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Cho Y, Lee CH, Jeong EG, Kim MH, Hong JH, Ko Y, Lee B, Yun G, Kim BJ, Jung J, Jung J, Lee JS. Prevalence of Rare Genetic Variations and Their Implications in NGS-data Interpretation. Sci Rep 2017; 7:9810. [PMID: 28851938 PMCID: PMC5574920 DOI: 10.1038/s41598-017-09247-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/21/2017] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) technology has improved enough to discover mutations associated with genetic diseases. Our study evaluated the feasibility of targeted NGS as a primary screening tool to detect causal variants and subsequently predict genetic diseases. We performed parallel computations on 3.7-megabase-targeted regions to detect disease-causing mutations in 103 participants consisting of 81 patients and 22 controls. Data analysis of the participants took about 6 hours using local databases and 200 nodes of a supercomputer. All variants in the selected genes led on average to 3.6 putative diseases for each patient while variants restricted to disease-causing genes identified the correct disease. Notably, only 12% of predicted causal variants were recorded as causal mutations in public databases: 88% had no or insufficient records. In this study, most genetic diseases were caused by rare mutations and public records were inadequate. Most rare variants, however, were not associated with genetic diseases. These data implied that novel, rare variants should not be ignored but interpreted in conjunction with additional clinical data. This step is needed so appropriate advice can be given to primary doctors and parents, thus fulfilling the purpose of this method as a primary screen for rare genetic diseases.
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Affiliation(s)
- Yangrae Cho
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
- DFTBA, CALS, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chul-Ho Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Eun-Goo Jeong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Min-Ho Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jong Hui Hong
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin-si, Gyeonggi-do, 17035, Republic of Korea
| | - Bomnun Lee
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Gilly Yun
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Byong Joon Kim
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongcheol Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea
| | - Jongsun Jung
- Syntekabio Incorporated, Techno-2ro B-512, Yuseong-gu, Daejeon, 34025, Republic of Korea.
| | - Jin-Sung Lee
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW. Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing. Genet Med 2015; 17:337-47. [PMID: 25255367 DOI: 10.1038/gim.2014.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/31/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study. METHODS The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation. RESULTS We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively. CONCLUSION Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns.
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Affiliation(s)
| | | | | | | | | | - Kevin Strauss
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Holmes Morton
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin W Naylor
- 1] Parabase Genomics, Boston, Massachusetts, USA [2] Division of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
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Grigorenko EL. Genomic sciences for developmentalists: a merge of science and practice. New Dir Child Adolesc Dev 2015; 2015:5-12. [PMID: 25732010 DOI: 10.1002/cad.20083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The etiological forces of development have been a central question for the developmental sciences (however defined) since their crystallization as a distinct branch of scientific inquiry. Although the history of these sciences contains examples of extreme positions capitalizing on either the predominance of the genome (i.e., the accumulation of genetic factors driving development) or the environmentome (i.e., the accumulation of environmental factors driving development), the moderate view of development as the emergence of a person from a particular genome and within a specific context has settled into the driver's seat and is disputed no longer. Yet, although there is a converging theoretical perspective, a gap between this perspective and practice remains. In other words, society needs to translate this position into praxis. This opinion exemplifies the current state of corresponding knowledge in the developmental sciences, with a particular emphasis on the understanding of the role of the genome in child and adolescent development, and offers a set of comments on how this translation is being shaped by the newest technologies in the genomic sciences.
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Affiliation(s)
- Elena L Grigorenko
- Child Study Center, Yale University, New Haven, CT, USA; Laboratory of Translational Science of Early Childhood, St. Petersburg State University, St. Petersburg, Russian Federation
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Abstract
That each of us is truly biologically unique, extending to even monozygotic, "identical" twins, is not fully appreciated. Now that it is possible to perform a comprehensive "omic" assessment of an individual, including one's DNA and RNA sequence and at least some characterization of one's proteome, metabolome, microbiome, autoantibodies, and epigenome, it has become abundantly clear that each of us has truly one-of-a-kind biological content. Well beyond the allure of the matchless fingerprint or snowflake concept, these singular, individual data and information set up a remarkable and unprecedented opportunity to improve medical treatment and develop preventive strategies to preserve health.
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Affiliation(s)
- Eric J Topol
- The Scripps Translational Science Institute, The Scripps Research Institute and Scripps Health, La Jolla, CA 92037, USA.
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