Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes

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Albrechtsen, A. (author)

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes

Article/chapterEnglish2013

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2012-11-19
Springer Science and Business Media LLC,2013
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LIBRIS-ID:oai:DiVA.org:umu-64936
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-64936URI
https://doi.org/10.1007/s00125-012-2756-1DOI
https://lup.lub.lu.se/record/3476925URI

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Language:English
Summary in:English

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SwePubSwePub

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) > 1% with common metabolic phenotypes. The study comprised three stages. We performed medium-depth (8x) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI > 27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. Exome sequencing identified 70,182 polymorphisms with MAF > 1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 x 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 x 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 x 10(-10)). We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Klinisk medicin Endokrinologi och diabetes hsv//swe
MEDICAL AND HEALTH SCIENCES Clinical Medicine Endocrinology and Diabetes hsv//eng
Exome sequencing
Genetic epidemiology
Genetics
Lipids
Next-generation sequencing
Obesity
Type 2 diabetes
Exome sequencing
Genetic epidemiology
Genetics
Lipids
Next-generation sequencing
Obesity
Type 2 diabetes

Added entries (persons, corporate bodies, meetings, titles ...)

Grarup, N. (author)
Li, Y. (author)
Sparso, T. (author)
Tian, G. (author)
Cao, H. (author)
Jiang, T. (author)
Kim, S. Y. (author)
Korneliussen, T. (author)
Li, Q. (author)
Nie, C. (author)
Wu, R. (author)
Skotte, L. (author)
Morris, A. P. (author)
Ladenvall, ClaesLund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups(Swepub:lu)med-cll (author)
Cauchi, S. (author)
Stancakova, A. (author)
Andersen, G. (author)
Astrup, A. (author)
Banasik, K. (author)
Bennett, A. J. (author)
Bolund, L. (author)
Charpentier, G. (author)
Chen, Y. (author)
Dekker, J. M. (author)
Doney, A. S. F. (author)
Dorkhan, MozhganLund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups(Swepub:lu)endo-mdo (author)
Forsen, T. (author)
Frayling, T. M. (author)
Groves, C. J. (author)
Gui, Y. (author)
Hallmans, GöranUmeå universitet,Näringsforskning,Enheten för biobanksforskning(Swepub:umu)goha0001 (author)
Hattersley, A. T. (author)
He, K. (author)
Hitman, G. A. (author)
Holmkvist, J. (author)
Huang, S. (author)
Jiang, H. (author)
Jin, X. (author)
Justesen, J. M. (author)
Kristiansen, K. (author)
Kuusisto, J. (author)
Lajer, M. (author)
Lantieri, O. (author)
Li, W. (author)
Liang, H. (author)
Liao, Q. (author)
Liu, X. (author)
Ma, T. (author)
Ma, X. (author)
Manijak, M. P. (author)
Sterner, MariaLund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups(Swepub:lu)med-ms1 (author)
Mokrosinski, J. (author)
Morris, A. D. (author)
Mu, B. (author)
Nielsen, A. A. (author)
Nijpels, G. (author)
Nilsson, PeterLund University,Lunds universitet,Internmedicin - epidemiologi,Forskargrupper vid Lunds universitet,Internal Medicine - Epidemiology,Lund University Research Groups(Swepub:lu)medf-pni (author)
Palmer, C. N. A. (author)
Rayner, N. W. (author)
Renstrom, F. (author)
Ribel-Madsen, R. (author)
Robertson, N. (author)
Rolandsson, OlovUmeå universitet,Allmänmedicin(Swepub:umu)olro0005 (author)
Rossing, P. (author)
Schwartz, T. W. (author)
Slagboom, P. E. (author)
Sterner, M. (author)
Tang, M. (author)
Tarnow, L. (author)
Tuomi, T. (author)
van't Riet, E. (author)
van Leeuwen, N. (author)
Varga, T. V. (author)
Vestmar, M. A. (author)
Walker, M. (author)
Wang, B. (author)
Wang, Y. (author)
Wu, H. (author)
Xi, F. (author)
Yengo, L. (author)
Yu, C. (author)
Zhang, X. (author)
Zhang, J. (author)
Zhang, Q. (author)
Zhang, W. (author)
Zheng, H. (author)
Zhou, Y. (author)
Altshuler, D. (author)
't Hart, L. M. (author)
Franks, Paul W.Umeå universitet,Medicin(Swepub:umu)pafr0003 (author)
Balkau, B. (author)
Froguel, P. (author)
McCarthy, M. I. (author)
Laakso, M. (author)
Groop, LeifLund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups(Swepub:lu)endo-lgr (author)
Christensen, C. (author)
Brandslund, I. (author)
Lauritzen, T. (author)
Witte, D. R. (author)
Linneberg, A. (author)
Jorgensen, T. (author)
Hansen, T. (author)
Wang, J. (author)
Nielsen, R. (author)
Pedersen, O. (author)
Genomik, diabetes och endokrinologiForskargrupper vid Lunds universitet (creator_code:org_t)

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In:Diabetologia: Springer Science and Business Media LLC56:2, s. 298-3100012-186X1432-0428

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By the author/editor: Albrechtsen, A.; Grarup, N.; Li, Y.; Sparso, T.; Tian, G.; Cao, H.; show more...; Jiang, T.; Kim, S. Y.; Korneliussen, T.; Li, Q.; Nie, C.; Wu, R.; Skotte, L.; Morris, A. P.; Ladenvall, Claes; Cauchi, S.; Stancakova, A.; Andersen, G.; Astrup, A.; Banasik, K.; Bennett, A. J.; Bolund, L.; Charpentier, G.; Chen, Y.; Dekker, J. M.; Doney, A. S. F.; Dorkhan, Mozhgan; Forsen, T.; Frayling, T. M.; Groves, C. J.; Gui, Y.; Hallmans, Göran; Hattersley, A. T ...; He, K.; Hitman, G. A.; Holmkvist, J.; Huang, S.; Jiang, H.; Jin, X.; Justesen, J. M.; Kristiansen, K.; Kuusisto, J.; Lajer, M.; Lantieri, O.; Li, W.; Liang, H.; Liao, Q.; Liu, X.; Ma, T.; Ma, X.; Manijak, M. P.; Sterner, Maria; Mokrosinski, J.; Morris, A. D.; Mu, B.; Nielsen, A. A.; Nijpels, G.; Nilsson, Peter; Palmer, C. N. A.; Rayner, N. W.; Renstrom, F.; Ribel-Madsen, R.; Robertson, N.; Rolandsson, Olov; Rossing, P.; Schwartz, T. W.; Slagboom, P. E.; Sterner, M.; Tang, M.; Tarnow, L.; Tuomi, T.; van't Riet, E.; van Leeuwen, N.; Varga, T. V.; Vestmar, M. A.; Walker, M.; Wang, B.; Wang, Y.; Wu, H.; Xi, F.; Yengo, L.; Yu, C.; Zhang, X.; Zhang, J.; Zhang, Q.; Zhang, W.; Zheng, H.; Zhou, Y.; Altshuler, D.; 't Hart, L. M.; Franks, Paul W.; Balkau, B.; Froguel, P.; McCarthy, M. I.; Laakso, M.; Groop, Leif; Christensen, C.; Brandslund, I.; Lauritzen, T.; Witte, D. R.; Linneberg, A.; Jorgensen, T.; Hansen, T.; Wang, J.; Nielsen, R.; Pedersen, O.; show less...

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