基因组测序在罕见病诊断中的应用。
Genome Sequencing for Diagnosing Rare Diseases.
机构信息
From 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.).
出版信息
N Engl J Med. 2024 Jun 6;390(21):1985-1997. doi: 10.1056/NEJMoa2314761.
BACKGROUND
Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.
METHODS
We sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center.
RESULTS
We sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) - 8.2% of families in the initial cohort - had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments.
CONCLUSIONS
The diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.).
背景
即使进行广泛的测试，例如外显子组测序，也可能难以发现导致罕见疾病的遗传变异。基因组测序的诊断率，特别是在阴性评估后，仍然定义不明确。
方法
我们对怀疑患有罕见单基因疾病且遗传检测未发现诊断的具有不同表型的家庭进行了基因组测序和分析，还对另一个独立临床中心的复制队列进行了基因组测序和分析。
结果
我们对 822 个家庭（初始队列中有 744 个，复制队列中有 78 个）进行了测序，并对 744 个家庭中的 218 个家庭做出了分子诊断（29.3%）。在这 218 个家庭中，有 61 个家庭（初始队列的 28.0%——占 8.2%）的变异需要进行基因组测序才能确定诊断，包括编码变异、内含子变异、小结构变异、拷贝数中性倒位、复杂重排和串联重复扩展。在先前非诊断性外显子组测序后做出分子诊断的大多数家庭（63.5%）的变异可以通过重新分析外显子组序列数据（53.4%）或通过其他分析方法，例如对拷贝数变异调用外显子组序列数据（10.8%）检测到。我们在复制队列中获得了类似的结果：在做出分子诊断的 33%的家庭中，或队列的 8%中，需要进行基因组测序，这表明这些发现既适用于研究环境，也适用于临床环境。
结论
在一个大型、多样化的研究队列和一个先前接受过基因检测的小临床队列中，基因组测序的诊断率约为 8%，包括几种以前通过外显子组测序或其他技术未检测到的致病性变异。（由国家人类基因组研究所等资助）。
Zotero 插件