1
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De La Vega FM, Chowdhury S, Moore B, Frise E, McCarthy J, Hernandez EJ, Wong T, James K, Guidugli L, Agrawal PB, Genetti CA, Brownstein CA, Beggs AH, Löscher BS, Franke A, Boone B, Levy SE, Õunap K, Pajusalu S, Huentelman M, Ramsey K, Naymik M, Narayanan V, Veeraraghavan N, Billings P, Reese MG, Yandell M, Kingsmore SF. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med 2021; 13:153. [PMID: 34645491 PMCID: PMC8515723 DOI: 10.1186/s13073-021-00965-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Clinical interpretation of genetic variants in the context of the patient's phenotype is becoming the largest component of cost and time expenditure for genome-based diagnosis of rare genetic diseases. Artificial intelligence (AI) holds promise to greatly simplify and speed genome interpretation by integrating predictive methods with the growing knowledge of genetic disease. Here we assess the diagnostic performance of Fabric GEM, a new, AI-based, clinical decision support tool for expediting genome interpretation. METHODS We benchmarked GEM in a retrospective cohort of 119 probands, mostly NICU infants, diagnosed with rare genetic diseases, who received whole-genome or whole-exome sequencing (WGS, WES). We replicated our analyses in a separate cohort of 60 cases collected from five academic medical centers. For comparison, we also analyzed these cases with current state-of-the-art variant prioritization tools. Included in the comparisons were trio, duo, and singleton cases. Variants underpinning diagnoses spanned diverse modes of inheritance and types, including structural variants (SVs). Patient phenotypes were extracted from clinical notes by two means: manually and using an automated clinical natural language processing (CNLP) tool. Finally, 14 previously unsolved cases were reanalyzed. RESULTS GEM ranked over 90% of the causal genes among the top or second candidate and prioritized for review a median of 3 candidate genes per case, using either manually curated or CNLP-derived phenotype descriptions. Ranking of trios and duos was unchanged when analyzed as singletons. In 17 of 20 cases with diagnostic SVs, GEM identified the causal SVs as the top candidate and in 19/20 within the top five, irrespective of whether SV calls were provided or inferred ab initio by GEM using its own internal SV detection algorithm. GEM showed similar performance in absence of parental genotypes. Analysis of 14 previously unsolved cases resulted in a novel finding for one case, candidates ultimately not advanced upon manual review for 3 cases, and no new findings for 10 cases. CONCLUSIONS GEM enabled diagnostic interpretation inclusive of all variant types through automated nomination of a very short list of candidate genes and disorders for final review and reporting. In combination with deep phenotyping by CNLP, GEM enables substantial automation of genetic disease diagnosis, potentially decreasing cost and expediting case review.
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Affiliation(s)
- Francisco M. De La Vega
- Fabric Genomics Inc., Oakland, CA USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA USA
- Current Address: Tempus Labs Inc., Redwood City, CA 94065 USA
| | - Shimul Chowdhury
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Barry Moore
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
| | | | | | - Edgar Javier Hernandez
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
| | - Terence Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Kiely James
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA USA
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Catherine A. Brownstein
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel & University Hospital Schleswig-Holstein, Kiel, Germany
| | - Braden Boone
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Shawn E. Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Matt Huentelman
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Marcus Naymik
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ USA
| | | | | | | | - Mark Yandell
- Fabric Genomics Inc., Oakland, CA USA
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT USA
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2
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Friedman J, Bird LM, Haas R, Robbins SL, Nahas SA, Dimmock DP, Yousefzadeh MJ, Witt MA, Niedernhofer LJ, Chowdhury S. Ending a diagnostic odyssey: Moving from exome to genome to identify cockayne syndrome. Mol Genet Genomic Med 2021; 9:e1623. [PMID: 34076366 PMCID: PMC8372079 DOI: 10.1002/mgg3.1623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 01/04/2023] Open
Abstract
Background Cockayne syndrome (CS) is a rare autosomal recessive disorder characterized by growth failure and multisystemic degeneration. Excision repair cross‐complementation group 6 (ERCC6 OMIM: *609413) is the gene most frequently mutated in CS. Methods A child with pre and postnatal growth failure and progressive neurologic deterioration with multisystem involvement, and with nondiagnostic whole‐exome sequencing, was screened for causal variants with whole‐genome sequencing (WGS). Results WGS identified biallelic ERCC6 variants, including a previously unreported intronic variant. Pathogenicity of these variants was established by demonstrating reduced levels of ERCC6 mRNA and protein expression, normal unscheduled DNA synthesis, and impaired recovery of RNA synthesis in patient fibroblasts following UV‐irradiation. Conclusion The study confirms the pathogenicity of a previously undescribed upstream intronic variant, highlighting the power of genome sequencing to identify noncoding variants. In addition, this report provides evidence for the utility of a combination approach of genome sequencing plus functional studies to provide diagnosis in a child for whom a lengthy diagnostic odyssey, including exome sequencing, was previously unrevealing.
