Literature DB >> 28496993

Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic.

David Bick1, Pamela C Fraser2, Michael F Gutzeit3, Jeremy M Harris4, Tina M Hambuch5, Daniel C Helbling6, Howard J Jacob1, Juliet N Kersten3, Steven R Leuthner7, Thomas May1,8, Paula E North7, Sasha Z Prisco9, Bryce A Schuler10, Mary Shimoyama11, Kimberly A Strong12, Scott K Van Why13, Regan Veith14, James Verbsky15, Arthur M Weborg4, Brandon M Wilk4, Rodney E Willoughby13, Elizabeth A Worthey4, David P Dimmock16.   

Abstract

A pilot program was initiated using whole genome sequencing (WGS) to diagnose suspected genetic disorders in the Genetics Clinic at Children's Hospital of Wisconsin. Twenty-two patients underwent WGS between 2010 and 2013. Initially, we obtained a 14% (3/22) diagnosis rate over 2 years; with subsequent reanalysis, this increased to 36% (8/22). Disease causing variants were identified in SKIV2L, CECR1, DGKE, PYCR2, RYR1, PDGFRB, EFTUD2, and BCS1L. In 75% (6/8) of diagnosed cases, the diagnosis affected treatment and/or medical surveillance. Additionally, one case demonstrated a homozygous A18V variant in VLDLR that appears to be associated with a previously undescribed phenotype.

Entities:  

Keywords:  clinic; diagnosis; genome; sequencing

Year:  2016        PMID： 28496993      PMCID： PMC5423809          DOI： 10.1055/s-0036-1593968

Source DB:  PubMed          Journal:  J Pediatr Genet        ISSN： 2146-460X


  56 in total

1.  Genome sequencing identifies major causes of severe intellectual disability.

Authors:  Christian Gilissen; Jayne Y Hehir-Kwa; Djie Tjwan Thung; Maartje van de Vorst; Bregje W M van Bon; Marjolein H Willemsen; Michael Kwint; Irene M Janssen; Alexander Hoischen; Annette Schenck; Richard Leach; Robert Klein; Rick Tearle; Tan Bo; Rolph Pfundt; Helger G Yntema; Bert B A de Vries; Tjitske Kleefstra; Han G Brunner; Lisenka E L M Vissers; Joris A Veltman
Journal:  Nature       Date:  2014-06-04       Impact factor: 49.962

2.  Actionable, pathogenic incidental findings in 1,000 participants' exomes.

Authors:  Michael O Dorschner; Laura M Amendola; Emily H Turner; Peggy D Robertson; Brian H Shirts; Carlos J Gallego; Robin L Bennett; Kelly L Jones; Mari J Tokita; James T Bennett; Jerry H Kim; Elisabeth A Rosenthal; Daniel S Kim; Holly K Tabor; Michael J Bamshad; Arno G Motulsky; C Ronald Scott; Colin C Pritchard; Tom Walsh; Wylie Burke; Wendy H Raskind; Peter Byers; Fuki M Hisama; Deborah A Nickerson; Gail P Jarvik
Journal:  Am J Hum Genet       Date:  2013-09-19       Impact factor: 11.025

3.  A large health system's approach to utilization of the genetic counselor CPT® 96040 code.

Authors:  Shanna L Gustafson; Gail Pfeiffer; Charis Eng
Journal:  Genet Med       Date:  2011-12       Impact factor: 8.822

4.  The NIH Undiagnosed Diseases Program and Network: Applications to modern medicine.

Authors:  William A Gahl; John J Mulvihill; Camilo Toro; Thomas C Markello; Anastasia L Wise; Rachel B Ramoni; David R Adams; Cynthia J Tifft
Journal:  Mol Genet Metab       Date:  2016-01-22       Impact factor: 4.797

Review 5.  Recommendations for the integration of genomics into clinical practice.

Authors:  Sarah Bowdin; Adel Gilbert; Emma Bedoukian; Christopher Carew; Margaret P Adam; John Belmont; Barbara Bernhardt; Leslie Biesecker; Hans T Bjornsson; Miriam Blitzer; Lisa C A D'Alessandro; Matthew A Deardorff; Laurie Demmer; Alison Elliott; Gerald L Feldman; Ian A Glass; Gail Herman; Lucia Hindorff; Fuki Hisama; Louanne Hudgins; A Micheil Innes; Laird Jackson; Gail Jarvik; Raymond Kim; Bruce Korf; David H Ledbetter; Mindy Li; Eriskay Liston; Christian Marshall; Livija Medne; M Stephen Meyn; Nasim Monfared; Cynthia Morton; John J Mulvihill; Sharon E Plon; Heidi Rehm; Amy Roberts; Cheryl Shuman; Nancy B Spinner; D James Stavropoulos; Kathleen Valverde; Darrel J Waggoner; Alisha Wilkens; Ronald D Cohn; Ian D Krantz
Journal:  Genet Med       Date:  2016-05-12       Impact factor: 8.822

6.  Patient decisions for disclosure of secondary findings among the first 200 individuals undergoing clinical diagnostic exome sequencing.

