☆ 4.6 Article

Genomic Position Mapping Discrepancies of Commercial SNP Chips

PLOS ONE (2012)

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PLOS ONE

卷 7, 期 2, 页码 -

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PUBLIC LIBRARY SCIENCE

DOI: 10.1371/journal.pone.0031025

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Multidisciplinary Sciences

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European Commission [KBBE-2A-222664]

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Reagent

摘要

The field of genetics has come to rely heavily on commercial genotyping arrays and accompanying annotations for insights into genotype-phenotype associations. However, in order to avoid errors and false leads, it is imperative that the annotation of SNP chromosomal positions is accurate and unambiguous. We report on genomic positional discrepancies of various SNP chips for human, cattle and mouse species, and discuss their causes and consequences.

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Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Yongkang Kim, Young Jin Kim, Min-Seok Kwon, Juyoung Lee, Selyeong Lee, Keng-Han Lin, Taylor J. Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P. Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benjamin F. Voight, Bok-Ghee Han, Christopher P. Jenkinson, Teemu Kuulasmaa, Johanna Kuusisto, Alisa Manning, Maggie C. Y. Ng, Nicholette D. Palmer, Beverley Balkau, Alena Stancakova, Hanna E. Abboud, Heiner Boeing, Vilmantas Giedraitis, Dorairaj Prabhakaran, Omri Gottesman, James Scott, Jason Carey, Phoenix Kwan, George Grant, Joshua D. Smith, Benjamin M. Neale, Shaun Purcell, Adam S. Butterworth, Joanna M. M. Howson, Heung Man Lee, Yingchang Lu, Soo-Heon Kwak, Wei Zhao, John Danesh, Vincent K. L. Lam, Kyong Soo Park, Danish Saleheen, Wing Yee So, Claudia H. T. Tam, Uzma Afzal, David Aguilar, Rector Arya, Tin Aung, Edmund Chan, Carmen Navarro, Ching-Yu Cheng, Domenico Palli, Adolfo Correa, Joanne E. Curran, Dennis Rybin, Vidya S. Farook, Sharon P. Fowler, Barry I. Freedman, Michael Griswold, Daniel Esten Hale, Pamela J. Hicks, Chiea-Chuen Khor, Satish Kumar, Benjamin Lehne, Dorothee Thuillier, Wei Yen Lim, Jianjun Liu, Marie Loh, Solomon K. Musani, Sobha Puppala, William R. Scott, Loic Yengo, Sian-Tsung Tan, Herman A. Taylor, Farook Thameem, Gregory Wilson, Tien Yin Wong, Pal Rasmus Njolstad, Jonathan C. Levy, Massimo Mangino, Lori L. Bonnycastle, Thomas Schwarzmayr, Joao Fadista, Gabriela L. Surdulescu, Christian Herder, Christopher J. Groves, Thomas Wieland, Jette Bork-Jensen, Ivan Brandslund, Cramer Christensen, Heikki A. Koistinen, Alex S. F. Doney, Leena Kinnunen, Tonu Esko, Andrew J. Farmer, Liisa Hakaste, Dylan Hodgkiss, Jasmina Kravic, Valeriya Lyssenko, Mette Hollensted, Marit E. Jorgensen, Torben Jorgensen, Claes Ladenvall, Johanne Marie Justesen, Annemari Karajamaki, Jennifer Kriebel, Wolfgang Rathmann, Lars Lannfelt, Torsten Lauritzen, Narisu Narisu, Allan Linneberg, Olle Melander, Lili Milani, Matt Neville, Marju Orho-Melander, Lu Qi, Qibin Qi, Michael Roden, Olov Rolandsson, Amy Swift, Anders H. Rosengren, Kathleen Stirrups, Andrew R. Wood, Evelin Mihailov, Christine Blancher, Mauricio O. Carneiro, Jared Maguire, Ryan Poplin, Khalid Shakir, Timothy Fennell, Mark DePristo, Martin Hrabe de Angelis, Panos Deloukas, Anette P. Gjesing, Goo Jun, Peter M. Nilsson, Jacquelyn Murphy, Robert Onofrio, Barbara Thorand, Torben Hansen, Christa Meisinger, Frank B. Hu, Bo Isomaa, Fredrik Karpe, Liming Liang, Annette Peters, Cornelia Huth, Stephen P. O'Rahilly, Colin N. A. Palmer, Oluf Pedersen, Rainer Rauramaa, Jaakko Tuomilehto, Veikko Salomaa, Richard M. Watanabe, Ann-Christine Syvanen, Richard N. Bergman, Dwaipayan Bharadwaj, Erwin P. Bottinger, Yoon Shin Cho, Giriraj R. Chandak, Juliana Cn Chan, Kee Seng Chia, Mark J. Daly, Shah B. Ebrahim, Claudia Langenberg, Paul Elliott, Kathleen A. Jablonski, Donna M. Lehman, Weiping Jia, Ronald C. W. Ma, Toni I. Pollin, Manjinder Sandhu, Nikhil Tandon, Philippe Froguel, Ines Barroso, Yik Ying Teo, Eleftheria Zeggini, Ruth J. F. Loos, Kerrin S. Small, Janina S. Ried, Ralph A. DeFronzo, Harald Grallert, Benjamin Glaser, Andres Metspalu, Nicholas J. Wareham, Mark Walker, Eric Banks, Christian Gieger, Erik Ingelsson, Hae Kyung Im, Thomas Illig, Paul W. Franks, Gemma Buck, Joseph Trakalo, David Buck, Inga Prokopenko, Reedik Magi, Lars Lind, Yossi Farjoun, Katharine R. Owen, Anna L. Gloyn, Konstantin Strauch, Tiinamaija Tuomi, Jaspal Singh Kooner, Jong-Young Lee, Taesung Park, Peter Donnelly, Andrew D. Morris, Andrew T. Hattersley, Donald W. Bowden, Francis S. Collins, Gil Atzmon, John C. Chambers, Timothy D. Spector, Markku Laakso, Tim M. Strom, Graeme I. Bell, John Blangero, Ravindranath Duggirala, EShyong Tai, Gilean McVean, Craig L. Hanis, James G. Wilson, Mark Seielstad, Timothy M. Frayling, James B. Meigs, Nancy J. Cox, Rob Sladek, Eric S. Lander, Stacey Gabriel, Karen L. Mohlke, Thomas Meitinger, Leif Groop, Goncalo Abecasis, Laura J. Scott, Andrew P. Morris, Hyun Min Kang, David Altshuler, Noel P. Burtt, Jose C. Florez, Michael Boehnke, Mark I. McCarthy