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Affiliation(s)
- Jennifer Friedman
- Department of NeurosciencesUniversity of California San DiegoSan DiegoCAUSA
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Neurology Rady Children’s HospitalSan DiegoCAUSA
- Rady Children’s Institute for Genomic MedicineSan DiegoCAUSA
| | - Lynne M. Bird
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Genetics/DysmorphologyRady Children’s Hospital San DiegoSan DiegoCAUSA
| | - Richard Haas
- Department of NeurosciencesUniversity of California San DiegoSan DiegoCAUSA
- Department of PediatricsUniversity of California San DiegoSan DiegoCAUSA
- Division of Neurology Rady Children’s HospitalSan DiegoCAUSA
| | - Shira L. Robbins
- Viterbi Family Department of Ophthalmology at the Shiley Eye InstituteUniversity of California San DiegoLa JollaCAUSA
| | | | | | - Matthew J. Yousefzadeh
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
| | - Mariah A. Witt
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
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3
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Kingsmore SF, Henderson A, Owen MJ, Clark MM, Hansen C, Dimmock D, Chambers CD, Jeliffe-Pawlowski LL, Hobbs C. Measurement of genetic diseases as a cause of mortality in infants receiving whole genome sequencing. NPJ Genom Med 2020; 5:49. [PMID: 33154820 PMCID: PMC7608690 DOI: 10.1038/s41525-020-00155-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding causes of infant mortality shapes public health policy and prioritizes diseases for investments in surveillance, intervention and medical research. Rapid genomic sequencing has created a novel opportunity to decrease infant mortality associated with treatable genetic diseases. Herein, we sought to measure the contribution of genetic diseases to mortality among infants by secondary analysis of babies enrolled in two clinical studies and a systematic literature review. Among 312 infants who had been admitted to an ICU at Rady Children's Hospital between November 2015 and September 2018 and received rapid genomic sequencing, 30 (10%) died in infancy. Ten (33%) of the infants who died were diagnosed with 11 genetic diseases. The San Diego Study of Outcomes in Mothers and Infants platform identified differences between in-hospital and out-of-hospital causes of infant death. Similarly, in six published studies, 195 (21%) of 918 infant deaths were associated with genetic diseases by genomic sequencing. In 195 infant deaths associated with genetic diseases, locus heterogeneity was 70%. Treatment guidelines existed for 70% of the genetic diseases diagnosed, suggesting that rapid genomic sequencing has substantial potential to decrease infant mortality among infants in ICUs. Further studies are needed in larger, comprehensive, unbiased patient sets to determine the generalizability of these findings.
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Affiliation(s)
| | - Audrey Henderson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Michelle M. Clark
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | - David Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
| | | | - Laura L. Jeliffe-Pawlowski
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA USA
| | - Charlotte Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123 USA
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4
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Ng A, Galosi S, Salz L, Wong T, Schwager C, Amudhavalli S, Gelineau-Morel R, Chowdhury S, Friedman J. Failure to thrive - an overlooked manifestation of KMT2B-related dystonia: a case presentation. BMC Neurol 2020; 20:246. [PMID: 32546208 PMCID: PMC7296679 DOI: 10.1186/s12883-020-01798-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Background KMT2B-related dystonia is a recently described form of childhood onset dystonia that may improve with deep brain stimulation. Prior reports have focused on neurologic features including prominent bulbar involvement without detailing general health consequences that may result from orolingual dysfunction. We describe a family with novel KMT2B mutation with several members with failure to thrive to highlight this non-neurologic, but consequential impact of mutation in this gene. Case presentation We present a case of a 15-year old female who was admitted and evaluated for failure to thrive. On exam, she had severe speech dysfluency, limited ability to protrude the tongue, and generalized dystonia involving the oromandibular region, right upper and left lower extremity with left foot inversion contracture. The proband and her parents underwent whole genome sequencing. A previously undescribed variant, c.4960 T > C (p.Cys1654Arg), was identified in the KMT2B gene in the proband and mother, and this variant was subsequently confirmed in two maternal cousins, one with failure to thrive. Literature review identified frequent reports of prominent bulbar involvement but failure to thrive is rarely mentioned. Conclusion Failure to thrive is a common pediatric clinical condition that has consequences for growth and development. In the presence of an abnormal neurologic exam, a search for a specific underlying genetic etiology should be pursued. With this case series, we highlight an unusual potentially treatable cause of failure to thrive, reinforce the importance of precise molecular diagnosis for patients with failure to thrive and an abnormal neurologic exam, and underscore the importance of cascade screening of family members.
