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

Affiliations

¹ Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
² Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
³ Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.
⁴ 1] Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA. [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
⁵ 1] Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA. [3] Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁶ Department of Physiology and Biophysics, Cornell University, New York, New York, USA.
⁷ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁸ 1] Department of Pathology, University of Utah, Salt Lake City, Utah, USA. [2] Institute for Clinical and Experimental Pathology, Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, Utah, USA.
⁹ College of American Pathologists, Northfield, Illinois, USA.
¹⁰ National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹¹ Division of Laboratory Services, Centers for Medicare and Medicaid Services, Baltimore, Maryland, USA.
¹² Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA.
¹³ National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA.
¹⁴ Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹⁵ Division of Select Agents and Toxins, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹⁶ GenomeQuest, Westborough, Massachusetts, USA.
¹⁷ Clinical Services, Illumina, San Diego, California, USA.
¹⁸ Thermo Fisher Scientific, South San Francisco, California, USA.
¹⁹ Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas, USA.
²⁰ National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia USA.
²¹ Illumina, San Diego, California, USA.
²² SoftGenetics, State College, Pennsylvania, USA.
²³ Oncology, Illumina, San Diego, California, USA.
²⁴ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
²⁵ Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
²⁶ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.

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

Good laboratory practice for clinical next-generation sequencing informatics pipelines

Amy S Gargis et al. Nat Biotechnol. 2015 Jul.

. 2015 Jul;33(7):689-93.

doi: 10.1038/nbt.3237.

Authors

Affiliations

¹ Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
² Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
³ Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.
⁴ 1] Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA. [2] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.
⁵ 1] Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. [2] Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA. [3] Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁶ Department of Physiology and Biophysics, Cornell University, New York, New York, USA.
⁷ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.
⁸ 1] Department of Pathology, University of Utah, Salt Lake City, Utah, USA. [2] Institute for Clinical and Experimental Pathology, Associated Regional and University Pathologists (ARUP) Laboratories, Salt Lake City, Utah, USA.
⁹ College of American Pathologists, Northfield, Illinois, USA.
¹⁰ National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹¹ Division of Laboratory Services, Centers for Medicare and Medicaid Services, Baltimore, Maryland, USA.
¹² Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland, USA.
¹³ National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA.
¹⁴ Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹⁵ Division of Select Agents and Toxins, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
¹⁶ GenomeQuest, Westborough, Massachusetts, USA.
¹⁷ Clinical Services, Illumina, San Diego, California, USA.
¹⁸ Thermo Fisher Scientific, South San Francisco, California, USA.
¹⁹ Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology &Immunology, Baylor College of Medicine, Houston, Texas, USA.
²⁰ National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia USA.
²¹ Illumina, San Diego, California, USA.
²² SoftGenetics, State College, Pennsylvania, USA.
²³ Oncology, Illumina, San Diego, California, USA.
²⁴ Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
²⁵ Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
²⁶ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, USA.

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

No abstract available

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Figures

**Figure 1**
Model for tertiary analysis of sequence variants. The purpose of tertiary analysis is to identify variants to be reported to the physician for medical decision making. The variants identified during secondary analysis are filtered and prioritized, with consideration of their gene associations. ESP, Exome Sequencing Project; WES, whole-exome sequencing; WGS, whole-genome sequencing.

See this image and copyright information in PMC

References

1. Gargis AS, et al. Nat. Biotechnol. 2012;30:1033–1036. - PMC - PubMed
1. Rehm HL, et al. Genet. Med. 2013;15:733–747. - PMC - PubMed
1. Craig DW, et al. Nat. Methods. 2008;5:887–893. - PMC - PubMed
1. Bell CJ, et al. Sci. Transl. Med. 2011;3:65ra64. - PMC - PubMed
1. Zook JM, et al. Nat. Biotechnol. 2014;32:246–251. - PubMed

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Good laboratory practice for clinical next-generation sequencing informatics pipelines

Affiliations

Good laboratory practice for clinical next-generation sequencing informatics pipelines

Authors

Affiliations

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources