ClinVar: improving access to variant interpretations and supporting evidence.
Melissa J. Landrum,Jennifer M. Lee,Mark L. Benson,Garth Brown,Chen Chao,Shanmuga Chitipiralla,Baoshan Gu,Jennifer Hart,Douglas W. Hoffman,Wonhee Jang,Karen Karapetyan,Kenneth S. Katz,Chunlei Liu,Zenith Maddipatla,Malheiro Aj,Kurt McDaniel,Michael Ovetsky,George R. Riley,George Zhou,J. Bradley Holmes,Brandi L. Kattman,Donna Maglott +21 more
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ClinVar continues to make improvements to its search and retrieval functions.Abstract:
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.read more
Citations
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Journal ArticleDOI
The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero,Juan Manuel Ramírez-Anguita,Josep Saüch-Pitarch,Francesco Ronzano,Emilio Centeno,Ferran Sanz,Laura I. Furlong +6 more
TL;DR: The DisGeNET platform, a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.
Journal ArticleDOI
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.
Daniel Taliun,Daniel N. Harris,Michael D. Kessler,Jedidiah Carlson,Jedidiah Carlson,Zachary A. Szpiech,Raul Torres,Sarah A Gagliano Taliun,André Corvelo,Stephanie M. Gogarten,Hyun Min Kang,Achilleas N. Pitsillides,Jonathon LeFaive,Seung-been Lee,Xiaowen Tian,Brian L. Browning,Sayantan Das,Anne-Katrin Emde,Wayne E. Clarke,Douglas Loesch,Amol C. Shetty,Thomas W. Blackwell,Albert V. Smith,Quenna Wong,Xiaoming Liu,Matthew P. Conomos,Dean Bobo,François Aguet,Christine M. Albert,Alvaro Alonso,Kristin G. Ardlie,Dan E. Arking,Stella Aslibekyan,Paul L. Auer,John Barnard,R. Graham Barr,Lucas Barwick,Lewis C. Becker,Rebecca L. Beer,Emelia J. Benjamin,Lawrence F. Bielak,John Blangero,Michael Boehnke,Donald W. Bowden,Jennifer A. Brody,Esteban G. Burchard,Brian E. Cade,Brian E. Cade,James F. Casella,Brandon Chalazan,Daniel I. Chasman,Daniel I. Chasman,Yii-Der Ida Chen,Michael H. Cho,Seung Hoan Choi,Mina K. Chung,Mina K. Chung,Mina K. Chung,Clary B. Clish,Adolfo Correa,Joanne E. Curran,Brian Custer,Dawood Darbar,Michelle Daya,Mariza de Andrade,Dawn L. DeMeo,Susan K. Dutcher,Patrick T. Ellinor,Leslie S. Emery,Celeste Eng,Diane Fatkin,Diane Fatkin,Diane Fatkin,Tasha E. Fingerlin,Lukas Forer,Myriam Fornage,Nora Franceschini,Christian Fuchsberger,Stephanie M. Fullerton,Soren Germer,Mark T. Gladwin,Daniel J. Gottlieb,Daniel J. Gottlieb,Xiuqing Guo,Michael E. Hall,Jiang He,Nancy L. Heard-Costa,Susan R. Heckbert,Marguerite R. Irvin,Jill M. Johnsen,Andrew D. Johnson,Robert C. Kaplan,Sharon L.R. Kardia,Tanika N. Kelly,Shannon Kelly,Eimear E. Kenny,Douglas P. Kiel,Robert Klemmer,Barbara A. Konkle,Charles Kooperberg,Anna Köttgen,Anna Köttgen,Leslie A. Lange,Jessica Lasky-Su,Daniel Levy,Daniel Levy,Xihong Lin,Keng-Han Lin,Chunyu Liu,Ruth J. F. Loos,Lori Garman,Robert E. Gerszten,Steven A. Lubitz,Kathryn L. Lunetta,Angel C.Y. Mak,Ani Manichaikul,Alisa K. Manning,Alisa K. Manning,Rasika A. Mathias,David D. McManus,Stephen T. McGarvey,James B. Meigs,Deborah A. Meyers,Julie L. Mikulla,Mollie A. Minear,Braxton D. Mitchell,Braxton D. Mitchell,Sanghamitra Mohanty,May E. Montasser,Courtney G. Montgomery,Alanna C. Morrison,Joanne M. Murabito,Andrea Natale,Pradeep Natarajan,Sarah C. Nelson,Kari E. North,Jeffrey R. O'Connell,Nicholette D. Palmer,Nathan Pankratz,Gina M. Peloso,Patricia A. Peyser,Jacob Pleiness,Wendy S. Post,Bruce M. Psaty,D. C. Rao,Susan Redline,Susan Redline,Alexander P. Reiner,Alexander P. Reiner,Dan M. Roden,Jerome I. Rotter,Ingo Ruczinski,Chloé Sarnowski,Sebastian Schoenherr,David A. Schwartz,Jeong-Sun Seo,Sudha Seshadri,Vivien A. Sheehan,Wayne Huey-Herng Sheu,M. Benjamin Shoemaker,Nicholas L. Smith,Nicholas L. Smith,Nicholas L. Smith,Jennifer A. Smith,Nona Sotoodehnia,Adrienne M. Stilp,Weihong Tang,Kent D. Taylor,Marilyn J. Telen,Timothy A. Thornton,Russell P. Tracy,David Van Den Berg,Ramachandran S. Vasan,Karine A. Viaud-Martinez,Scott I. Vrieze,Daniel E. Weeks,Bruce S. Weir,Scott T. Weiss,Lu-Chen Weng,Cristen J. Willer,Yingze Zhang,Xutong Zhao,Donna K. Arnett,Allison E. Ashley-Koch,Kathleen C. Barnes,Eric Boerwinkle,Eric Boerwinkle,Stacey Gabriel,Richard A. Gibbs,Kenneth Rice,Stephen S. Rich,Edwin K. Silverman,Pankaj Qasba,Weiniu Gan,George J. Papanicolaou,Deborah A. Nickerson,Sharon R. Browning,Michael C. Zody,Sebastian Zöllner,James G. Wilson,L. Adrienne Cupples,Cathy C. Laurie,Cashell E. Jaquish,Ryan D. Hernandez,Timothy D. O’Connor,Gonçalo R. Abecasis +205 more
TL;DR: The Trans-Omics for Precision Medicine (TOPMed) project as discussed by the authors aims to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases.
