Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

详细信息    查看全文

• 作者：Keren J. Carss¹ ; ² ; ¹⁸ ; Gavin Arno² ; ³ ; ⁴ ; ¹⁸ ; Marie Erwood¹ ; ² ; Jonathan Stephens¹ ; ² ; Alba Sanchis-Juan¹ ; ² ; Sarah Hull³ ; ⁴ ; Karyn Megy¹ ; ² ; Detelina Grozeva² ; ⁵ ; Eleanor Dewhurst¹ ; ² ; Samantha Malka³ ; ⁴ ; Vincent Plagnol⁶ ; Christopher Penkett¹ ; ² ; Kathleen Stirrups¹ ; ² ; Roberta Rizzo⁴ ; Genevieve Wright⁴ ; Dragana Josifova² ; ⁷ ; Maria Bitner-Glindzicz² ; ⁸ ; Richard H. Scott² ; ⁹ ; Emma Clement² ; ¹⁰ ; Louise Allen² ; ¹¹ ; Ruth Armstrong² ; ¹² ; Angela F. Brady² ; ¹³ ; Jenny Carmichael² ; ¹² ; Manali Chitre² ; ¹² ; Robert H.H. Henderson² ; ⁴ ; ¹⁰ ; Jane Hurst² ; ¹⁰ ; Robert E. MacLaren² ; ⁴ ; ¹⁴ ; Elaine Murphy² ; ¹⁵ ; Joan Paterson² ; ¹² ; Elisabeth Rosser² ; ¹⁰ ; Dorothy A. Thompson² ; ¹⁶ ; Emma Wakeling² ; ¹³ ; Willem H. Ouwehand¹ ; ² ; Michel Michaelides² ; ³ ; ⁴ ; Anthony T. Moore² ; ³ ; ⁴ ; ¹⁷ ; NIHR-BioResource Rare Diseases Consortium Timothy Aitman ; Hana Alachkar ; Sonia Ali ; Louise Allen ; David Allsup ; Gautum Ambegaonkar ; Julie Anderson ; Richard Antrobus ; Ruth Armstrong ; Gavin Arno ; Gururaj Arumugakani ; Sofie Ashford ; William Astle ; Antony Attwood ; Steve Austin ; Chiara Bacchelli ; Tamam Bakchoul ; Tadbir K. Bariana ; Helen Baxendale ; David Bennett ; Claire Bethune ; Shahnaz Bibi ; Maria Bitner-Glindzicz ; Marta Bleda ; Harm Boggard ; Paula Bolton-Maggs ; Claire Booth ; John R. Bradley ; Angie Brady ; Matthew Brown ; Michael Browning ; Christine Bryson ; Siobhan Burns ; Paul Calleja ; Natalie Canham ; Jenny Carmichael ; Keren Carss ; Mark Caulfield ; Elizabeth Chalmers ; Anita Chandra ; Patrick Chinnery ; Manali Chitre ; Colin Church ; Emma Clement ; Naomi Clements-Brod ; Virginia Clowes ; Gerry Coghlan ; Peter Collins ; Nichola Cooper ; Amanda Creaser-Myers ; Rosa DaCosta ; Louise Daugherty ; Sophie Davies ; John Davis ; Minka De Vries ; Patrick Deegan ; Sri V.V. Deevi ; Charu Deshpande ; Lisa Devlin ; Eleanor Dewhurst ; Rainer Doffinger ; Natalie Dormand ; Elizabeth Drewe ; David Edgar ; William Egner ; Wendy N. Erber ; Marie Erwood ; Tamara Everington ; Remi Favier ; Helen Firth ; Debra Fletcher ; Frances Flinter ; James C. Fox ; Amy Frary ; Kathleen Freson ; Bruce Furie ; Abigail Furnell ; Daniel Gale ; Alice Gardham ; Michael Gattens ; Neeti Ghali ; Pavandeep K. Ghataorhe ; Rohit Ghurye ; Simon Gibbs ; Kimberley Gilmour ; Paul Gissen ; Sarah Goddard ; Keith Gomez ; Pavel Gordins ; Stefan Grä ; f ; Daniel Greene ; Alan Greenhalgh ; Andreas Greinacher ; Sofia Grigoriadou ; Detelina Grozeva ; Scott Hackett ; Charaka Hadinnapola ; Rosie Hague ; Matthias Haimel ; Csaba Halmagyi ; Tracey Hammerton ; Daniel Hart ; Grant Hayman ; Johan W.M. Heemskerk ; Robert Henderson ; Anke Hensiek ; Yvonne Henskens ; Archana Herwadkar ; Simon Holden ; Muriel Holder ; Susan Holder ; Fengyuan Hu ; Aarnoud Huissoon ; Marc Humbert ; Jane Hurst ; Roger James ; Stephen Jolles ; Dragana Josifova ; Rashid Kazmi ; David Keeling ; Peter