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Affiliation(s)
- Andrew Ng
- University of California San Diego, San Diego, CA, USA.,Rady Children's Hospital, San Diego, CA, USA
| | | | - Lisa Salz
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Terence Wong
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Jennifer Friedman
- University of California San Diego, San Diego, CA, USA. .,Rady Children's Hospital, San Diego, CA, USA. .,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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5
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Zhao M, Havrilla JM, Fang L, Chen Y, Peng J, Liu C, Wu C, Sarmady M, Botas P, Isla J, Lyon GJ, Weng C, Wang K. Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. NAR Genom Bioinform 2020; 2:lqaa032. [PMID: 32500119 PMCID: PMC7252576 DOI: 10.1093/nargab/lqaa032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/10/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPacket descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed and acts as a real-time phenotype-driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients' de-identified HPO term data from the Children's Hospital of Philadelphia.
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Affiliation(s)
- Mengge Zhao
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - James M Havrilla
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Li Fang
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ying Chen
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacqueline Peng
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Chao Wu
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pablo Botas
- Foundation 29, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Julián Isla
- Foundation 29, Pozuelo de Alarcon, 28223 Madrid, Spain.,Dravet Syndrome European Federation, 29200 Brest, France
| | - Gholson J Lyon
- Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY 10314, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY 10032, USA
| | - Kai Wang
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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6
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Clark MM, Hildreth A, Batalov S, Ding Y, Chowdhury S, Watkins K, Ellsworth K, Camp B, Kint CI, Yacoubian C, Farnaes L, Bainbridge MN, Beebe C, Braun JJA, Bray M, Carroll J, Cakici JA, Caylor SA, Clarke C, Creed MP, Friedman J, Frith A, Gain R, Gaughran M, George S, Gilmer S, Gleeson J, Gore J, Grunenwald H, Hovey RL, Janes ML, Lin K, McDonagh PD, McBride K, Mulrooney P, Nahas S, Oh D, Oriol A, Puckett L, Rady Z, Reese MG, Ryu J, Salz L, Sanford E, Stewart L, Sweeney N, Tokita M, Van Der Kraan L, White S, Wigby K, Williams B, Wong T, Wright MS, Yamada C, Schols P, Reynders J, Hall K, Dimmock D, Veeraraghavan N, Defay T, Kingsmore SF. Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation. Sci Transl Med 2020; 11:11/489/eaat6177. [PMID: 31019026 DOI: 10.1126/scitranslmed.aat6177] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 10/24/2018] [Accepted: 04/01/2019] [Indexed: 12/19/2022]
Abstract
By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children's deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient's CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient's genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments.
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Affiliation(s)
- Michelle M Clark
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Amber Hildreth
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA.,Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kelly Watkins
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Brandon Camp
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | | | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Matthew N Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Codified Genomics, LLC, Houston, TX 77033, USA
| | - Curtis Beebe
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Joshua J A Braun
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Margaret Bray
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
| | - Jeanne Carroll
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Julie A Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sara A Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Mitchell P Creed
- University of Kansas School of Medicine, Kansas City, MO 66160, USA
| | - Jennifer Friedman
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA
| | | | | | - Mary Gaughran
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | | | - Joseph Gleeson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA 92093, USA
| | | | | | - Raymond L Hovey
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Marie L Janes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kejia Lin
- Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Kyle McBride
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Patrick Mulrooney
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Daeheon Oh
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Albert Oriol
- Rady Children's Hospital, San Diego, CA 92123, USA
| | - Laura Puckett
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Zia Rady
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Julie Ryu
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Lisa Salz
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Nathaly Sweeney
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Luca Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sarah White
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Terence Wong
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Meredith S Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Catherine Yamada
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - John Reynders
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay
- Alexion Pharmaceuticals Inc., New Haven, CT 06510, USA
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7
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Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, Bainbridge MN, Carroll J, Caylor SA, Clarke C, Ding Y, Ellsworth K, Farnaes L, Hildreth A, Hobbs C, James K, Kint CI, Lenberg J, Nahas S, Prince L, Reyes I, Salz L, Sanford E, Schols P, Sweeney N, Tokita M, Veeraraghavan N, Watkins K, Wigby K, Wong T, Chowdhury S, Wright MS, Dimmock D, Bezares Z, Bloss C, Braun JJ, Diaz C, Mashburn D, Tamang D, Orendain D, Friedman J, Gleeson J, Barea J, Chiang G, Cohenmeyer C, Coufal NG, Evans M, Honold J, Hovey RL, Kimball A, Lane B, Le C, Le J, Leibel S, Moyer L, Mulrooney P, Oh D, Ordonez P, Oriol A, Ortiz-Arechiga M, Puckett L, Speziale M, Suttner D, Van Der Kraan L, Knight G, Sauer C, Song R, White S, Wise A, Yamada C. A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants. Am J Hum Genet 2019; 105:719-733. [PMID: 31564432 DOI: 10.1016/j.ajhg.2019.08.009] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/23/2019] [Indexed: 12/21/2022] Open
Abstract
The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.
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