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Genome Sequencing for Diagnosing Rare Diseases.
Monica H Wojcik1, Gabrielle Lemire1, Eva Berger1
1From the Division of Newborn Medicine (M.H.W., P.B.A.), the Manton Center for Orphan Disease Research (M.H.W., W.W., S.L.S., J.A.M., J.L., C.A.G., H.T.G., A.H.B., P.B.A., A.O.-L.), Division of Genetics and Genomics (M.H.W., G.L., S.L.S., L.P., E.G., H.T.G., V.S.G., A.H.B., P.B.A., A.O.-L.), Department of Pediatrics (S. Shril, R.S., F.H., W.K.C.), and the Division of Hematology and Oncology (M.W., J.M.V., V.G.S., L.D.C.), Boston Children's Hospital, Harvard Medical School, the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School (M.W., J.M.V., V.G.S., L.D.C.), the Center for Genomic Medicine (A.S.-J., J.G., J.M.F., H.B., M.T., C.A.-T., H.L.R., A.O.-L.) and the Pediatric Surgical Research Laboratories (H.B.), Massachusetts General Hospital, the Department of Neurology, Harvard Medical School (A.S.-J., V.S.G., J.M.F., H.B., M.T.), the Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School (E.A.P., E.M.P., K.M.B.), and the Department of Neurology, Brigham and Women's Hospital (V.S.G.), Boston, the Broad Center for Mendelian Genomics (M.H.W., G.L., B.W., G.E.V., S.L.S., H.S., M.S.-B., E.G.S., A.S.-J., K.A.R., L.P., I.O.-O., M.O., E.O., B.E.M., D.M., A.L., E.G., J.G., V.S.G., J.M.F., E. Evangelista, E. England, S. DiTroia, K.R.C., H.B., A.H.B., S.M.B., M.T., C.A.-T., H.L.R., A.O.-L.), Program in Medical and Population Genetics (M.W., J.M.V., V.G.S., L.D.C., A.H.B., P.B.A.), and the Stanley Center for Psychiatric Research (M.T.), Broad Institute of MIT and Harvard, and the Harvard Stem Cell Institute (V.G.S., L.D.C.), Cambridge - all in Massachusetts; the Institute of Human Genetics, University of Leipzig Medical Center (E.B., V. Strehlow, M.R., D.P., K.P., H.O., J.H., T.B., R.A.J.), and the Division of Neuropediatrics, Hospital for Children and Adolescents, University Hospital Leipzig (A.M., J.G.-A.), Leipzig, the Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf (D.W.), Heidelberg University, Medical Faculty of Heidelberg, Center for Child and Adolescent Medicine, Division of Pediatric Epileptology, Heidelberg (S. Syrbe), and the Department of Epileptology, Krankenhaus Mara, Bethel Epilepsy Center, Medical School OWL, Bielefeld University, Bielefeld (T.P.) - all in Germany; the Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Center, Cairo (M.S.Z.); the Victorian Clinical Genetics Service (S.M.W., T.Y.T., L.G., J.C.), the Centre for Population Genomics (D.M.), and the Brain and Mitochondrial Research Group (J.C.), Murdoch Children's Research Institute, Parkville, VIC, the Department of Paediatrics, University of Melbourne, Melbourne (S.M.W., T.Y.T., L.G., J.C.), the Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead (L.B.W., R.G.M., S.T.C., S.J.B.), the Discipline of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney (L.B.W., R.G.M., S.T.C., S.J.B.), and Functional Neuromics, Children's Medical Research Institute (R.G.M., S.T.C., S.J.B.), Westmead, NSW, the Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, WA (G.R., N.L.), the Centre for Population Genomics, Garvan Institute of Medical Research, Sydney (D.M.), and the Department of Neurology, Central Adelaide Local Health Network/Royal Adelaide Hospital, Adelaide Medical School, University of Adelaide, and the Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA (R.G.) - all in Australia; the John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom (A.T., V. Straub); the Fred A. Litwin Family Centre in Genetic Medicine, University Health Network (J.S., C.F.M.), the Department of Molecular Genetics (J.S.), the Faculty of Medicine (C.F.M.), and the Department of Laboratory Medicine and Pathobiology (J.P.L.-E.), University of Toronto, and Pathology and Laboratory Medicine and the Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health (J.P.L.-E.) - all in Toronto; the Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, and the Department of Genetics and Personalized Medicine, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia (K.R., S.P., K.Õ., K.T.O.); Molecular Diagnostics, New York Genome Center (V.O.), and the Department of Pathology and Cell Biology, Columbia University Irving Medical Center (M.G.) - both in New York; the Department of Neurosciences, University of California, San Diego, La Jolla, and Rady Children's Institute for Genomic Medicine, San Diego - both in California (J.G.G.); and the Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD (S. Donkervoort, C.G.B.).
Genome sequencing significantly improves rare disease diagnosis, identifying genetic variants missed by exome sequencing. This advanced genetic testing offers a diagnostic yield of approximately 8% for previously undiagnosed cases.
Area of Science:
- Genomics
- Rare Diseases
- Genetic Diagnostics
Background:
- Rare monogenic diseases often remain undiagnosed despite extensive genetic testing like exome sequencing.
- The diagnostic utility of whole genome sequencing (WGS) after prior negative genetic evaluations is not well-established.
Purpose of the Study:
- To evaluate the diagnostic yield of whole genome sequencing (WGS) in families with rare monogenic diseases who previously had negative genetic testing results.
- To identify the types of genetic variants detectable by WGS that are missed by exome sequencing.
Main Methods:
- Whole genome sequencing was performed on 822 families with suspected rare monogenic diseases and undiagnosed phenotypes.
- Data from an initial cohort of 744 families and a replication cohort of 78 families were analyzed.
- Previous exome sequencing data was reanalyzed, and additional analytic methods were applied.
Main Results:
- A molecular diagnosis was achieved in 29.3% of the initial cohort (218/744 families).
- Genome sequencing was crucial for identifying pathogenic variants in 8.2% of the initial cohort, including complex rearrangements and repeat expansions missed by exome sequencing.
- Reanalysis of exome data or application of additional methods identified variants in 63.5% of diagnosed cases.
Conclusions:
- Whole genome sequencing provides a significant diagnostic yield of approximately 8% in individuals with rare diseases previously tested by other methods.
- WGS identifies diverse pathogenic variants, including structural variants and repeat expansions, not detectable by exome sequencing.
- These findings support the clinical utility of WGS for diagnosing rare genetic disorders.
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