TY - JOUR
T1 - Assembling and validating bioinformatic pipelines for next-generation sequencing clinical assays
AU - SoRelle, Jeffrey A.
AU - Wachsmann, Megan
AU - Cantarel, Brandi L.
N1 - Publisher Copyright:
© 2020 College of American Pathologists. All rights reserved.
PY - 2020/9
Y1 - 2020/9
N2 - Context.-Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and genetic annotation databases are important for determining genetic alterations associated with disease. The analysis methods are often tuned to the assay to maximize accuracy. Once a pipeline has been developed, it must be validated to determine accuracy and reproducibility for samples similar to real-world cases. In silico proficiency testing or institutional data exchange will ensure consistency among clinical laboratories. Objective.-To provide molecular pathologists a step-by-step guide to bioinformatics analysis and validation design in order to navigate the regulatory and validation standards of implementing a bioinformatic pipeline as a part of a new clinical NGS assay. Data Sources.-This guide uses published studies on genomic analysis, bioinformatics methods, and methods comparison studies to inform the reader on what resources, including open source software tools and databases, are available for genetic variant detection and interpretation. Conclusions.-This review covers 4 key concepts: (1) bioinformatic analysis design for detecting genetic variation, (2) the resources for assessing genetic effects, (3) analysis validation assessment experiments and data sets, including a diverse set of samples to mimic real-world challenges that assess accuracy and reproducibility, and (4) if concordance between clinical laboratories will be improved by proficiency testing designed to test bioinformatic pipelines.
AB - Context.-Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and genetic annotation databases are important for determining genetic alterations associated with disease. The analysis methods are often tuned to the assay to maximize accuracy. Once a pipeline has been developed, it must be validated to determine accuracy and reproducibility for samples similar to real-world cases. In silico proficiency testing or institutional data exchange will ensure consistency among clinical laboratories. Objective.-To provide molecular pathologists a step-by-step guide to bioinformatics analysis and validation design in order to navigate the regulatory and validation standards of implementing a bioinformatic pipeline as a part of a new clinical NGS assay. Data Sources.-This guide uses published studies on genomic analysis, bioinformatics methods, and methods comparison studies to inform the reader on what resources, including open source software tools and databases, are available for genetic variant detection and interpretation. Conclusions.-This review covers 4 key concepts: (1) bioinformatic analysis design for detecting genetic variation, (2) the resources for assessing genetic effects, (3) analysis validation assessment experiments and data sets, including a diverse set of samples to mimic real-world challenges that assess accuracy and reproducibility, and (4) if concordance between clinical laboratories will be improved by proficiency testing designed to test bioinformatic pipelines.
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U2 - 10.5858/arpa.2019-0476-RA
DO - 10.5858/arpa.2019-0476-RA
M3 - Review article
C2 - 32045276
AN - SCOPUS:85087502820
SN - 0003-9985
VL - 144
SP - 1118
EP - 1130
JO - Archives of Pathology and Laboratory Medicine
JF - Archives of Pathology and Laboratory Medicine
IS - 9
ER -