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Clinical testing of BRCA1 and BRCA2: A worldwide snapshot of technological practices

Clinical testing of BRCA1 and BRCA2: A worldwide snapshot of technological practices
Clinical testing of BRCA1 and BRCA2: A worldwide snapshot of technological practices

Clinical testing of BRCA1 and BRCA2 began over 20 years ago. With the expiration and overturning of the BRCA patents, limitations on which laboratories could offer commercial testing were lifted. These legal changes occurred approximately the same time as the widespread adoption of massively parallel sequencing (MPS) technologies. Little is known about how these changes impacted laboratory practices for detecting genetic alterations in hereditary breast and ovarian cancer genes. Therefore, we sought to examine current laboratory genetic testing practices for BRCA1/BRCA2. We employed an online survey of 65 questions covering four areas: laboratory characteristics, details on technological methods, variant classification, and client-support information. Eight United States (US) laboratories and 78 non-US laboratories completed the survey. Most laboratories (93%; 80/86) used MPS platforms to identify variants. Laboratories differed widely on: (1) technologies used for large rearrangement detection; (2) criteria for minimum read depths; (3) non-coding regions sequenced; (4) variant classification criteria and approaches; (5) testing volume ranging from 2 to 2.5 × 105 tests annually; and (6) deposition of variants into public databases. These data may be useful for national and international agencies to set recommendations for quality standards for BRCA1/BRCA2 clinical testing. These standards could also be applied to testing of other disease genes.

Toland, Amanda Ewart
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Forman, Andrea
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Couch, Fergus J.
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Culver, Julie O.
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Eccles, Diana M.
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Foulkes, William D.
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Hogervorst, Frans B.L.
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Houdayer, Claude
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Levy-Lahad, Ephrat
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Monteiro, Alvaro N.
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Neuhausen, Susan L.
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Plon, Sharon E.
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Sharan, Shyam K.
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Spurdle, Amanda B.
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Szabo, Csilla
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Brody, Lawrence C.
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Toland, Amanda Ewart
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Forman, Andrea
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Couch, Fergus J.
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Culver, Julie O.
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Eccles, Diana M.
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Foulkes, William D.
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Hogervorst, Frans B.L.
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Houdayer, Claude
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Levy-Lahad, Ephrat
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Monteiro, Alvaro N.
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Neuhausen, Susan L.
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Plon, Sharon E.
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Sharan, Shyam K.
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Spurdle, Amanda B.
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Szabo, Csilla
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Brody, Lawrence C.
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Toland, Amanda Ewart, Forman, Andrea, Couch, Fergus J., Culver, Julie O., Eccles, Diana M., Foulkes, William D., Hogervorst, Frans B.L., Houdayer, Claude, Levy-Lahad, Ephrat, Monteiro, Alvaro N., Neuhausen, Susan L., Plon, Sharon E., Sharan, Shyam K., Spurdle, Amanda B., Szabo, Csilla and Brody, Lawrence C. (2018) Clinical testing of BRCA1 and BRCA2: A worldwide snapshot of technological practices. npj Genomic Medicine, 3 (1). (doi:10.1038/s41525-018-0046-7).

Record type: Article

Abstract

Clinical testing of BRCA1 and BRCA2 began over 20 years ago. With the expiration and overturning of the BRCA patents, limitations on which laboratories could offer commercial testing were lifted. These legal changes occurred approximately the same time as the widespread adoption of massively parallel sequencing (MPS) technologies. Little is known about how these changes impacted laboratory practices for detecting genetic alterations in hereditary breast and ovarian cancer genes. Therefore, we sought to examine current laboratory genetic testing practices for BRCA1/BRCA2. We employed an online survey of 65 questions covering four areas: laboratory characteristics, details on technological methods, variant classification, and client-support information. Eight United States (US) laboratories and 78 non-US laboratories completed the survey. Most laboratories (93%; 80/86) used MPS platforms to identify variants. Laboratories differed widely on: (1) technologies used for large rearrangement detection; (2) criteria for minimum read depths; (3) non-coding regions sequenced; (4) variant classification criteria and approaches; (5) testing volume ranging from 2 to 2.5 × 105 tests annually; and (6) deposition of variants into public databases. These data may be useful for national and international agencies to set recommendations for quality standards for BRCA1/BRCA2 clinical testing. These standards could also be applied to testing of other disease genes.

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Accepted/In Press date: 16 January 2018
e-pub ahead of print date: 15 February 2018
Published date: 1 December 2018

Identifiers

Local EPrints ID: 418390
URI: https://eprints.soton.ac.uk/id/eprint/418390
PURE UUID: 756bf0fd-6925-49c9-8934-69c9f0582f9c

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Date deposited: 06 Mar 2018 17:30
Last modified: 13 Mar 2019 18:48

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Contributors

Author: Amanda Ewart Toland
Author: Andrea Forman
Author: Fergus J. Couch
Author: Julie O. Culver
Author: Diana M. Eccles
Author: William D. Foulkes
Author: Frans B.L. Hogervorst
Author: Claude Houdayer
Author: Ephrat Levy-Lahad
Author: Alvaro N. Monteiro
Author: Susan L. Neuhausen
Author: Sharon E. Plon
Author: Shyam K. Sharan
Author: Amanda B. Spurdle
Author: Csilla Szabo
Author: Lawrence C. Brody

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