BACKGROUND: High density genotyping arrays have become established as a valuable research tool in human genetics. Currently, more than 300 genome wide association studies were published for human reporting about 1,000 SNPs that are associated with a phenotype. Also in animal sciences high density genotyping arrays are harnessed to analyse genetic variation. To exploit the full potential of this technology single nucleotide polymorphisms (SNPs) on the chips should be well characterized and their chromosomal position should be precisely known. This, however, is a challenge if the genome sequence is still subject to changes. RESULTS: We have developed a mapping strategy and a suite of software scripts to update the chromosomal positions of oligomer sequences used for SNP genotyping on high density arrays. We describe the mapping procedure in detail so that scientists with moderate bioinformatics skills can reproduce it. We furthermore present a case study in which we re-mapped 54,001 oligomer sequences from Ilumina's BovineSNP50 beadchip to the bovine genome sequence. We found in 992 cases substantial discrepancies between the manufacturer's annotations and our results. The software scripts in the Perl and R programming languages are provided as supplements. CONCLUSIONS: The positions of oligomer sequences in the genome are volatile even within one build of the genome. To facilitate the analysis of data from a GWAS or from an expression study, especially with species whose genome assembly is still unstable, it is recommended to update the oligomer positions before data analysis.
BACKGROUND: High density genotyping arrays have become established as a valuable research tool in human genetics. Currently, more than 300 genome wide association studies were published for human reporting about 1,000 SNPs that are associated with a phenotype. Also in animal sciences high density genotyping arrays are harnessed to analyse genetic variation. To exploit the full potential of this technology single nucleotide polymorphisms (SNPs) on the chips should be well characterized and their chromosomal position should be precisely known. This, however, is a challenge if the genome sequence is still subject to changes. RESULTS: We have developed a mapping strategy and a suite of software scripts to update the chromosomal positions of oligomer sequences used for SNP genotyping on high density arrays. We describe the mapping procedure in detail so that scientists with moderate bioinformatics skills can reproduce it. We furthermore present a case study in which we re-mapped 54,001 oligomer sequences from Ilumina's BovineSNP50 beadchip to the bovine genome sequence. We found in 992 cases substantial discrepancies between the manufacturer's annotations and our results. The software scripts in the Perl and R programming languages are provided as supplements. CONCLUSIONS: The positions of oligomer sequences in the genome are volatile even within one build of the genome. To facilitate the analysis of data from a GWAS or from an expression study, especially with species whose genome assembly is still unstable, it is recommended to update the oligomer positions before data analysis.
Authors: Curtis P Van Tassell; Timothy P L Smith; Lakshmi K Matukumalli; Jeremy F Taylor; Robert D Schnabel; Cynthia Taylor Lawley; Christian D Haudenschild; Stephen S Moore; Wesley C Warren; Tad S Sonstegard Journal: Nat Methods Date: 2008-02-24 Impact factor: 28.547
Authors: Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio Journal: Proc Natl Acad Sci U S A Date: 2009-05-27 Impact factor: 11.205
Authors: J B Cole; P M VanRaden; J R O'Connell; C P Van Tassell; T S Sonstegard; R D Schnabel; J F Taylor; G R Wiggans Journal: J Dairy Sci Date: 2009-06 Impact factor: 4.034
