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

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

doi:10.1038/nbt.2403

Cited by 431 publications

(422 citation statements)

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“…Extracted cfDNA can be used to generate a collection of DNA fragments, that is generally termed as gene library (7,10). In particular, when all of the known coding exons in a genome are captured an 'exome sequencing' is obtained; this approach is usually carried out in research practice (7,10).…”

Section: Library Preparation and Sequencingmentioning

confidence: 99%

“…In particular, when all of the known coding exons in a genome are captured an 'exome sequencing' is obtained; this approach is usually carried out in research practice (7,10). Conversely, a target library composed by specific clinical relevant gene regions is obtained when narrow next generation panels are implemented (8,11).…”

Section: Library Preparation and Sequencingmentioning

confidence: 99%

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Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients

Malapelle¹,

Pisapia²,

Rocco³

et al. 2016

Transl. Lung Cancer Res.

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The advent of genomic based personalized medicine has led to multiple advances in the molecular characterization of many tumor types, such as non-small cell lung cancer (NSCLC). NSCLC is diagnosed in most cases on small tissue samples that may be not always sufficient for EGFR mutational assessment to select patients for first and second generations' tyrosine kinase inhibitors (TKIs) therapy. In patients without tissue availability at presentation, the analysis of cell free DNA (cfDNA) derived from liquid biopsy samples, in particular from plasma, represent an established alternative to provide EGFR mutational testing for treatment decision making. In addition, a new paradigm for TKIs resistance management was recently approved by Food and Drug Administration, supporting the liquid biopsy based genotyping prior to tissue based genotyping for the detection of T790M mutation to select patients for third generation TKIs. In these settings, real time PCR (RT-PCR) and digital PCR 'targeted' methods, which detect known mutations by specific probes, have extensively been adopted. Taking into account the restricted reference range and the limited multiplexing power of these targeted methods, the performance of liquid biopsy analyses may be further improved by next generation sequencing (NGS). While most tissue based NGS genotyping is well established, liquid biopsy NGS application is challenging, requiring a careful validation of the whole process, from blood collection to variant calling. Here we review this evolving field, highlighting those methodological points that are crucial to accurately select NSCLC patients for TKIs treatment administration by NGS on cfDNA.

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Section: Library Preparation and Sequencingmentioning

confidence: 99%

Section: Library Preparation and Sequencingmentioning

confidence: 99%

Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients

Malapelle¹,

Pisapia²,

Rocco³

et al. 2016

Transl. Lung Cancer Res.

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“…Different sample collection and processing methods, sequencing chemistries, instruments, protocols, and data analysis methods are known to affect NGS assay results. 8,9 In addition, regulatory compliance, such as the Code of Federal Regulations title 21 part 812 for investigational device exemption (Code of Federal Regulations, http://www.accessdata.fda.gov/scripts/cdrh/ cfdocs/cfcfr/CFRsearch.cfm?CFRPartZ812, last accessed October 13, 2016) for the FDA must be achieved for use of assays in clinical trials.…”

mentioning

confidence: 99%

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial

Lih

Harrington

Sims

et al. 2017

The Journal of Molecular Diagnostics

124

101

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The National Cancer InstituteeMolecular Analysis for Therapy Choice (NCI-MATCH) trial is a national signal-finding precision medicine study that relies on genomic assays to screen and enroll patients with relapsed or refractory cancer after standard treatments. We report the analytical validation processes for the next-generation sequencing (NGS) assay that was tailored for regulatory compliant use in the trial. The Oncomine Cancer Panel assay and the Personal Genome Machine were used in four networked laboratories accredited for the Clinical Laboratory Improvement Amendments. Using formalin-fixed paraffin-embedded clinical specimens and cell lines, we found that the assay achieved overall sensitivity of 96.98% for 265 known mutations and 99.99% specificity. High reproducibility in detecting all reportable variants was observed, with a 99.99% mean interoperator pairwise concordance across the four laboratories. The limit of detection for each variant type was 2.8% for single-nucleotide variants, 10.5% for insertion/deletions, 6.8% for large insertion/deletions (gap !4 bp), and four copies for gene amplification. The assay system from biopsy collection through reporting was tested and found to be fully fit for purpose. Our results indicate that the NCI-MATCH NGS assay met the criteria for the intended clinical use and that high reproducibility of a complex NGS assay is achievable across multiple clinical laboratories. Our validation approaches can serve as a template for development and validation of other NGS assays for precision medicine. (J Mol Diagn 2017, 19: 313e327; http://dx

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“…Samples were selected for end-to-end process validation with additional samples being run by NGS alone to satisfy NGS assay specific validation requirements [9][10][11][12].…”

Section: Ngs Assay Validationmentioning

confidence: 99%

Clinical Validation of a Next Generation Sequencing Panel Test for Hereditary Colorectal Cancer

MJ¹,

LM²

2016

J Med Diagn Meth

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Background: Application of next generation sequencing (NGS) is revolutionizing the clinical molecular diagnostics industry. As this occurs, guidelines for validating NGS processes are limited, non-specific, and rapidly evolving. NGS validation projects are complex and expensive, so the validation experiments must be carefully considered, while being certain all current and evolving regulatory requirements are met.

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

Cited by 431 publications

References 1 publication

Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients

Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial

Clinical Validation of a Next Generation Sequencing Panel Test for Hereditary Colorectal Cancer

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