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J Pediatr Genet. 2017 Jun;6(2):61-76. doi: 10.1055/s-0036-1593968. Epub 2016 Nov 28.

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

Author information

1
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States.
2
Aerodigestive and Genomic Services, Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States.
3
Children's Hospital of Wisconsin, Milwaukee, Wisconsin, United States.
4
Software Development and Informatics, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States.
5
Pediatric Genetics, Invitae Corporation, San Francisco, California, United States.
6
Human Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
7
Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
8
University of California, San Francisco, California, United States.
9
Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States.
10
Medical Scientist Training Program, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
11
Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
12
Ethics and Genomics Program, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States.
13
Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
14
Genetics Department, Children's Hospitals and Clinics of Minnesota, Minneapolis, Minnesota, United States.
15
Division of Rheumatology, Department of Pediatrics, CIRL and Clinical and Translational Research, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
16
Rady Children's Institute for Genomic Medicine, San Diego, California, United States.

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.

KEYWORDS:

clinic; diagnosis; genome; sequencing

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