Posted ContentDOI
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Daniel Taliun,Daniel N. Harris,Michael D. Kessler,Jedidiah Carlson,Jedidiah Carlson,Zachary A. Szpiech,Zachary A. Szpiech,Raul Torres,Sarah A Gagliano Taliun,André Corvelo,Stephanie M. Gogarten,Hyun Min Kang,Achilleas N. Pitsillides,Jonathon LeFaive,Seung-been Lee,Xiaowen Tian,Brian L. Browning,Sayantan Das,Anne-Katrin Emde,Wayne E. Clarke,Douglas Loesch,Amol C. Shetty,Thomas W. Blackwell,Quenna Wong,François Aguet,Christine M. Albert,Alvaro Alonso,Kristin G. Ardlie,Stella Aslibekyan,Paul L. Auer,John Barnard,R. Graham Barr,R. Graham Barr,Lewis C. Becker,Rebecca L. Beer,Emelia J. Benjamin,Lawrence F. Bielak,John Blangero,Michael Boehnke,Donald W. Bowden,Jennifer A. Brody,Esteban G. Burchard,Brian E. Cade,Brian E. Cade,James F. Casella,Brandon Chalazan,Yii-Der Ida Chen,Michael H. Cho,Seung Hoan Choi,Mina K. Chung,Mina K. Chung,Mina K. Chung,Clary B. Clish,Adolfo Correa,Joanne E. Curran,Brian Custer,Dawood Darbar,Michelle Daya,Mariza de Andrade,Dawn L. DeMeo,Susan K. Dutcher,Patrick T. Ellinor,Leslie S. Emery,Diane Fatkin,Diane Fatkin,Diane Fatkin,Lukas Forer,Myriam Fornage,Nora Franceschini,Christian Fuchsberger,Stephanie M. Fullerton,Soren Germer,Mark T. Gladwin,Daniel J. Gottlieb,Daniel J. Gottlieb,Xiuqing Guo,Michael E. Hall,Jiang He,Nancy L. Heard-Costa,Susan R. Heckbert,Marguerite R. Irvin,Jill M. Johnsen,Andrew D. Johnson,Sharon L.R. Kardia,Tanika N. Kelly,Shannon Kelly,Eimear E. Kenny,Douglas P. Kiel,Douglas P. Kiel,Robert Klemmer,Barbara A. Konkle,Charles Kooperberg,Anna Köttgen,Anna Köttgen,Leslie A. Lange,Jessica Lasky-Su,Daniel Levy,Daniel Levy,Xihong Lin,Keng-Han Lin,Chunyu Liu,Ruth J. F. Loos,Lori Garman,Robert E. Gerszten,Steven A. Lubitz,Kathryn L. Lunetta,Angel C.Y. Mak,Ani Manichaikul,Alisa K. Manning,Alisa K. Manning,Rasika A. Mathias,David D. McManus,Stephen T. McGarvey,James B. Meigs,Deborah A. Meyers,Julie L. Mikulla,Mollie A. Minear,Braxton D. Mitchell,Braxton D. Mitchell,Sanghamitra Mohanty,May E. Montasser,Courtney G. Montgomery,Alanna C. Morrison,Joanne M. Murabito,Andrea Natale,Pradeep Natarajan,Sarah C. Nelson,Kari E. North,Jeffrey R. O'Connell,Nicholette D. Palmer,Nathan Pankratz,Gina M. Peloso,Patricia A. Peyser,Wendy S. Post,Bruce M. Psaty,D. C. Rao,Susan Redline,Susan Redline,Alexander P. Reiner,Alexander P. Reiner,Dan M. Roden,Jerome I. Rotter,Ingo Ruczinski,Chloé Sarnowski,Sebastian Schoenherr,Jeong-Sun Seo,Sudha Seshadri,Vivien A. Sheehan,M. Benjamin Shoemaker,Albert V. Smith,Nicholas L. Smith,Jennifer A. Smith,Nona Sotoodehnia,Adrienne M. Stilp,Weihong Tang,Kent D. Taylor,Marilyn J. Telen,Timothy A. Thornton,Russell P. Tracy,David Van Den Berg,Ramachandran S. Vasan,Karine A. Viaud-Martinez,Scott I. Vrieze,Daniel E. Weeks,Bruce S. Weir,Scott T. Weiss,Lu-Chen Weng,Cristen J. Willer,Yingze Zhang,Xutong Zhao,Donna K. Arnett,Allison E. Ashley-Koch,Kathleen C. Barnes,Eric Boerwinkle,Eric Boerwinkle,Stacey Gabriel,Richard A. Gibbs,Kenneth Rice,Stephen S. Rich,Edwin K. Silverman,Pankaj Qasba,Weiniu Gan,George J. Papanicolaou,Deborah A. Nickerson,Sharon R. Browning,Michael C. Zody,Sebastian Zöllner,James G. Wilson,L. Adrienne Cupples,Cathy C. Laurie,Cashell E. Jaquish,Ryan D. Hernandez,Ryan D. Hernandez,Timothy D. O’Connor,Gonçalo R. Abecasis +194 more