Authors: Ben J Hayes; Phil J Bowman; Amanda J Chamberlain; Keith Savin; Curt P van Tassell; Tad S Sonstegard; Mike E Goddard Journal: PLoS One Date: 2009-08-18 Impact factor: 3.240
Authors: Christine G Elsik; Ross L Tellam; Kim C Worley; Richard A Gibbs; Donna M Muzny; George M Weinstock; David L Adelson; Evan E Eichler; Laura Elnitski; Roderic Guigó; Debora L Hamernik; Steve M Kappes; Harris A Lewin; David J Lynn; Frank W Nicholas; Alexandre Reymond; Monique Rijnkels; Loren C Skow; Evgeny M Zdobnov; Lawrence Schook; James Womack; Tyler Alioto; Stylianos E Antonarakis; Alex Astashyn; Charles E Chapple; Hsiu-Chuan Chen; Jacqueline Chrast; Francisco Câmara; Olga Ermolaeva; Charlotte N Henrichsen; Wratko Hlavina; Yuri Kapustin; Boris Kiryutin; Paul Kitts; Felix Kokocinski; Melissa Landrum; Donna Maglott; Kim Pruitt; Victor Sapojnikov; Stephen M Searle; Victor Solovyev; Alexandre Souvorov; Catherine Ucla; Carine Wyss; Juan M Anzola; Daniel Gerlach; Eran Elhaik; Dan Graur; Justin T Reese; Robert C Edgar; John C McEwan; Gemma M Payne; Joy M Raison; Thomas Junier; Evgenia V Kriventseva; Eduardo Eyras; Mireya Plass; Ravikiran Donthu; Denis M Larkin; James Reecy; Mary Q Yang; 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Oliver Jann; John W Keele; Matthew P Kent; Sigbjørn Lien; Stephanie D McKay; Sean McWilliam; Abhirami Ratnakumar; Robert D Schnabel; Timothy Smith; Warren M Snelling; Tad S Sonstegard; Roger T Stone; Yoshikazu Sugimoto; Akiko Takasuga; Jeremy F Taylor; Curtis P Van Tassell; Michael D Macneil; Antonio R R Abatepaulo; Colette A Abbey; Virpi Ahola; Iassudara G Almeida; Ariel F Amadio; Elen Anatriello; Suria M Bahadue; Fernando H Biase; Clayton R Boldt; Jeffery A Carroll; Wanessa A Carvalho; Eliane P Cervelatti; Elsa Chacko; Jennifer E Chapin; Ye Cheng; Jungwoo Choi; Adam J Colley; Tatiana A de Campos; Marcos De Donato; Isabel K F de Miranda Santos; Carlo J F de Oliveira; Heather Deobald; Eve Devinoy; Kaitlin E Donohue; Peter Dovc; Annett Eberlein; Carolyn J Fitzsimmons; Alessandra M Franzin; Gustavo R Garcia; Sem Genini; Cody J Gladney; Jason R Grant; Marion L Greaser; Jonathan A Green; Darryl L Hadsell; Hatam A Hakimov; Rob Halgren; Jennifer L Harrow; Elizabeth A Hart; Nicola Hastings; Marta Hernandez; Zhi-Liang Hu; Aaron Ingham; Terhi Iso-Touru; Catherine Jamis; Kirsty Jensen; Dimos Kapetis; Tovah Kerr; Sari S Khalil; Hasan Khatib; Davood Kolbehdari; Charu G Kumar; Dinesh Kumar; Richard Leach; Justin C-M Lee; Changxi Li; Krystin M Logan; Roberto Malinverni; Elisa Marques; William F Martin; Natalia F Martins; Sandra R Maruyama; Raffaele Mazza; Kim L McLean; Juan F Medrano; Barbara T Moreno; Daniela D Moré; Carl T Muntean; Hari P Nandakumar; Marcelo F G Nogueira; Ingrid Olsaker; Sameer D Pant; Francesca Panzitta; Rosemeire C P Pastor; Mario A Poli; Nathan Poslusny; Satyanarayana Rachagani; Shoba Ranganathan; Andrej Razpet; Penny K Riggs; Gonzalo Rincon; Nelida Rodriguez-Osorio; Sandra L Rodriguez-Zas; Natasha E Romero; Anne Rosenwald; Lillian Sando; Sheila M Schmutz; Libing Shen; Laura Sherman; Bruce R Southey; Ylva Strandberg Lutzow; Jonathan V Sweedler; Imke Tammen; Bhanu Prakash V L Telugu; Jennifer M Urbanski; Yuri T Utsunomiya; Chris P Verschoor; Ashley J Waardenberg; Zhiquan Wang; Robert Ward; Rosemarie Weikard; Thomas H Welsh; Stephen N White; Laurens G Wilming; Kris R Wunderlich; Jianqi Yang; Feng-Qi Zhao Journal: Science Date: 2009-04-24 Impact factor: 47.728
Authors: Lakshmi K Matukumalli; Cynthia T Lawley; Robert D Schnabel; Jeremy F Taylor; Mark F Allan; Michael P Heaton; Jeff O'Connell; Stephen S Moore; Timothy P L Smith; Tad S Sonstegard; Curtis P Van Tassell Journal: PLoS One Date: 2009-04-24 Impact factor: 3.240
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