Genomic diagnosis for children with intellectual disability and/or developmental delay
Kevin M. Bowling,Michelle L. Thompson,Michelle D. Amaral,Candice R. Finnila,Susan M. Hiatt,Krysta L. Engel,J. Nicholas Cochran,Kelly M. East,David E. Gray,Whitley V. Kelley,Neil E. Lamb,Edward J. Lose,Carla A. Rich,Shirley Simmons,Jana Whittle,Benjamin T. Weaver,Amy S. Nesmith,Richard M. Myers,Gregory S. Barsh,E. Martina Bebin,Gregory M. Cooper +20 more
TLDR
The data strongly support the value of large-scale sequencing, especially WGS within proband-parent trios, as both an effective first-choice diagnostic tool and means to advance clinical and research progress related to pediatric neurological disease.Abstract:
Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-parent trios. Whole-exome sequences (WES) were generated for 365 individuals (127 affected) and whole-genome sequences (WGS) were generated for 612 individuals (244 affected). Pathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11.3%). We found that a family history of neurological disease, especially the presence of an affected first-degree relative, reduces the pathogenic/likely pathogenic variant identification rate, reflecting both the disease relevance and ease of interpretation of de novo variants. We also found that improvements to genetic knowledge facilitated interpretation changes in many cases. Through systematic reanalyses, we have thus far reclassified 15 variants, with 11.3% of families who initially were found to harbor a VUS and 4.7% of families with a negative result eventually found to harbor a pathogenic or likely pathogenic variant. To further such progress, the data described here are being shared through ClinVar, GeneMatcher, and dbGaP. Our data strongly support the value of large-scale sequencing, especially WGS within proband-parent trios, as both an effective first-choice diagnostic tool and means to advance clinical and research progress related to pediatric neurological disease.read more
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CADD: predicting the deleteriousness of variants throughout the human genome.
Philipp Rentzsch,Daniela Witten,Gregory M. Cooper,Jay Shendure,Martin Kircher,Martin Kircher +5 more
TL;DR: The latest updates to CADD are reviewed, including the most recent version, 1.4, which supports the human genome build GRCh38, and also present updates to the website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications.
Journal ArticleDOI
Delineation of the genetic and clinical spectrum of Phelan-McDermid syndrome caused by SHANK3 point mutations
Silvia De Rubeis,Paige M. Siper,Allison Durkin,Jordana Weissman,François Muratet,Danielle Halpern,Maria del Pilar Trelles,Yitzchak Frank,Reymundo Lozano,A. Ting Wang,J. Lloyd Holder,Catalina Betancur,Joseph D. Buxbaum,Alexander Kolevzon +13 more
TL;DR: The findings expand the molecular and phenotypic spectrum of PMS caused by SHANK3 point mutations and suggest that, in general, speech impairment and motor deficits are more severe in the case of deletions.
Journal ArticleDOI
Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.
Ragan Hart,Barbara B. Biesecker,Carrie L. Blout,Kurt D. Christensen,Kurt D. Christensen,Laura M. Amendola,Katie Bergstrom,Sawona Biswas,Kevin M. Bowling,Laura K. Conlin,Laura K. Conlin,Greg M. Cooper,Matthew C. Dulik,Matthew C. Dulik,Kelly M. East,Jessica Everett,Candice R. Finnila,Arezou A. Ghazani,Marian J. Gilmore,Katrina A.B. Goddard,Gail P. Jarvik,Jennifer J. Johnston,Tia L. Kauffman,Whitley V. Kelley,Joel B. Krier,Katie L. Lewis,Amy L. McGuire,Carmit K. McMullen,Jeffrey Ou,Sharon E. Plon,Heidi L. Rehm,Heidi L. Rehm,Heidi L. Rehm,C. Sue Richards,Edward J. Romasko,Ane Miren Sagardia,Nancy B. Spinner,Michelle L. Thompson,Erin Turbitt,Jason L. Vassy,Jason L. Vassy,Jason L. Vassy,Benjamin S. Wilfond,David L. Veenstra,Jonathan S. Berg,Robert C. Green,Leslie G. Biesecker,Lucia A. Hindorff +47 more
TL;DR: The results suggest that disclosure of SFs shows little to no adverse impact on participants and adds only modestly to near-term health-care costs; additional studies are needed to confirm these findings.
Journal ArticleDOI
Genomic medicine for kidney disease
TL;DR: Pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients, and the creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.
