in a random sample of 146 individuals and compare them with the data reported in HapMap Caucasian population (n = 112). Genotyping was performed using Illumina golden gate genotyping assay following DNA extraction from saliva. Allele frequencies were determined by direct gene count method. Results GWAS studies confirmed 384 SNPs to be associated with disease risk (364) of Diabetes Type 1 and 2 (54 & 118 respectively), Coronary artery disease(71), myocardial infarction(9), cardiac failure(24), sudden cardiac arrest (38), atrial fibrillation(9), hypertension(18), obesity(10), metabolic syndrome(2) and stroke(11); or were associated with metabolic traits (20). The master table of their ‘ rs’ id, chromosomes, location and association is presented. Of the 384 SNPs, 44 were not in H-W equilibrium and were omitted. HapMap data were not available for 13 SNPs. We are reporting their allele frequencyon the Indian population for the first time. Of the remaining 307 disease association SNPs, statistically significant dif- ference (p<.05) from HapMap Caucasian population was observed in 53% of them (164 of 307) and the difference of >10% (considered major in population genetics) was found in 42% (130 of 307). Of the 20 metabolic associa- tion SNPs, 50% (10 of 20) had statistically significant dif- ference and in all of them it was >10%. Conclusions We are reporting the largest repository, documenting disease and related SNP and allele frequencies in Indian population. We have also highlighted clear differences with HapMap data and would caution against indiscri- minate use of HapMap for bench-to-bedside application of genetic knowledge in our population. Published: 21 January 2014 doi:10.1186/1755-8166-7-S1-P105 Cite this article as: Mankad et al.: Population allele frequencies of disease associated SNPs in India: a paradigm shift from HapMap. Molecular Cytogenetics 2014 7(Suppl 1):P105. Xcode Life Sciences, 6B, Eldorado, Nungambakkam High Road, Nungambakkam, Chennai, 600 034, India Mankad et al. Molecular Cytogenetics 2014, 7(Suppl 1):P105 http://www.molecularcytogenetics.org/content/7/S1/P105 © 2014 Mankad et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Transcript of Population allele frequencies of disease associated SNPs in India: a paradigm shift from HapMap
POSTER PRESENTATION Open Access
Population allele frequencies of diseaseassociated SNPs in India: a paradigm shift fromHapMapPankaj Mankad, Srisanth Balan*, Saleem Mohammed
From International Conference on Human Genetics and 39th Annual Meeting of the Indian Society ofHuman Genetics (ISHG)Ahmadabad, India. 23-25 January 2013
BackgroundOne of the challenges facing us in India, translating recentdiscoveries of chronic disease associated SNPs into clinicaldomain for prevention, is the lack of knowledge about thefrequency of the polymorphism in our population. Hence,using available HapMap data has become a norm. How-ever, it is anticipated that population genomics in Indiacould be different from the HapMap Caucasian popula-tion. Relative disease risk prediction based on relevantSNPs, both for personalized medicine and for populationgenetics, has little value without accurate information ofpopulation allele frequencies. We report allele frequencyof 384 SNPs directly related to chronic disease risk andmetabolic traits in the Indian population.
Materials and methodsWe report the allele in a random sample of 146 individualsand compare them with the data reported in HapMapCaucasian population (n = 112). Genotyping wasperformed using Illumina golden gate genotyping assayfollowing DNA extraction from saliva. Allele frequencieswere determined by direct gene count method.
ResultsGWAS studies confirmed 384 SNPs to be associated withdisease risk (364) of Diabetes Type 1 and 2 (54 & 118respectively), Coronary artery disease(71), myocardialinfarction(9), cardiac failure(24), sudden cardiac arrest(38), atrial fibrillation(9), hypertension(18), obesity(10),metabolic syndrome(2) and stroke(11); or were associatedwith metabolic traits (20). The master table of their ‘rs’
id, chromosomes, location and association is presented.Of the 384 SNPs, 44 were not in H-W equilibrium andwere omitted. HapMap data were not available for 13SNPs. We are reporting their allele frequencyon theIndian population for the first time. Of the remaining307 disease association SNPs, statistically significant dif-ference (p<.05) from HapMap Caucasian population wasobserved in 53% of them (164 of 307) and the differenceof >10% (considered major in population genetics) wasfound in 42% (130 of 307). Of the 20 metabolic associa-tion SNPs, 50% (10 of 20) had statistically significant dif-ference and in all of them it was >10%.
ConclusionsWe are reporting the largest repository, documentingdisease and related SNP and allele frequencies in Indianpopulation. We have also highlighted clear differenceswith HapMap data and would caution against indiscri-minate use of HapMap for bench-to-bedside applicationof genetic knowledge in our population.
Published: 21 January 2014
doi:10.1186/1755-8166-7-S1-P105Cite this article as: Mankad et al.: Population allele frequencies ofdisease associated SNPs in India: a paradigm shift from HapMap.Molecular Cytogenetics 2014 7(Suppl 1):P105.
Xcode Life Sciences, 6B, Eldorado, Nungambakkam High Road,Nungambakkam, Chennai, 600 034, India
Mankad et al. Molecular Cytogenetics 2014, 7(Suppl 1):P105http://www.molecularcytogenetics.org/content/7/S1/P105
© 2014 Mankad et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative CommonsAttribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction inany medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