TL;DR: The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation as well as resources and early insights from the sequence data.
Journal ArticleDOI
A reference map of the human binary protein interactome
Katja Luck,Dae-Kyum Kim,Luke Lambourne,Kerstin Spirohn,Bridget E. Begg,Wenting Bian,Ruth Brignall,Tiziana M. Cafarelli,Francisco J. Campos-Laborie,Benoit Charloteaux,Dong-Sic Choi,Atina G. Cote,Meaghan Daley,Steven Deimling,Alice Desbuleux,Amélie Dricot,Marinella Gebbia,Madeleine F. Hardy,Nishka Kishore,Jennifer J. Knapp,István Kovács,István Kovács,Irma Lemmens,Irma Lemmens,Miles W. Mee,Joseph C. Mellor,Carl Pollis,Carles Pons,Aaron Richardson,Sadie Schlabach,Bridget Teeking,Anupama Yadav,Mariana Babor,Dawit Balcha,Omer Basha,Christian Bowman-Colin,Suet-Feung Chin,Soon Gang Choi,Claudia Colabella,Georges Coppin,Cassandra D’Amata,David De Ridder,Steffi De Rouck,Steffi De Rouck,Miquel Duran-Frigola,Hanane Ennajdaoui,Florian Goebels,Liana Goehring,Anjali Gopal,Ghazal Haddad,Elodie Hatchi,Mohamed Helmy,Yves Jacob,Yves Jacob,Yoseph Kassa,Serena Landini,Roujia Li,Natascha van Lieshout,Andrew MacWilliams,Dylan Markey,Joseph N. Paulson,Joseph N. Paulson,Sudharshan Rangarajan,John Rasla,Ashyad Rayhan,Thomas Rolland,Adriana San-Miguel,Yun Shen,Dayag Sheykhkarimli,Gloria M. Sheynkman,Eyal Simonovsky,Murat Tasan,Alexander O. Tejeda,Vincent Tropepe,Jean-Claude Twizere,Yang Wang,Robert J. Weatheritt,Jochen Weile,Yu Xia,Yu Xia,Xinping Yang,Esti Yeger-Lotem,Quan Zhong,Patrick Aloy,Gary D. Bader,Javier De Las Rivas,Suzanne Gaudet,Tong Hao,Janusz Rak,Jan Tavernier,Jan Tavernier,David E. Hill,Marc Vidal,Frederick P. Roth,Michael A. Calderwood +94 more
TL;DR: The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.
Journal ArticleDOI
ClinVar: improvements to accessing data.
Melissa J. Landrum,Shanmuga Chitipiralla,Garth Brown,Chao Chen,Baoshan Gu,Jennifer Hart,Douglas W. Hoffman,Wonhee Jang,Kuljeet Kaur,Chunlei Liu,Vitaly Lyoshin,Zenith Maddipatla,Rama Maiti,Joseph Mitchell,Nuala A. O'Leary,George R. Riley,Wenyao Shi,George Zhou,Valerie A. Schneider,Donna Maglott,J. Bradley Holmes,Brandi L. Kattman +21 more
TL;DR: The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file, and ClinVar's search engine has been fine-tuned for improved retrieval of search results.
References
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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
The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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.
Journal ArticleDOI
ClinVar: public archive of relationships among sequence variation and human phenotype
Melissa J. Landrum,Jennifer M. Lee,George R. Riley,Wonhee Jang,Wendy S. Rubinstein,Deanna M. Church,Donna Maglott +6 more
TL;DR: To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations.
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