A window into clinical next-generation sequencing-based oncology testing practices

Rakesh Nagarajan*, Angela N. Bartley, Julia A. Bridge, Lawrence J Jennings, Suzanne Kamel-Reid, Annette Kim, Alexander J. Lazar, Neal I. Lindeman, Joel Moncur, Alex J. Rai, Mark J. Routbort, Patricia Vasalos, Jason D. Merker

*Corresponding author for this work

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Context: Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective: To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. Design: College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. Results: These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions: This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

Original languageEnglish (US)
Pages (from-to)1679-1685
Number of pages7
JournalArchives of Pathology and Laboratory Medicine
Volume141
Issue number12
DOIs
StatePublished - Dec 1 2017

Fingerprint

Precision Medicine
Neoplasms
Nucleotides
Surveys and Questionnaires
Pathologists

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Medical Laboratory Technology

Cite this

Nagarajan, Rakesh ; Bartley, Angela N. ; Bridge, Julia A. ; Jennings, Lawrence J ; Kamel-Reid, Suzanne ; Kim, Annette ; Lazar, Alexander J. ; Lindeman, Neal I. ; Moncur, Joel ; Rai, Alex J. ; Routbort, Mark J. ; Vasalos, Patricia ; Merker, Jason D. / A window into clinical next-generation sequencing-based oncology testing practices. In: Archives of Pathology and Laboratory Medicine. 2017 ; Vol. 141, No. 12. pp. 1679-1685.
@article{f07f2eada04849f0b23548415fe06ade,
title = "A window into clinical next-generation sequencing-based oncology testing practices",
abstract = "Context: Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective: To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. Design: College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. Results: These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions: This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.",
author = "Rakesh Nagarajan and Bartley, {Angela N.} and Bridge, {Julia A.} and Jennings, {Lawrence J} and Suzanne Kamel-Reid and Annette Kim and Lazar, {Alexander J.} and Lindeman, {Neal I.} and Joel Moncur and Rai, {Alex J.} and Routbort, {Mark J.} and Patricia Vasalos and Merker, {Jason D.}",
year = "2017",
month = "12",
day = "1",
doi = "10.5858/arpa.2016-0542-CP",
language = "English (US)",
volume = "141",
pages = "1679--1685",
journal = "Archives of Pathology and Laboratory Medicine",
issn = "0003-9985",
publisher = "College of American Pathologists",
number = "12",

}

Nagarajan, R, Bartley, AN, Bridge, JA, Jennings, LJ, Kamel-Reid, S, Kim, A, Lazar, AJ, Lindeman, NI, Moncur, J, Rai, AJ, Routbort, MJ, Vasalos, P & Merker, JD 2017, 'A window into clinical next-generation sequencing-based oncology testing practices', Archives of Pathology and Laboratory Medicine, vol. 141, no. 12, pp. 1679-1685. https://doi.org/10.5858/arpa.2016-0542-CP

A window into clinical next-generation sequencing-based oncology testing practices. / Nagarajan, Rakesh; Bartley, Angela N.; Bridge, Julia A.; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J.; Lindeman, Neal I.; Moncur, Joel; Rai, Alex J.; Routbort, Mark J.; Vasalos, Patricia; Merker, Jason D.

In: Archives of Pathology and Laboratory Medicine, Vol. 141, No. 12, 01.12.2017, p. 1679-1685.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A window into clinical next-generation sequencing-based oncology testing practices

AU - Nagarajan, Rakesh

AU - Bartley, Angela N.

AU - Bridge, Julia A.

AU - Jennings, Lawrence J

AU - Kamel-Reid, Suzanne

AU - Kim, Annette

AU - Lazar, Alexander J.

AU - Lindeman, Neal I.

AU - Moncur, Joel

AU - Rai, Alex J.

AU - Routbort, Mark J.

AU - Vasalos, Patricia

AU - Merker, Jason D.

PY - 2017/12/1

Y1 - 2017/12/1

N2 - Context: Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective: To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. Design: College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. Results: These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions: This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

AB - Context: Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective: To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. Design: College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. Results: These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions: This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

UR - http://www.scopus.com/inward/record.url?scp=85037033412&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85037033412&partnerID=8YFLogxK

U2 - 10.5858/arpa.2016-0542-CP

DO - 10.5858/arpa.2016-0542-CP

M3 - Article

C2 - 29028368

AN - SCOPUS:85037033412

VL - 141

SP - 1679

EP - 1685

JO - Archives of Pathology and Laboratory Medicine

JF - Archives of Pathology and Laboratory Medicine

SN - 0003-9985

IS - 12

ER -