Literature DB >> 26154004

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Amy S Gargis1, Lisa Kalman1, David P Bick2, Cristina da Silva3, David P Dimmock2, Birgit H Funke4, Sivakumar Gowrisankar4, Madhuri R Hegde3, Shashikant Kulkarni5, Christopher E Mason6, Rakesh Nagarajan7, Karl V Voelkerding8, Elizabeth A Worthey2, Nazneen Aziz9, John Barnes10, Sarah F Bennett11, Himani Bisht12, Deanna M Church13, Zoya Dimitrova14, Shaw R Gargis15, Nabil Hafez16, Tina Hambuch17, Fiona C L Hyland18, Ruth Ann Luna19, Duncan MacCannell20, Tobias Mann21, Megan R McCluskey22, Timothy K McDaniel23, Lilia M Ganova-Raeva14, Heidi L Rehm4, Jeffrey Reid24, David S Campo14, Richard B Resnick16, Perry G Ridge25, Marc L Salit26, Pavel Skums14, Lee-Jun C Wong24, Barbara A Zehnbauer1, Justin M Zook26, Ira M Lubin1.   

Abstract

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Year:  2015        PMID: 26154004      PMCID: PMC6504172          DOI: 10.1038/nbt.3237

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  11 in total

1.  Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Authors:  Justin M Zook; Brad Chapman; Jason Wang; David Mittelman; Oliver Hofmann; Winston Hide; Marc Salit
Journal:  Nat Biotechnol       Date:  2014-02-16       Impact factor: 54.908

2.  Carrier testing for severe childhood recessive diseases by next-generation sequencing.

Authors:  Callum J Bell; Darrell L Dinwiddie; Neil A Miller; Shannon L Hateley; Elena E Ganusova; Joann Mudge; Ray J Langley; Lu Zhang; Clarence C Lee; Faye D Schilkey; Vrunda Sheth; Jimmy E Woodward; Heather E Peckham; Gary P Schroth; Ryan W Kim; Stephen F Kingsmore
Journal:  Sci Transl Med       Date:  2011-01-12       Impact factor: 17.956

3.  A standard variation file format for human genome sequences.

Authors:  Martin G Reese; Barry Moore; Colin Batchelor; Fidel Salas; Fiona Cunningham; Gabor T Marth; Lincoln Stein; Paul Flicek; Mark Yandell; Karen Eilbeck
Journal:  Genome Biol       Date:  2010-08-26       Impact factor: 13.583

4.  Point-counterpoint. Ethics and genomic incidental findings.

Authors:  Amy L McGuire; Steven Joffe; Barbara A Koenig; Barbara B Biesecker; Laurence B McCullough; Jennifer S Blumenthal-Barby; Timothy Caulfield; Sharon F Terry; Robert C Green
Journal:  Science       Date:  2013-05-16       Impact factor: 47.728

5.  Not-so-incidental findings: the ACMG recommendations on the reporting of incidental findings in clinical whole genome and whole exome sequencing.

Authors:  Megan Allyse; Marsha Michie
Journal:  Trends Biotechnol       Date:  2013-05-09       Impact factor: 19.536

6.  Assuring the quality of next-generation sequencing in clinical laboratory practice.

Authors:  Amy S Gargis; Lisa Kalman; Meredith W Berry; David P Bick; David P Dimmock; Tina Hambuch; Fei Lu; Elaine Lyon; Karl V Voelkerding; Barbara A Zehnbauer; Richa Agarwala; Sarah F Bennett; Bin Chen; Ephrem L H Chin; John G Compton; Soma Das; Daniel H Farkas; Matthew J Ferber; Birgit H Funke; Manohar R Furtado; Lilia M Ganova-Raeva; Ute Geigenmüller; Sandra J Gunselman; Madhuri R Hegde; Philip L F Johnson; Andrew Kasarskis; Shashikant Kulkarni; Thomas Lenk; C S Jonathan Liu; Megan Manion; Teri A Manolio; Elaine R Mardis; Jason D Merker; Mangalathu S Rajeevan; Martin G Reese; Heidi L Rehm; Birgitte B Simen; Joanne M Yeakley; Justin M Zook; Ira M Lubin
Journal:  Nat Biotechnol       Date:  2012-11       Impact factor: 54.908

7.  ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Authors:  C Sue Richards; Sherri Bale; Daniel B Bellissimo; Soma Das; Wayne W Grody; Madhuri R Hegde; Elaine Lyon; Brian E Ward
Journal:  Genet Med       Date:  2008-04       Impact factor: 8.822

