Zachary A Szpiech1, Alexandra Blant2, Trevor J Pemberton2. 1. Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, CA 94158, USA. 2. Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
Abstract
SUMMARY: Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method ( Pemberton et al., 2012 ) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method. AVAILABILITY AND IMPLEMENTATION: GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub ( https://github.com/szpiech/garlic ) under the GNU General Public License version 3. CONTACT: zachary.szpiech@ucsf.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Runs of homozygosity (ROH) are important genomic features that manifest when identical-by-descent haplotypes are inherited from parents. Their length distributions and genomic locations are informative about population history and they are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. Here, we present software implementing a model-based method ( Pemberton et al., 2012 ) for inferring ROH in genome-wide SNP datasets that incorporates population-specific parameters and a genotyping error rate as well as provides a length-based classification module to identify biologically interesting classes of ROH. Using simulations, we evaluate the performance of this method. AVAILABILITY AND IMPLEMENTATION: GARLIC is written in C ++. Source code and pre-compiled binaries (Windows, OSX and Linux) are hosted on GitHub ( https://github.com/szpiech/garlic ) under the GNU General Public License version 3. CONTACT: zachary.szpiech@ucsf.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Todd Lencz; Christophe Lambert; Pamela DeRosse; Katherine E Burdick; T Vance Morgan; John M Kane; Raju Kucherlapati; Anil K Malhotra Journal: Proc Natl Acad Sci U S A Date: 2007-12-05 Impact factor: 11.205
Authors: Russell L McLaughlin; Kevin P Kenna; Alice Vajda; Mark Heverin; Susan Byrne; Colette G Donaghy; Simon Cronin; Daniel G Bradley; Orla Hardiman Journal: Genomics Date: 2015-01-23 Impact factor: 5.736
Authors: Tie-Lin Yang; Yan Guo; Li-Shu Zhang; Qing Tian; Han Yan; Christopher J Papasian; Robert R Recker; Hong-Wen Deng Journal: J Clin Endocrinol Metab Date: 2010-05-13 Impact factor: 5.958
Authors: Peter K Joshi; Tonu Esko; Ozren Polašek; James F Wilson; Hannele Mattsson; Niina Eklund; Ilaria Gandin; Teresa Nutile; Anne U Jackson; Claudia Schurmann; Albert V Smith; Weihua Zhang; Yukinori Okada; Alena Stančáková; Jessica D Faul; Wei Zhao; Traci M Bartz; Maria Pina Concas; Nora Franceschini; Stefan Enroth; Veronique Vitart; Stella Trompet; Xiuqing Guo; Daniel I Chasman; Jeffery R O'Connel; Tanguy Corre; Suraj S Nongmaithem; Yuning Chen; Massimo Mangino; Daniela Ruggiero; Michela Traglia; Aliki-Eleni Farmaki; Tim Kacprowski; Andrew Bjonnes; Ashley van der Spek; Ying Wu; Anil K Giri; Lisa R Yanek; Lihua Wang; Edith Hofer; Cornelius A Rietveld; Olga McLeod; Marilyn C Cornelis; Cristian Pattaro; Niek