Authors:  Layla Shahmirzadi; Elizabeth C Chao; Erika Palmaer; Melissa C Parra; Sha Tang; Kelly D Farwell Gonzalez
Journal:  Genet Med       Date:  2013-10-10       Impact factor: 8.822

7.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

8.  A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

Authors:  Zornitza Stark; Tiong Y Tan; Belinda Chong; Gemma R Brett; Patrick Yap; Maie Walsh; Alison Yeung; Heidi Peters; Dylan Mordaunt; Shannon Cowie; David J Amor; Ravi Savarirayan; George McGillivray; Lilian Downie; Paul G Ekert; Christiane Theda; Paul A James; Joy Yaplito-Lee; Monique M Ryan; Richard J Leventer; Emma Creed; Ivan Macciocca; Katrina M Bell; Alicia Oshlack; Simon Sadedin; Peter Georgeson; Charlotte Anderson; Natalie Thorne; Clara Gaff; Susan M White
Journal:  Genet Med       Date:  2016-03-03       Impact factor: 8.822

9.  A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases.

Authors:  Neil A Miller; Emily G Farrow; Margaret Gibson; Laurel K Willig; Greyson Twist; Byunggil Yoo; Tyler Marrs; Shane Corder; Lisa Krivohlavek; Adam Walter; Josh E Petrikin; Carol J Saunders; Isabelle Thiffault; Sarah E Soden; Laurie D Smith; Darrell L Dinwiddie; Suzanne Herd; Julie A Cakici; Severine Catreux; Mike Ruehle; Stephen F Kingsmore
Journal:  Genome Med       Date:  2015-09-30       Impact factor: 11.117

10.  Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory.

Authors:  Samuel P Strom; Hane Lee; Kingshuk Das; Eric Vilain; Stanley F Nelson; Wayne W Grody; Joshua L Deignan
Journal:  Genet Med       Date:  2014-01-09       Impact factor: 8.822
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  27 in total

1.  Heterozygous variants in MYBPC1 are associated with an expanded neuromuscular phenotype beyond arthrogryposis.

Authors:  Vandana Shashi; Janelle Geist; Youngha Lee; Yongjin Yoo; Unbeom Shin; Kelly Schoch; Jennifer Sullivan; Nicholas Stong; Edward Smith; Joan Jasien; Peter Kranz; Yoonsung Lee; Yong Beom Shin; Nathan T Wright; Murim Choi; Aikaterini Kontrogianni-Konstantopoulos
Journal:  Hum Mutat       Date:  2019-05-05       Impact factor: 4.878

2.  A head-to-head evaluation of the diagnostic efficacy and costs of trio versus singleton exome sequencing analysis.

Authors:  Tiong Yang Tan; Sebastian Lunke; Belinda Chong; Dean Phelan; Miriam Fanjul-Fernandez; Justine E Marum; Vanessa Siva Kumar; Zornitza Stark; Alison Yeung; Natasha J Brown; Chloe Stutterd; Martin B Delatycki; Simon Sadedin; Melissa Martyn; Ilias Goranitis; Natalie Thorne; Clara L Gaff; Susan M White
Journal:  Eur J Hum Genet       Date:  2019-07-18       Impact factor: 4.246

3.  Severe Neonatal RYR1 Myopathy With Pathological Features of Congenital Muscular Dystrophy.

Authors:  Daniel C Helbling; David Mendoza; Julie McCarrier; Mark A Vanden Avond; Matthew M Harmelink; Paul E Barkhaus; Donald Basel; Michael W Lawlor
Journal:  J Neuropathol Exp Neurol       Date:  2019-03-01       Impact factor: 3.685

Review 4.  Management of syndromic diarrhea/tricho-hepato-enteric syndrome: A review of the literature.

Authors:  Alexandre Fabre; Patrice Bourgeois; Marie-Edith Coste; Céline Roman; Vincent Barlogis; Catherine Badens
Journal:  Intractable Rare Dis Res       Date:  2017-08

5.  The future of DNA sequencing.

Authors:  Eric D Green; Edward M Rubin; Maynard V Olson
Journal:  Nature       Date:  2017-10-11       Impact factor: 49.962

Review 6.  Genomic medicine for undiagnosed diseases.

Authors:  Anastasia L Wise; Teri A Manolio; George A Mensah; Josh F Peterson; Dan M Roden; Cecelia Tamburro; Marc S Williams; Eric D Green
Journal:  Lancet       Date:  2019-08-05       Impact factor: 79.321

7.  Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder.

Authors:  Ning Liu; Kelly Schoch; Xi Luo; Loren D M Pena; Venkata Hemanjani Bhavana; Mary K Kukolich; Sarah Stringer; Zöe Powis; Kelly Radtke; Cameron Mroske; Kristen L Deak; Marie T McDonald; Allyn McConkie-Rosell; M Louise Markert; Peter G Kranz; Nicholas Stong; Anna C Need; David Bick; Michelle D Amaral; Elizabeth A Worthey; Shawn Levy; Michael F Wangler; Hugo J Bellen; Vandana Shashi; Shinya Yamamoto
Journal:  Hum Mol Genet       Date:  2018-07-15       Impact factor: 6.150

8.  Genome-Wide Sequencing for Unexplained Developmental Disabilities or Multiple Congenital Anomalies: A Health Technology Assessment.

Authors: 
Journal:  Ont Health Technol Assess Ser       Date:  2020-03-06

Review 9.  Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature.

Authors:  Hadley Stevens Smith; J Michael Swint; Seema R Lalani; Jose-Miguel Yamal; Marcia C de Oliveira Otto; Stephan Castellanos; Amy Taylor; Brendan H Lee; Heidi V Russell
Journal:  Genet Med       Date:  2018-05-14       Impact factor: 8.822

10.  A patient with germ-line gain-of-function PDGFRB p.N666H mutation and marked clinical response to imatinib.

Authors:  Dinel Pond; Florence A Arts; Nancy J Mendelsohn; Jean-Baptiste Demoulin; Gunter Scharer; Yoav Messinger
Journal:  Genet Med       Date:  2017-07-20       Impact factor: 8.822
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