Format

Send to

Choose Destination

See 1 citation:

J Mol Diagn. 2018 Jan;20(1):4-27. doi: 10.1016/j.jmoldx.2017.11.003. Epub 2017 Nov 21.

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

Author information

1
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address: roys@upmc.edu.
2
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; PathGroup, Nashville, Tennessee.
3
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Division of Molecular and Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
4
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Genetics and Genomics Center, Icahn School of Medicine, Mount Sinai Hospital, New York, New York; Sema4 Laboratory, Branford, Connecticut.
5
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
6
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Invitae, San Francisco, California.
7
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Color Genomics, Inc., Burlingame, California.
8
The Association for Molecular Pathology, Bethesda, Maryland.
9
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; ARUP Laboratories, Salt Lake City, Utah.
10
Next Generation Sequencing Bioinformatics Pipeline Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia.

Abstract

Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. To address this unmet need, the Association of Molecular Pathology, with organizational representation from the College of American Pathologists and the American Medical Informatics Association, has developed a set of 17 best practice consensus recommendations for the validation of clinical NGS bioinformatics pipelines. Recommendations include practical guidance for laboratories regarding NGS bioinformatics pipeline design, development, and operation, with additional emphasis on the role of a properly trained and qualified molecular professional to achieve optimal NGS testing quality.

PMID:
29154853
DOI:
10.1016/j.jmoldx.2017.11.003
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center