8.  ACMG recommendations on incidental findings are flawed scientifically and ethically.

Authors:  Neil A Holtzman
Journal:  Genet Med       Date:  2013-09       Impact factor: 8.822

9.  ACMG clinical laboratory standards for next-generation sequencing.

Authors:  Heidi L Rehm; Sherri J Bale; Pinar Bayrak-Toydemir; Jonathan S Berg; Kerry K Brown; Joshua L Deignan; Michael J Friez; Birgit H Funke; Madhuri R Hegde; Elaine Lyon
Journal:  Genet Med       Date:  2013-07-25       Impact factor: 8.822

10.  Identification of genetic variants using bar-coded multiplexed sequencing.

Authors:  David W Craig; John V Pearson; Szabolcs Szelinger; Aswin Sekar; Margot Redman; Jason J Corneveaux; Traci L Pawlowski; Trisha Laub; Gary Nunn; Dietrich A Stephan; Nils Homer; Matthew J Huentelman
Journal:  Nat Methods       Date:  2008-09-14       Impact factor: 28.547

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  56 in total

1.  Omics-driven startups challenge healthcare model.

Authors:  Cormac Sheridan
Journal:  Nat Biotechnol       Date:  2015-09       Impact factor: 54.908

Review 2.  Genomics of Immune Diseases and New Therapies.

Authors:  Michael Lenardo; Bernice Lo; Carrie L Lucas
Journal:  Annu Rev Immunol       Date:  2015-12-23       Impact factor: 28.527

3.  Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

Authors:  Erin H Graf; Keith E Simmon; Keith D Tardif; Weston Hymas; Steven Flygare; Karen Eilbeck; Mark Yandell; Robert Schlaberg
Journal:  J Clin Microbiol       Date:  2016-01-27       Impact factor: 5.948

4.  Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

Authors:  Ira M Lubin; Nazneen Aziz; Lawrence J Babb; Dennis Ballinger; Himani Bisht; Deanna M Church; Shaun Cordes; Karen Eilbeck; Fiona Hyland; Lisa Kalman; Melissa Landrum; Edward R Lockhart; Donna Maglott; Gabor Marth; John D Pfeifer; Heidi L Rehm; Somak Roy; Zivana Tezak; Rebecca Truty; Mollie Ullman-Cullere; Karl V Voelkerding; Elizabeth A Worthey; Alexander W Zaranek; Justin M Zook
Journal:  J Mol Diagn       Date:  2017-03-18       Impact factor: 5.568

Review 5.  Reference standards for next-generation sequencing.

Authors:  Simon A Hardwick; Ira W Deveson; Tim R Mercer
Journal:  Nat Rev Genet       Date:  2017-06-19       Impact factor: 53.242

Review 6.  Preparing pathology for precision medicine: challenges and opportunities.

Authors:  Karen L Kaul
Journal:  Virchows Arch       Date:  2017-05-16       Impact factor: 4.064

Review 7.  Integrating Advanced Molecular Technologies into Public Health.

Authors:  Marta Gwinn; Duncan R MacCannell; Rima F Khabbaz
Journal:  J Clin Microbiol       Date:  2016-12-28       Impact factor: 5.948

Review 8.  Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.

Authors:  Lawrence J Jennings; Maria E Arcila; Christopher Corless; Suzanne Kamel-Reid; Ira M Lubin; John Pfeifer; Robyn L Temple-Smolkin; Karl V Voelkerding; Marina N Nikiforova
Journal:  J Mol Diagn       Date:  2017-03-21       Impact factor: 5.568

9.  Defining KIR and HLA Class I Genotypes at Highest Resolution via High-Throughput Sequencing.

Authors:  Paul J Norman; Jill A Hollenbach; Neda Nemat-Gorgani; Wesley M Marin; Steven J Norberg; Elham Ashouri; Jyothi Jayaraman; Emily E Wroblewski; John Trowsdale; Raja Rajalingam; Jorge R Oksenberg; Jacques Chiaroni; Lisbeth A Guethlein; James A Traherne; Mostafa Ronaghi; Peter Parham
Journal:  Am J Hum Genet       Date:  2016-08-04       Impact factor: 11.025

Review 10.  Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.

Authors:  Aquillah M Kanzi; James Emmanuel San; Benjamin Chimukangara; Eduan Wilkinson; Maryam Fish; Veron Ramsuran; Tulio de Oliveira
Journal:  Front Genet       Date:  2020-10-23       Impact factor: 4.599

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