Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India

Richa Saxena, Danish Saleheen, Latonya F. Been, Martha L. Garavito, Timothy Braun, Andrew Bjonnes, Robin Young, Weang Kee Ho, Asif Rasheed, Philippe Frossard, Xueling Sim, Neelam Hassanali, Venkatesan Radha, Manickam Chidambaram, Samuel Liju, Simon D. Rees, Daniel Peng Keat Ng, Tien Yin Wong, Toshimasa Yamauchi, Kazuo Hara & 28 others Yasushi Tanaka, Hiroshi Hirose, Mark I. McCarthy, Andrew P. Morris, Abdul Basit, Anthony H. Barnett, Prasad Katulanda, David Matthews, Viswanathan Mohan, Gurpreet S. Wander, Jai Rup Singh, Narinder K. Mehra, Sarju Ralhan, M. Ilyas Kamboh, John J. Mulvihill, Hiroshi Maegawa, Kazuyuki Tobe, Shiro Maeda, Yoon S. Cho, E. Shyong Tai, M. Ann Kelly, John C. Chambers, Jaspal S. Kooner, Takashi Kadowaki, Panos Deloukas, Daniel J. Rader, John Danesh, Dharambir K. Sanghera

Research output: Contribution to journalArticle

94 Citations (Scopus)

Abstract

We performed a genome-wide association study (GWAS) and a multistage meta-analysis of type 2 diabetes (T2D) in Punjabi Sikhs from India. Our discovery GWAS in 1,616 individuals (842 case subjects) was followed by in silico replication of the top 513 independent single nucleotide polymorphisms (SNPs) (P < 10-3) in Punjabi Sikhs (n = 2,819; 801 case subjects). We further replicated 66 SNPs (P < 10-4) through genotyping in a Punjabi Sikh sample (n = 2,894; 1,711 case subjects). On combined meta-analysis in Sikh populations (n = 7,329; 3,354 case subjects), we identified a novel locus in association with T2D at 13q12 represented by a directly genotyped intronic SNP (rs9552911, P = 1.82 × 10-8) in the SGCG gene. Next, we undertook in silico replication (stage 2b) of the top 513 signals (P < 10-3) in 29,157 non-Sikh South Asians (10,971 case subjects) and de novo genotyping of up to 31 top signals (P < 10-4) in 10,817 South Asians (5,157 case subjects) (stage 3b). In combined South Asian meta-analysis, we observed six suggestive associations (P < 10-5 to < 10-7), including SNPs at HMG1L1/CTCFL, PLXNA4, SCAP, and chr5p11. Further evaluation of 31 top SNPs in 33,707 East Asians (16,746 case subjects) (stage 3c) and 47,117 Europeans (8,130 case subjects) (stage 3d), and joint meta-analysis of 128,127 individuals (44,358 case subjects) from 27 multiethnic studies, did not reveal any additional loci nor was there any evidence of replication for the new variant. Our findings provide new evidence on the presence of a population-specific signal in relation to T2D, which may provide additional insights into T2D pathogenesis.

Original languageEnglish
Pages (from-to)1746-1755
Number of pages10
JournalDiabetes
Volume62
Issue number5
DOIs
Publication statusPublished - 2013 May

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Genome-Wide Association Study
Type 2 Diabetes Mellitus
Single Nucleotide Polymorphism
India
Meta-Analysis
Computer Simulation
Population
Joints
Genes

ASJC Scopus subject areas

  • Internal Medicine
  • Endocrinology, Diabetes and Metabolism

Cite this

Saxena, R., Saleheen, D., Been, L. F., Garavito, M. L., Braun, T., Bjonnes, A., ... Sanghera, D. K. (2013). Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. Diabetes, 62(5), 1746-1755. https://doi.org/10.2337/db12-1077

Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. / Saxena, Richa; Saleheen, Danish; Been, Latonya F.; Garavito, Martha L.; Braun, Timothy; Bjonnes, Andrew; Young, Robin; Ho, Weang Kee; Rasheed, Asif; Frossard, Philippe; Sim, Xueling; Hassanali, Neelam; Radha, Venkatesan; Chidambaram, Manickam; Liju, Samuel; Rees, Simon D.; Ng, Daniel Peng Keat; Wong, Tien Yin; Yamauchi, Toshimasa; Hara, Kazuo; Tanaka, Yasushi; Hirose, Hiroshi; McCarthy, Mark I.; Morris, Andrew P.; Basit, Abdul; Barnett, Anthony H.; Katulanda, Prasad; Matthews, David; Mohan, Viswanathan; Wander, Gurpreet S.; Singh, Jai Rup; Mehra, Narinder K.; Ralhan, Sarju; Kamboh, M. Ilyas; Mulvihill, John J.; Maegawa, Hiroshi; Tobe, Kazuyuki; Maeda, Shiro; Cho, Yoon S.; Tai, E. Shyong; Kelly, M. Ann; Chambers, John C.; Kooner, Jaspal S.; Kadowaki, Takashi; Deloukas, Panos; Rader, Daniel J.; Danesh, John; Sanghera, Dharambir K.

In: Diabetes, Vol. 62, No. 5, 05.2013, p. 1746-1755.

