Interpreting epidemiological research

Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1

C. Eng, L. C. Brody, T. M U Wagner, P. Devilee, Jan Vijg, C. Szabo, S. V. Tavtigian, K. L. Nathanson, E. Ostrander, T. S. Frank, Ake Borg, Lawrence C. Brody, Fergus Couch, Peter Devilee, Douglas F. Easton, Charis Eng, Thomas S. Frank, David F. Goldgar, Katherine A. Nathanson, Susan Neuhausen & 16 others Elaine Ostrander, Csilla Szabo, Sean V. Tavtigian, Teresa M U Wagner, Anne Lise Borresen-Dale, Graham Casey, Stephen Friend, Andrew Futreal, Simon A. Gayther, Patricia Murphy, Kelly A. Owens, Mark Rabin, Elizabeth Schubert, Donna F. Shattuck, Barbara L. Weber, Roger Wiseman

Research output: Contribution to journalArticle

128 Citations (Scopus)

Abstract

While sequence analysis is considered by many to be the most sensitive method of detecting unknown mutations in large genes such as BRCA1, most published estimates of the prevalence of mutations in this gene have been derived from studies that have used other methods of gene analysis. In order to determine the relative sensitivity of techniques that are widely used in research on BRCA1, a set of blinded samples containing 58 distinct mutations were analysed by four separate laboratories. Each used one of the following methods: single strand conformational polymorphism analysis (SSCP), conformation sensitive gel electrophoresis (CSGE), two dimensional gene scanning (TDGS), and denaturing high performance liquid chromatography (DHPLC). Only the laboratory using DHPLC correctly identified each of the mutations. The laboratory using TDGS correctly identified 91% of the mutations but produced three apparent false positive results. The laboratories using SSCP and CSGE detected abnormal migration for 72% and 76% of the mutations, respectively, but subsequently confirmed and reported only 65% and 60% of mutations, respectively. False negatives therefore resulted not only from failure of the techniques to distinguish wild type from mutant, but also from failure to confirm the mutation by sequence analysis as well as from human errors leading to misreporting of results. These findings characterise sources of error in commonly used methods of mutation detection that should be addressed by laboratories using these methods. Based upon sources of error identified in this comparison, it is likely that mutations in BRCA1 and BRCA2 are more prevalent than some studies have previously reported. The findings of this comparison provide a basis for interpreting studies of mutations in susceptibility genes across many inherited cancer syndromes.

Original languageEnglish (US)
Pages (from-to)824-833
Number of pages10
JournalJournal of Medical Genetics
Volume38
Issue number12
StatePublished - 2001
Externally publishedYes

Fingerprint

Mutation
Research
Genes
Sequence Analysis
Research Design
High Pressure Liquid Chromatography
Electrophoresis, Gel, Two-Dimensional
Electrophoresis
Gels
Neoplasms

Keywords

  • BRCA1
  • Cancer genetics
  • Mutation detection

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Interpreting epidemiological research : Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1. / Eng, C.; Brody, L. C.; Wagner, T. M U; Devilee, P.; Vijg, Jan; Szabo, C.; Tavtigian, S. V.; Nathanson, K. L.; Ostrander, E.; Frank, T. S.; Borg, Ake; Brody, Lawrence C.; Couch, Fergus; Devilee, Peter; Easton, Douglas F.; Eng, Charis; Frank, Thomas S.; Goldgar, David F.; Nathanson, Katherine A.; Neuhausen, Susan; Ostrander, Elaine; Szabo, Csilla; Tavtigian, Sean V.; Wagner, Teresa M U; Borresen-Dale, Anne Lise; Casey, Graham; Friend, Stephen; Futreal, Andrew; Gayther, Simon A.; Murphy, Patricia; Owens, Kelly A.; Rabin, Mark; Schubert, Elizabeth; Shattuck, Donna F.; Weber, Barbara L.; Wiseman, Roger.

In: Journal of Medical Genetics, Vol. 38, No. 12, 2001, p. 824-833.