Verweij; Clemens Baumbach; Abdel Abdellaoui; Helen R Warren; Dragana Vuckovic; Hao Mei; Claude Bouchard; John R B Perry; Stefania Cappellani; Saira S Mirza; Miles C Benton; Ulrich Broeckel; Sarah E Medland; Penelope A Lind; Giovanni Malerba; Alexander Drong; Loic Yengo; Lawrence F Bielak; Degui Zhi; Peter J van der Most; Daniel Shriner; Reedik Mägi; Gibran Hemani; Tugce Karaderi; Zhaoming Wang; Tian Liu; Ilja Demuth; Jing Hua Zhao; Weihua Meng; Lazaros Lataniotis; Sander W van der Laan; Jonathan P Bradfield; Andrew R Wood; Amelie Bonnefond; Tarunveer S Ahluwalia; Leanne M Hall; Erika Salvi; Seyhan Yazar; Lisbeth Carstensen; Hugoline G de Haan; Mark Abney; Uzma Afzal; Matthew A Allison; Najaf Amin; Folkert W Asselbergs; Stephan J L Bakker; R Graham Barr; Sebastian E Baumeister; Daniel J Benjamin; Sven Bergmann; Eric Boerwinkle; Erwin P Bottinger; Archie Campbell; Aravinda Chakravarti; Yingleong Chan; Stephen J Chanock; Constance Chen; Y-D Ida Chen; Francis S Collins; John Connell; Adolfo Correa; L Adrienne Cupples; George Davey Smith; Gail Davies; Marcus Dörr; Georg Ehret; Stephen B Ellis; Bjarke Feenstra; Mary F Feitosa; Ian Ford; Caroline S Fox; Timothy M Frayling; Nele Friedrich; Frank Geller; Generation Scotland; Irina Gillham-Nasenya; Omri Gottesman; Misa Graff; Francine Grodstein; Charles Gu; Chris Haley; Christopher J Hammond; Sarah E Harris; Tamara B Harris; Nicholas D Hastie; Nancy L Heard-Costa; Kauko Heikkilä; Lynne J Hocking; Georg Homuth; Jouke-Jan Hottenga; Jinyan Huang; Jennifer E Huffman; Pirro G Hysi; M Arfan Ikram; Erik Ingelsson; Anni Joensuu; Åsa Johansson; Pekka Jousilahti; J Wouter Jukema; Mika Kähönen; Yoichiro Kamatani; Stavroula Kanoni; Shona M Kerr; Nazir M Khan; Philipp Koellinger; Heikki A Koistinen; Manraj K Kooner; Michiaki Kubo; Johanna Kuusisto; Jari Lahti; Lenore J Launer; Rodney A Lea; Benjamin Lehne; Terho Lehtimäki; David C M Liewald; Lars Lind; Marie Loh; Marja-Liisa Lokki; Stephanie J London; Stephanie J Loomis; Anu Loukola; Yingchang Lu; Thomas Lumley; Annamari Lundqvist; Satu Männistö; Pedro Marques-Vidal; Corrado Masciullo; Angela Matchan; Rasika A Mathias; Koichi Matsuda; James B Meigs; Christa Meisinger; Thomas Meitinger; Cristina Menni; Frank D Mentch; Evelin Mihailov; Lili Milani; May E Montasser; Grant W Montgomery; Alanna Morrison; Richard H Myers; Rajiv Nadukuru; Pau Navarro; Mari Nelis; Markku S Nieminen; Ilja M Nolte; George T O'Connor; Adesola Ogunniyi; Sandosh Padmanabhan; Walter R Palmas; James S Pankow; Inga Patarcic; Francesca Pavani; Patricia A Peyser; Kirsi Pietilainen; Neil Poulter; Inga Prokopenko; Sarju Ralhan; Paul Redmond; Stephen S Rich; Harri Rissanen; Antonietta Robino; Lynda M Rose; Richard Rose; Cinzia Sala; Babatunde Salako; Veikko Salomaa; Antti-Pekka Sarin; Richa Saxena; Helena Schmidt; Laura J Scott; William R Scott; Bengt Sennblad; Sudha Seshadri; Peter Sever; Smeeta Shrestha; Blair H Smith; Jennifer