Research output: Contribution to journalArticle

Saxena, R, Saleheen, D, Been, LF, Garavito, ML, Braun, T, Bjonnes, A, Young, R, Ho, WK, Rasheed, A, Frossard, P, Sim, X, Hassanali, N, Radha, V, Chidambaram, M, Liju, S, Rees, SD, Ng, DPK, Wong, TY, Yamauchi, T, Hara, K, Tanaka, Y, Hirose, H, McCarthy, MI, Morris, AP, Basit, A, Barnett, AH, Katulanda, P, Matthews, D, Mohan, V, Wander, GS, Singh, JR, Mehra, NK, Ralhan, S, Kamboh, MI, Mulvihill, JJ, Maegawa, H, Tobe, K, Maeda, S, Cho, YS, Tai, ES, Kelly, MA, Chambers, JC, Kooner, JS, Kadowaki, T, Deloukas, P, Rader, DJ, Danesh, J & Sanghera, DK 2013, 'Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India', Diabetes, vol. 62, no. 5, pp. 1746-1755. https://doi.org/10.2337/db12-1077
Saxena, Richa ; Saleheen, Danish ; Been, Latonya F. ; Garavito, Martha L. ; Braun, Timothy ; Bjonnes, Andrew ; Young, Robin ; Ho, Weang Kee ; Rasheed, Asif ; Frossard, Philippe ; Sim, Xueling ; Hassanali, Neelam ; Radha, Venkatesan ; Chidambaram, Manickam ; Liju, Samuel ; Rees, Simon D. ; Ng, Daniel Peng Keat ; Wong, Tien Yin ; Yamauchi, Toshimasa ; Hara, Kazuo ; Tanaka, Yasushi ; Hirose, Hiroshi ; McCarthy, Mark I. ; Morris, Andrew P. ; Basit, Abdul ; Barnett, Anthony H. ; Katulanda, Prasad ; Matthews, David ; Mohan, Viswanathan ; Wander, Gurpreet S. ; Singh, Jai Rup ; Mehra, Narinder K. ; Ralhan, Sarju ; Kamboh, M. Ilyas ; Mulvihill, John J. ; Maegawa, Hiroshi ; Tobe, Kazuyuki ; Maeda, Shiro ; Cho, Yoon S. ; Tai, E. Shyong ; Kelly, M. Ann ; Chambers, John C. ; Kooner, Jaspal S. ; Kadowaki, Takashi ; Deloukas, Panos ; Rader, Daniel J. ; Danesh, John ; Sanghera, Dharambir K. / Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. In: Diabetes. 2013 ; Vol. 62, No. 5. pp. 1746-1755.
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abstract = "We performed a genome-wide association study (GWAS) and a multistage meta-analysis of type 2 diabetes (T2D) in Punjabi Sikhs from India. Our discovery GWAS in 1,616 individuals (842 case subjects) was followed by in silico replication of the top 513 independent single nucleotide polymorphisms (SNPs) (P < 10-3) in Punjabi Sikhs (n = 2,819; 801 case subjects). We further replicated 66 SNPs (P < 10-4) through genotyping in a Punjabi Sikh sample (n = 2,894; 1,711 case subjects). On combined meta-analysis in Sikh populations (n = 7,329; 3,354 case subjects), we identified a novel locus in association with T2D at 13q12 represented by a directly genotyped intronic SNP (rs9552911, P = 1.82 × 10-8) in the SGCG gene. Next, we undertook in silico replication (stage 2b) of the top 513 signals (P < 10-3) in 29,157 non-Sikh South Asians (10,971 case subjects) and de novo genotyping of up to 31 top signals (P < 10-4) in 10,817 South Asians (5,157 case subjects) (stage 3b). In combined South Asian meta-analysis, we observed six suggestive associations (P < 10-5 to < 10-7), including SNPs at HMG1L1/CTCFL, PLXNA4, SCAP, and chr5p11. Further evaluation of 31 top SNPs in 33,707 East Asians (16,746 case subjects) (stage 3c) and 47,117 Europeans (8,130 case subjects) (stage 3d), and joint meta-analysis of 128,127 individuals (44,358 case subjects) from 27 multiethnic studies, did not reveal any additional loci nor was there any evidence of replication for the new variant. Our findings provide new evidence on the presence of a population-specific signal in relation to T2D, which may provide additional insights into T2D pathogenesis.",
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T1 - Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India

AU - Saxena, Richa

AU - Saleheen, Danish

AU - Been, Latonya F.

AU - Garavito, Martha L.

AU - Braun, Timothy

AU - Bjonnes, Andrew

AU - Young, Robin

AU - Ho, Weang Kee

AU - Rasheed, Asif

AU - Frossard, Philippe

AU - Sim, Xueling

AU - Hassanali, Neelam

AU - Radha, Venkatesan

AU - Chidambaram, Manickam

AU - Liju, Samuel

AU - Rees, Simon D.

AU - Ng, Daniel Peng Keat

AU - Wong, Tien Yin

AU - Yamauchi, Toshimasa

AU - Hara, Kazuo

AU - Tanaka, Yasushi

AU - Hirose, Hiroshi

AU - McCarthy, Mark I.

AU - Morris, Andrew P.

AU - Basit, Abdul

AU - Barnett, Anthony H.

AU - Katulanda, Prasad

AU - Matthews, David

AU - Mohan, Viswanathan

AU - Wander, Gurpreet S.

AU - Singh, Jai Rup

AU - Mehra, Narinder K.

AU - Ralhan, Sarju

AU - Kamboh, M. Ilyas

AU - Mulvihill, John J.

AU - Maegawa, Hiroshi

AU - Tobe, Kazuyuki

AU - Maeda, Shiro

AU - Cho, Yoon S.

AU - Tai, E. Shyong

AU - Kelly, M. Ann

AU - Chambers, John C.

AU - Kooner, Jaspal S.

AU - Kadowaki, Takashi

AU - Deloukas, Panos

AU - Rader, Daniel J.

AU - Danesh, John

AU - Sanghera, Dharambir K.

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