Research output: Contribution to journalArticle

Eng, C, Brody, LC, Wagner, TMU, Devilee, P, Vijg, J, Szabo, C, Tavtigian, SV, Nathanson, KL, Ostrander, E, Frank, TS, Borg, A, Brody, LC, Couch, F, Devilee, P, Easton, DF, Eng, C, Frank, TS, Goldgar, DF, Nathanson, KA, Neuhausen, S, Ostrander, E, Szabo, C, Tavtigian, SV, Wagner, TMU, Borresen-Dale, AL, Casey, G, Friend, S, Futreal, A, Gayther, SA, Murphy, P, Owens, KA, Rabin, M, Schubert, E, Shattuck, DF, Weber, BL & Wiseman, R 2001, 'Interpreting epidemiological research: Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1', Journal of Medical Genetics, vol. 38, no. 12, pp. 824-833.
Eng, C. ; Brody, L. C. ; Wagner, T. M U ; Devilee, P. ; Vijg, Jan ; Szabo, C. ; Tavtigian, S. V. ; Nathanson, K. L. ; Ostrander, E. ; Frank, T. S. ; Borg, Ake ; Brody, Lawrence C. ; Couch, Fergus ; Devilee, Peter ; Easton, Douglas F. ; Eng, Charis ; Frank, Thomas S. ; Goldgar, David F. ; Nathanson, Katherine A. ; Neuhausen, Susan ; Ostrander, Elaine ; Szabo, Csilla ; Tavtigian, Sean V. ; Wagner, Teresa M U ; Borresen-Dale, Anne Lise ; Casey, Graham ; Friend, Stephen ; Futreal, Andrew ; Gayther, Simon A. ; Murphy, Patricia ; Owens, Kelly A. ; Rabin, Mark ; Schubert, Elizabeth ; Shattuck, Donna F. ; Weber, Barbara L. ; Wiseman, Roger. / Interpreting epidemiological research : Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1. In: Journal of Medical Genetics. 2001 ; Vol. 38, No. 12. pp. 824-833.
@article{16d8faefbe014b158d094c68418d3fa9,
title = "Interpreting epidemiological research: Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1",
abstract = "While sequence analysis is considered by many to be the most sensitive method of detecting unknown mutations in large genes such as BRCA1, most published estimates of the prevalence of mutations in this gene have been derived from studies that have used other methods of gene analysis. In order to determine the relative sensitivity of techniques that are widely used in research on BRCA1, a set of blinded samples containing 58 distinct mutations were analysed by four separate laboratories. Each used one of the following methods: single strand conformational polymorphism analysis (SSCP), conformation sensitive gel electrophoresis (CSGE), two dimensional gene scanning (TDGS), and denaturing high performance liquid chromatography (DHPLC). Only the laboratory using DHPLC correctly identified each of the mutations. The laboratory using TDGS correctly identified 91{\%} of the mutations but produced three apparent false positive results. The laboratories using SSCP and CSGE detected abnormal migration for 72{\%} and 76{\%} of the mutations, respectively, but subsequently confirmed and reported only 65{\%} and 60{\%} of mutations, respectively. False negatives therefore resulted not only from failure of the techniques to distinguish wild type from mutant, but also from failure to confirm the mutation by sequence analysis as well as from human errors leading to misreporting of results. These findings characterise sources of error in commonly used methods of mutation detection that should be addressed by laboratories using these methods. Based upon sources of error identified in this comparison, it is likely that mutations in BRCA1 and BRCA2 are more prevalent than some studies have previously reported. The findings of this comparison provide a basis for interpreting studies of mutations in susceptibility genes across many inherited cancer syndromes.",
keywords = "BRCA1, Cancer genetics, Mutation detection",
author = "C. Eng and Brody, {L. C.} and Wagner, {T. M U} and P. Devilee and Jan Vijg and C. Szabo and Tavtigian, {S. V.} and Nathanson, {K. L.} and E. Ostrander and Frank, {T. S.} and Ake Borg and Brody, {Lawrence C.} and Fergus Couch and Peter Devilee and Easton, {Douglas F.} and Charis Eng and Frank, {Thomas S.} and Goldgar, {David F.} and Nathanson, {Katherine A.} and Susan Neuhausen and Elaine Ostrander and Csilla Szabo and Tavtigian, {Sean V.} and Wagner, {Teresa M U} and Borresen-Dale, {Anne Lise} and Graham Casey and Stephen Friend and Andrew Futreal and Gayther, {Simon A.} and Patricia Murphy and Owens, {Kelly A.} and Mark Rabin and Elizabeth Schubert and Shattuck, {Donna F.} and Weber, {Barbara L.} and Roger Wiseman",
year = "2001",
language = "English (US)",
volume = "38",
pages = "824--833",
journal = "Journal of Medical Genetics",
issn = "0022-2593",
publisher = "BMJ Publishing Group",
number = "12",

}

TY - JOUR

T1 - Interpreting epidemiological research

T2 - Blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1

AU - Eng, C.