A Smith; Nicole Soranzo; Nona Sotoodehnia; Lorraine Southam; Alice V Stanton; Maria G Stathopoulou; Konstantin Strauch; Rona J Strawbridge; Matthew J Suderman; Nikhil Tandon; Sian-Tsun Tang; Kent D Taylor; Bamidele O Tayo; Anna Maria Töglhofer; Maciej Tomaszewski; Natalia Tšernikova; Jaakko Tuomilehto; Andre G Uitterlinden; Dhananjay Vaidya; Astrid van Hylckama Vlieg; Jessica van Setten; Tuula Vasankari; Sailaja Vedantam; Efthymia Vlachopoulou; Diego Vozzi; Eero Vuoksimaa; Melanie Waldenberger; Erin B Ware; William Wentworth-Shields; John B Whitfield; Sarah Wild; Gonneke Willemsen; Chittaranjan S Yajnik; Jie Yao; Gianluigi Zaza; Xiaofeng Zhu; The BioBank Japan Project; Rany M Salem; Mads Melbye; Hans Bisgaard; Nilesh J Samani; Daniele Cusi; David A Mackey; Richard S Cooper; Philippe Froguel; Gerard Pasterkamp; Struan F A Grant; Hakon Hakonarson; Luigi Ferrucci; Robert A Scott; Andrew D Morris; Colin N A Palmer; George Dedoussis; Panos Deloukas; Lars Bertram; Ulman Lindenberger; Sonja I Berndt; Cecilia M Lindgren; Nicholas J Timpson; Anke Tönjes; Patricia B Munroe; Thorkild I A Sørensen; Charles N Rotimi; Donna K Arnett; Albertine J Oldehinkel; Sharon L R Kardia; Beverley Balkau; Giovanni Gambaro; Andrew P Morris; Johan G Eriksson; Margie J Wright; Nicholas G Martin; Steven C Hunt; John M Starr; Ian J Deary; Lyn R Griffiths; Henning Tiemeier; Nicola Pirastu; Jaakko Kaprio; Nicholas J Wareham; Louis Pérusse; James G Wilson; Giorgia Girotto; Mark J Caulfield; Olli Raitakari; Dorret I Boomsma; Christian Gieger; Pim van der Harst; Andrew A Hicks; Peter Kraft; Juha Sinisalo; Paul Knekt; Magnus Johannesson; Patrik K E Magnusson; Anders Hamsten; Reinhold Schmidt; Ingrid B Borecki; Erkki Vartiainen; Diane M Becker; Dwaipayan Bharadwaj; Karen L Mohlke; Michael Boehnke; Cornelia M van Duijn; Dharambir K Sanghera; Alexander Teumer; Eleftheria Zeggini; Andres Metspalu; Paolo Gasparini; Sheila Ulivi; Carole Ober; Daniela Toniolo; Igor Rudan; David J Porteous; Marina Ciullo; Tim D Spector; Caroline Hayward; Josée Dupuis; Ruth J F Loos; Alan F Wright; Giriraj R Chandak; Peter Vollenweider; Alan Shuldiner; Paul M Ridker; Jerome I Rotter; Naveed Sattar; Ulf Gyllensten; Kari E North; Mario Pirastu; Bruce M Psaty; David R Weir; Markku Laakso; Vilmundur Gudnason; Atsushi Takahashi; John C Chambers; Jaspal S Kooner; David P Strachan; Harry Campbell; Joel N Hirschhorn; Markus Perola Journal: Nature Date: 2015-07-01 Impact factor: 49.962
Authors: Javier Prado-Martinez; Peter H Sudmant; Jeffrey M Kidd; Heng Li; Joanna L Kelley; Belen Lorente-Galdos; Krishna R Veeramah; August E Woerner; Timothy D O'Connor; Gabriel Santpere; Alexander Cagan; Christoph Theunert; Ferran Casals; Hafid Laayouni; Kasper Munch; Asger Hobolth; Anders E Halager; Maika Malig; Jessica Hernandez-Rodriguez; Irene Hernando-Herraez; Kay Prüfer; Marc Pybus; Laurel Johnstone; Michael Lachmann; Can Alkan; Dorina