SCIENTIFIC DATA (2018)

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Article Biochemistry & Molecular Biology

Genome-wide meta-analysis identifies BARX1 and EML4-MTA3 as new loci associated with infantile hypertrophic pyloric stenosis

Joao Fadista, Line Skotte, Frank Geller, Jonas Bybjerg-Grauholm, Sanne Gortz, Paul A. Romitti, Michele Caggana, Denise M. Kay, Hans Matsson, Heather A. Boyd, David M. Hougaard, Agneta Nordenskjold, James L. Mills, Mads Melbye, Bjarke Feenstra

HUMAN MOLECULAR GENETICS (2019)

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Article Genetics & Heredity

Genome-wide Study Identifies Association between HLA-B*55:01 and Self-Reported Penicillin Allergy

Kristi Krebs, Jonas Bovijn, Neil Zheng, Maarja Lepamets, Jenny C. Censin, Tuuli Jurgenson, Dage Sarg, Erik Abner, Triin Laisk, Yang Luo, Line Skotte, Frank Geller, Wei Wang, Adam Auton, Soumya Raychaudhuri, Tonu Esko, Andres Metspalu, Sven Laur, Dan M. Roden, Wei-Qi Wei, Michael Holmes, Cecilia M. Lindgren, Elizabeth J. Phillips, Reedik Magi, Lili Milani, Joao Fadista

AMERICAN JOURNAL OF HUMAN GENETICS (2020)

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Article Multidisciplinary Sciences

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Ana Vinuela, Arushi Varshney, Martijn van de Bunt, Rashmi B. Prasad, Olof Asplund, Amanda Bennett, Michael Boehnke, Andrew A. Brown, Michael R. Erdos, Joao Fadista, Ola Hansson, Gad Hatem, Cedric Howald, Apoorva K. Iyengar, Paul Johnson, Ulrika Krus, Patrick E. MacDonald, Anubha Mahajan, Jocelyn E. Manning Fox, Narisu Narisu, Vibe Nylander, Peter Orchard, Nikolay Oskolkov, Nikolaos I. Panousis, Anthony Payne, Michael L. Stitzel, Swarooparani Vadlamudi, Ryan Welch, Francis S. Collins, Karen L. Mohlke, Anna L. Gloyn, Laura J. Scott, Emmanouil T. Dermitzakis, Leif Groop, Stephen C. J. Parker, Mark I. McCarthy

NATURE COMMUNICATIONS (2020)

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Article Endocrinology & Metabolism

Integrating genetics with newborn metabolomics in infantile hypertrophic pyloric stenosis

Joao Fadista, Line Skotte, Julie Courraud, Frank Geller, Sanne Gortz, Jan Wohlfahrt, Mads Melbye, Arieh S. Cohen, Bjarke Feenstra

Summary: The study found lower levels of certain metabolites in IHPS cases, possibly reflecting different feeding patterns in the first days of life. Additionally, more IHPS cases than controls had a diagnosis of neonatal difficulty in feeding at breast.

METABOLOMICS (2021)

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Article Medicine, General & Internal

Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity

Joao Fadista, Luke M. Kraven, Juha Karjalainen, Shea J. Andrews, Frank Geller, J. Kenneth Baillie, Louise Wain, R. Gisli Jenkins, Bjarke Feenstra

Summary: There is a positive genetic correlation between IPF and COVID-19 severity, but the causal relationship between IPF and COVID-19 severity is not clear. However, one specific IPF risk gene shows a causal effect on COVID-19 severity, while another IPF risk gene appears to have a protective effect against COVID-19 hospitalization in older adults.

EBIOMEDICINE (2021)

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Article Mathematical & Computational Biology

Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes

Amitabh Sharma, Arda Halu, Julius L. Decano, Megha Padi, Yang-Yu Liu, Rashmi B. Prasad, Joao Fadista, Marc Santolini, Jorg Menche, Scott T. Weiss, Marc Vidal, Edwin K. Silverman, Masanori Aikawa, Albert-Laszlo Barabasi, Leif Groop, Joseph Loscalzo

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2018)

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Article Endocrinology & Metabolism

Glucose-Induced Changes in Gene Expression in Human Pancreatic Islets: Causes or Consequences of Chronic Hyperglycemia

Emilia Ottosson-Laakso, Ulrika Krus, Petter Storm, Rashmi B. Prasad, Nikolay Oskolkov, Emma Ahlqvist, Joao Fadista, Ola Hansson, Leif Groop, Petter Vikman

DIABETES (2017)

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Article Endocrinology & Metabolism

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk

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DIABETES (2017)

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