AU - Brody, L. C.

AU - Wagner, T. M U

AU - Devilee, P.

AU - Vijg, Jan

AU - Szabo, C.

AU - Tavtigian, S. V.

AU - Nathanson, K. L.

AU - Ostrander, E.

AU - Frank, T. S.

AU - Borg, Ake

AU - Brody, Lawrence C.

AU - Couch, Fergus

AU - Devilee, Peter

AU - Easton, Douglas F.

AU - Eng, Charis

AU - Frank, Thomas S.

AU - Goldgar, David F.

AU - Nathanson, Katherine A.

AU - Neuhausen, Susan

AU - Ostrander, Elaine

AU - Szabo, Csilla

AU - Tavtigian, Sean V.

AU - Wagner, Teresa M U

AU - Borresen-Dale, Anne Lise

AU - Casey, Graham

AU - Friend, Stephen

AU - Futreal, Andrew

AU - Gayther, Simon A.

AU - Murphy, Patricia

AU - Owens, Kelly A.

AU - Rabin, Mark

AU - Schubert, Elizabeth

AU - Shattuck, Donna F.

AU - Weber, Barbara L.

AU - Wiseman, Roger

PY - 2001

Y1 - 2001

N2 - While sequence analysis is considered by many to be the most sensitive method of detecting unknown mutations in large genes such as BRCA1, most published estimates of the prevalence of mutations in this gene have been derived from studies that have used other methods of gene analysis. In order to determine the relative sensitivity of techniques that are widely used in research on BRCA1, a set of blinded samples containing 58 distinct mutations were analysed by four separate laboratories. Each used one of the following methods: single strand conformational polymorphism analysis (SSCP), conformation sensitive gel electrophoresis (CSGE), two dimensional gene scanning (TDGS), and denaturing high performance liquid chromatography (DHPLC). Only the laboratory using DHPLC correctly identified each of the mutations. The laboratory using TDGS correctly identified 91% of the mutations but produced three apparent false positive results. The laboratories using SSCP and CSGE detected abnormal migration for 72% and 76% of the mutations, respectively, but subsequently confirmed and reported only 65% and 60% of mutations, respectively. False negatives therefore resulted not only from failure of the techniques to distinguish wild type from mutant, but also from failure to confirm the mutation by sequence analysis as well as from human errors leading to misreporting of results. These findings characterise sources of error in commonly used methods of mutation detection that should be addressed by laboratories using these methods. Based upon sources of error identified in this comparison, it is likely that mutations in BRCA1 and BRCA2 are more prevalent than some studies have previously reported. The findings of this comparison provide a basis for interpreting studies of mutations in susceptibility genes across many inherited cancer syndromes.

AB - While sequence analysis is considered by many to be the most sensitive method of detecting unknown mutations in large genes such as BRCA1, most published estimates of the prevalence of mutations in this gene have been derived from studies that have used other methods of gene analysis. In order to determine the relative sensitivity of techniques that are widely used in research on BRCA1, a set of blinded samples containing 58 distinct mutations were analysed by four separate laboratories. Each used one of the following methods: single strand conformational polymorphism analysis (SSCP), conformation sensitive gel electrophoresis (CSGE), two dimensional gene scanning (TDGS), and denaturing high performance liquid chromatography (DHPLC). Only the laboratory using DHPLC correctly identified each of the mutations. The laboratory using TDGS correctly identified 91% of the mutations but produced three apparent false positive results. The laboratories using SSCP and CSGE detected abnormal migration for 72% and 76% of the mutations, respectively, but subsequently confirmed and reported only 65% and 60% of mutations, respectively. False negatives therefore resulted not only from failure of the techniques to distinguish wild type from mutant, but also from failure to confirm the mutation by sequence analysis as well as from human errors leading to misreporting of results. These findings characterise sources of error in commonly used methods of mutation detection that should be addressed by laboratories using these methods. Based upon sources of error identified in this comparison, it is likely that mutations in BRCA1 and BRCA2 are more prevalent than some studies have previously reported. The findings of this comparison provide a basis for interpreting studies of mutations in susceptibility genes across many inherited cancer syndromes.

KW - BRCA1

KW - Cancer genetics

KW - Mutation detection

UR - http://www.scopus.com/inward/record.url?scp=18244377693&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=18244377693&partnerID=8YFLogxK

M3 - Article

VL - 38

SP - 824

EP - 833

JO - Journal of Medical Genetics

JF - Journal of Medical Genetics

SN - 0022-2593

IS - 12

ER -