Twigg; Natalia Petit; Carl Baker; Fereydoun Hormozdiari; Marcos Fernandez-Callejo; Marc Dabad; Michael L Wilson; Laurie Stevison; Cristina Camprubí; Tiago Carvalho; Aurora Ruiz-Herrera; Laura Vives; Marta Mele; Teresa Abello; Ivanela Kondova; Ronald E Bontrop; Anne Pusey; Felix Lankester; John A Kiyang; Richard A Bergl; Elizabeth Lonsdorf; Simon Myers; Mario Ventura; Pascal Gagneux; David Comas; Hans Siegismund; Julie Blanc; Lidia Agueda-Calpena; Marta Gut; Lucinda Fulton; Sarah A Tishkoff; James C Mullikin; Richard K Wilson; Ivo G Gut; Mary Katherine Gonder; Oliver A Ryder; Beatrice H Hahn; Arcadi Navarro; Joshua M Akey; Jaume Bertranpetit; David Reich; Thomas Mailund; Mikkel H Schierup; Christina Hvilsom; Aida M Andrés; Jeffrey D Wall; Carlos D Bustamante; Michael F Hammer; Evan E Eichler; Tomas Marques-Bonet Journal: Nature Date: 2013-07-03 Impact factor: 49.962
Authors: Kay Prüfer; Fernando Racimo; Nick Patterson; Flora Jay; Sriram Sankararaman; Susanna Sawyer; Anja Heinze; Gabriel Renaud; Peter H Sudmant; Cesare de Filippo; Heng Li; Swapan Mallick; Michael Dannemann; Qiaomei Fu; Martin Kircher; Martin Kuhlwilm; Michael Lachmann; Matthias Meyer; Matthias Ongyerth; Michael Siebauer; Christoph Theunert; Arti Tandon; Priya Moorjani; Joseph Pickrell; James C Mullikin; Samuel H Vohr; Richard E Green; Ines Hellmann; Philip L F Johnson; Hélène Blanche; Howard Cann; Jacob O Kitzman; Jay Shendure; Evan E Eichler; Ed S Lein; Trygve E Bakken; Liubov V Golovanova; Vladimir B Doronichev; Michael V Shunkov; Anatoli P Derevianko; Bence Viola; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo Journal: Nature Date: 2013-12-18 Impact factor: 49.962
Authors: Francisco C Ceballos; Peter K Joshi; David W Clark; Michèle Ramsay; James F Wilson Journal: Nat Rev Genet Date: 2018-01-15 Impact factor: 53.242
Authors: Shyamalika Gopalan; Richard E W Berl; Justin W Myrick; Zachary H Garfield; Austin W Reynolds; Barnabas K Bafens; Gillian Belbin; Mira Mastoras; Cole Williams; Michelle Daya; Akmel N Negash; Marcus W Feldman; Barry S Hewlett; Brenna M Henn Journal: Curr Biol Date: 2022-03-09 Impact factor: 10.900
Authors: Richard M Merkhofer; Mary B O'Neill; Caitlin S Pepperell; Bruce S Klein; Donny Xiong; Nydiaris Hernandez-Santos; Hannah Dobson; J Scott Fites; Abigail C Shockey; Marcel Wuethrich Journal: mBio Date: 2019-06-18 Impact factor: 7.867
Authors: Priyanka Nakka; Samuel Pattillo Smith; Anne H O'Donnell-Luria; Kimberly F McManus; Joanna L Mountain; Sohini Ramachandran; J Fah Sathirapongsasuti Journal: Am J Hum Genet Date: 2019-10-10 Impact factor: 11.025
Authors: Sergey A Kornilov; Mei Tan; Abdullah Aljughaiman; Oxana Yu Naumova; Elena L Grigorenko Journal: Front Genet Date: 2019-09-18 Impact factor: 4.599
Authors: Zachary A Szpiech; Angel C Y Mak; Marquitta J White; Donglei Hu; Celeste Eng; Esteban G Burchard; Ryan D Hernandez Journal: Am J Hum Genet Date: 2019-09-19 Impact factor: 11.025