Kelleher ; Anne M. Kelly ; Fiona Kennedy ; David Kiely ; Nathalie Kingston ; Ania Koziell ; Deepa Krishnakumar ; Taco W. Kuijpers ; Dinakantha Kumararatne ; Manju Kurian ; Michael A. Laffan ; Michele P. Lambert ; Hana Lango Allen ; Allan Lawrie ; Sara Lear ; Melissa Lees ; Claire Lentaigne ; Ri Liesner ; Rachel Linger ; Hilary Longhurst ; Lorena Lorenzo ; Rajiv Machado ; Rob Mackenzie ; Robert MacLaren ; Eamonn Maher ; Jesmeen Maimaris ; Sarah Mangles ; Ania Manson ; Rutendo Mapeta ; Hugh S. Markus ; Jennifer Martin ; Larahmie Masati ; Mary Mathias ; Vera Matser ; Anna Maw ; Elizabeth McDermott ; Coleen McJannet ; Stuart Meacham ; Sharon Meehan ; Karyn Megy ; Sarju Mehta ; Michel Michaelides ; Carolyn M. Millar ; Shahin Moledina ; Anthony Moore ; Nicholas Morrell ; Andrew Mumford ; Sai Murng ; Elaine Murphy ; Sergey Nejentsev ; Sadia Noorani ; Paquita Nurden ; Eric Oksenhendler ; Willem H. Ouwehand ; Sofia Papadia ; Soo-Mi Park ; Alasdair Parker ; John Pasi ; Chris Patch ; Joan Paterson ; Jeanette Payne ; Andrew Peacock ; Kathelijne Peerlinck ; Christopher J. Penkett ; Joanna Pepke-Zaba ; David J. Perry ; Val Pollock ; Gary Polwarth ; Mark Ponsford ; Waseem Qasim ; Isabella Quinti ; Stuart Rankin ; Julia Rankin ; F. Lucy Raymond ; Karola Rehnstrom ; Evan Reid ; Christopher J. Rhodes ; Michael Richards ; Sylvia Richardson ; Alex Richter ; Irene Roberts ; Matthew Rondina ; Elisabeth Rosser ; Catherine Roughley ; Kevin Rue-Albrecht ; Crina Samarghitean ; Alba Sanchis-Juan ; Richard Sandford ; Saikat Santra ; Ravishankar Sargur ; Sinisa Savic ; Sol Schulman ; Harald Schulze ; Richard Scott ; Marie Scully ; Suranjith Seneviratne ; Carrock Sewell ; Olga Shamardina ; Debbie Shipley ; Ilenia Simeoni ; Suthesh Sivapalaratnam ; Kenneth Smith ; Aman Sohal ; Laura Southgate ; Simon Staines ; Emily Staples ; Hans Stauss ; Penelope Stein ; Jonathan Stephens ; Kathleen Stirrups ; Sophie Stock ; Jay Suntharalingam ; R. Campbell Tait ; Kate Talks ; Yvonne Tan ; Jecko Thachil ; James Thaventhiran ; Ellen Thomas ; Moira Thomas ; Dorothy Thompson ; Adrian Thrasher ; Marc Tischkowitz ; Catherine Titterton ; Cheng-Hock Toh ; Mark Toshner ; Carmen Treacy ; Richard Trembath ; Salih Tuna ; Wojciech Turek ; Ernest Turro ; Chris Van Geet ; Marijke Veltman ; Julie Vogt ; Julie von Ziegenweldt ; Anton Vonk Noordegraaf ; Emma Wakeling ; Ivy Wanjiku ; Timothy Q. Warner ; Evangeline Wassmer ; Hugh Watkins ; Andrew Webster ; Steve Welch ; Sarah Westbury ; John Wharton ; Deborah Whitehorn ; Martin Wilkins ; Lisa Willcocks ; Catherine Williamson ; Geoffrey Woods ; John Wort ; Nigel Yeatman ; Patrick Yong ; Tim Young ; Ping Yu
• 关键词：retinal dystrophy ; whole-genome sequence ; copy-number variants ; rare sequence variant
• 刊名：The American Journal of Human Genetics
• 出版年：2017
• 出版时间：5 January 2017
• 年：2017
• 卷：100
• 期：1
• 页码：75-90
• 全文大小：1734 K
• 卷排序：100

文摘

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in CHM in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.