Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes Article Swipe
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· 2017
· Open Access
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· DOI: https://doi.org/10.1101/144410
Identification of coding variant associations for complex diseases offers a direct route to biological insight, but is dependent on appropriate inference concerning the causal impact of those variants on disease risk. We aggregated coding variant data for 81,412 type 2 diabetes (T2D) cases and 370,832 controls of diverse ancestry, identifying 40 distinct coding variant association signals (at 38 loci) reaching significance ( p <2.2×10 −7 ). Of these, 16 represent novel associations mapping outside known genome-wide association study (GWAS) signals. We make two important observations. First, despite a threefold increase in sample size over previous efforts, only five of the 40 signals are driven by variants with minor allele frequency <5%, and we find no evidence for low-frequency variants with allelic odds ratio >1.29. Second, we used GWAS data from 50,160 T2D cases and 465,272 controls of European ancestry to fine-map these associated coding variants in their regional context, with and without additional weighting to account for the global enrichment of complex trait association signals in coding exons. At the 37 signals for which we attempted fine-mapping, we demonstrate convincing support (posterior probability >80% under the “annotation-weighted” model) that coding variants are causal for the association at 16 (including novel signals involving POC5 p.His36Arg, ANKH p.Arg187Gln, WSCD2 p.Thr113Ile, PLCB3 p.Ser778Leu, and PNPLA3 p.Ile148Met). However, at 13 of the 37 loci, the associated coding variants represent “false leads” and naïve analysis could have led to an erroneous inference regarding the effector transcript mediating the signal. Accurate identification of validated targets is dependent on correct specification of the contribution of coding and non-coding mediated mechanisms at associated loci.
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/144410
- https://www.biorxiv.org/content/biorxiv/early/2017/12/13/144410.full.pdf
- OA Status
- green
- References
- 57
- OpenAlex ID
- https://openalex.org/W2801547246
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2801547246Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/144410Digital Object Identifier
- Title
-
Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetesWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2017Year of publication
- Publication date
-
2017-05-31Full publication date if available
- Authors
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Anubha Mahajan, Jennifer Wessel, Sara M. Willems, Zhao Wei, Neil R. Robertson, Audrey Y. Chu, Wei Gan, Hidetoshi Kitajima, Daniel Taliun, N. William Rayner, Xiuqing Guo, Yingchang Lu, Man Li, Richard A. Jensen, Yao Hu, Shaofeng Huo, Kurt K. Lohman, Weihua Zhang, James P. Cook, Bram P. Prins, Jason Flannick, Niels Grarup, Vassily Trubetskoy, Jasmina Kravić, Young Jin Kim, Denis Rybin, Hanieh Yaghootkar, Martina Müller‐Nurasyid, Karina Meidtner, Ruifang Li‐Gao, Tibor V. Varga, Jonathan Marten, Li Jin, Albert V. Smith, Ping An, Symen Ligthart, Stefan Gustafsson, Giovanni Malerba, Ayşe Demirkan, Juan Fernández Tajes, Valgerður Steinthórsdóttir, Matthias Wuttke, Cécile Lecœur, Michael Preuß, Lawrence F. Bielak, Marielisa Graff, Heather M. Highland, Anne E. Justice, Dajiang J. Liu, Eirini Marouli, Gina M. Peloso, Helen R. Warren, Saima Afaq, Shoaib Afzal, Emma Ahlqvist, Peter Almgren, Najaf Amin, Lia B. Bang, Alain G. Bertoni, Cristina Bombieri, Jette Bork‐Jensen, Ivan Brandslund, Jennifer A. Brody, Noël P. Burtt, Mickaël Canouil, Yii‐Der Ida Chen, Yoon Shin Cho, Cramer Christensen, Sophie V. Eastwood, Kai‐Uwe Eckardt, Krista Fischer, Giovanni Gambaro, Vilmantas Giedraitis, Megan L. Grove, Hugoline G. de Haan, Sophie Hackinger, Yang Hai, Sohee Han, Anne Tybjærg‐Hansen, Marie‐France Hivert, Bo Isomaa, Susanne Jäger, Marit E. Jørgensen, Torben Jørgensen, Annemari Käräjämäki, Bong-Jo Kim, Sung‐Soo Kim, Heikki A. Koistinen, Péter Kovács, Jennifer Kriebel, Florian Kronenberg, Kristi Läll, Leslie A. Lange, Jung‐Jin Lee, Benjamin Lehne, Huaixing Li, Keng‐Hung Lin, Allan Linneberg, Yongmei Liu, Jun LiuList of authors in order
- Landing page
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https://doi.org/10.1101/144410Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2017/12/13/144410.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2017/12/13/144410.full.pdfDirect OA link when available
- Concepts
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Coding (social sciences), Computer science, Identification (biology), Type 2 diabetes, Type 1 diabetes, Artificial intelligence, Mathematics, Medicine, Diabetes mellitus, Biology, Statistics, Botany, EndocrinologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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57Number of works referenced by this work
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