Journal ArticleDOI
Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature
Hadley Stevens Smith,J. Michael Swint,Seema R. Lalani,Jose-Miguel Yamal,Marcia C de Oliveira Otto,Stephan Castellanos,A.M. Taylor,Brendan Lee,Heidi V. Russell +8 more
TL;DR: Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes andMultidisciplinary implementation research is needed to demonstrate clinical utility and cost-effectiveness of CGS.
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Grant,Carla Gallo,Giovanni Poletti,Danish Saleheen,Asif Rasheed,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Yekaterina Vaydylevich,Audrey Duncanson,Michael Dunn,Jeffery A. Schloss +517 more
TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Journal ArticleDOI
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
Journal ArticleDOI
Analysis of protein-coding genetic variation in 60,706 humans
Monkol Lek,Konrad J. Karczewski,Konrad J. Karczewski,Eric Vallabh Minikel,Eric Vallabh Minikel,Kaitlin E. Samocha,Eric Banks,Timothy Fennell,Anne H. O’Donnell-Luria,Anne H. O’Donnell-Luria,Anne H. O’Donnell-Luria,James S. Ware,Andrew J. Hill,Andrew J. Hill,Andrew J. Hill,Beryl B. Cummings,Beryl B. Cummings,Taru Tukiainen,Taru Tukiainen,Daniel P. Birnbaum,Jack A. Kosmicki,Laramie E. Duncan,Laramie E. Duncan,Karol Estrada,Karol Estrada,Fengmei Zhao,Fengmei Zhao,James Zou,Emma Pierce-Hoffman,Emma Pierce-Hoffman,Joanne Berghout,David Neil Cooper,Nicole A. Deflaux,Mark A. DePristo,Ron Do,Jason Flannick,Jason Flannick,Menachem Fromer,Laura D. Gauthier,Jackie Goldstein,Jackie Goldstein,Namrata Gupta,Daniel P. Howrigan,Daniel P. Howrigan,Adam Kiezun,Mitja I. Kurki,Mitja I. Kurki,Ami Levy Moonshine,Pradeep Natarajan,Lorena Orozco,Gina M. Peloso,Gina M. Peloso,Ryan Poplin,Manuel A. Rivas,Valentin Ruano-Rubio,Samuel A. Rose,Douglas M. Ruderfer,Khalid Shakir,Peter D. Stenson,Christine Stevens,Brett Thomas,Brett Thomas,Grace Tiao,María Teresa Tusié-Luna,Ben Weisburd,Hong-Hee Won,Dongmei Yu,David Altshuler,David Altshuler,Diego Ardissino,Michael Boehnke,John Danesh,Stacey Donnelly,Roberto Elosua,Jose C. Florez,Jose C. Florez,Stacey Gabriel,Gad Getz,Gad Getz,Stephen J. Glatt,Christina M. Hultman,Sekar Kathiresan,Markku Laakso,Steven A. McCarroll,Steven A. McCarroll,Mark I. McCarthy,Mark I. McCarthy,Dermot P.B. McGovern,Ruth McPherson,Benjamin M. Neale,Benjamin M. Neale,Aarno Palotie,Shaun Purcell,Danish Saleheen,Jeremiah M. Scharf,Pamela Sklar,Patrick F. Sullivan,Patrick F. Sullivan,Jaakko Tuomilehto,Ming T. Tsuang,Hugh Watkins,Hugh Watkins,James G. Wilson,Mark J. Daly,Mark J. Daly,Daniel G. MacArthur,Daniel G. MacArthur +106 more
TL;DR: The aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC) provides direct evidence for the presence of widespread mutational recurrence.
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Analysis of protein-coding genetic variation in 60,706 humans
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Consensus Statement : Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies
David T. Miller,Margaret P Adam,Margaret P Adam,Swaroop Aradhya,Leslie G. Biesecker,Arthur R. Brothman,Nigel P. Carter,Deanna M. Church,John A. Crolla,Evan E. Eichler,Charles J. Epstein,W. Andrew Faucett,Lars Feuk,Jan M. Friedman,Ada Hamosh,Laird G. Jackson,Erin B. Kaminsky,Klaas Kok,Ian D. Krantz,Robert M. Kuhn,Charles Lee,James Ostell,Carla Rosenberg,Stephen W. Scherer,Nancy B. Spinner,Dimitri J. Stavropoulos,James Tepperberg,Erik C. Thorland,Joris Vermeesch,Darrel Waggoner,Michael S. Watson,Christa Lese Martin,David H. Ledbetter +32 more