Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash

M. García-Closas, K. M. Egan, J. Abruzzo, P. A. Newcomb, L. Titus-Ernstoff, T. Franklin, P. K. Bender, J. C. Beck, L. Le Marchand, A. Lum, M. Alavanja, R. B. Hayes, J. Rutter, Kenneth Buetow, L. A. Brinton, N. Rothman

Research output: Contribution to journalArticle

227 Citations (Scopus)

Abstract

Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 μg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 μg/mouthwash sample for phases 1 and 2, respectively. Most (94-100%) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61% of the brush extracts. PCR success rates for amplification of β-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100%). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although DNA isolated from either mouthwash or cytobrush samples collected by mail from adults is adequate for a wide range of PCR-based assays, a single mouthwash sample provides substantially larger amounts and higher molecular weight DNA than two cytobrush samples.

Original languageEnglish (US)
Pages (from-to)687-696
Number of pages10
JournalCancer Epidemiology Biomarkers and Prevention
Volume10
Issue number6
StatePublished - 2001
Externally publishedYes

Fingerprint

Mouthwashes
Cheek
Epidemiologic Studies
DNA
Chloroform
Phenol
Postal Service
Molecular Weight
Polymerase Chain Reaction
Breast Neoplasms
BRCA1 Gene
Globins
Gene Amplification
DNA Probes
Androgen Receptors
Microsatellite Repeats
Genes
Case-Control Studies
Reading

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

García-Closas, M., Egan, K. M., Abruzzo, J., Newcomb, P. A., Titus-Ernstoff, L., Franklin, T., ... Rothman, N. (2001). Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiology Biomarkers and Prevention, 10(6), 687-696.

Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. / García-Closas, M.; Egan, K. M.; Abruzzo, J.; Newcomb, P. A.; Titus-Ernstoff, L.; Franklin, T.; Bender, P. K.; Beck, J. C.; Le Marchand, L.; Lum, A.; Alavanja, M.; Hayes, R. B.; Rutter, J.; Buetow, Kenneth; Brinton, L. A.; Rothman, N.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 10, No. 6, 2001, p. 687-696.

Research output: Contribution to journalArticle

García-Closas, M, Egan, KM, Abruzzo, J, Newcomb, PA, Titus-Ernstoff, L, Franklin, T, Bender, PK, Beck, JC, Le Marchand, L, Lum, A, Alavanja, M, Hayes, RB, Rutter, J, Buetow, K, Brinton, LA & Rothman, N 2001, 'Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash', Cancer Epidemiology Biomarkers and Prevention, vol. 10, no. 6, pp. 687-696.
García-Closas M, Egan KM, Abruzzo J, Newcomb PA, Titus-Ernstoff L, Franklin T et al. Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. Cancer Epidemiology Biomarkers and Prevention. 2001;10(6):687-696.
García-Closas, M. ; Egan, K. M. ; Abruzzo, J. ; Newcomb, P. A. ; Titus-Ernstoff, L. ; Franklin, T. ; Bender, P. K. ; Beck, J. C. ; Le Marchand, L. ; Lum, A. ; Alavanja, M. ; Hayes, R. B. ; Rutter, J. ; Buetow, Kenneth ; Brinton, L. A. ; Rothman, N. / Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash. In: Cancer Epidemiology Biomarkers and Prevention. 2001 ; Vol. 10, No. 6. pp. 687-696.
@article{e40db5e73fea41a4aada4f543fcff168,
title = "Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash",
abstract = "Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 μg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 μg/mouthwash sample for phases 1 and 2, respectively. Most (94-100{\%}) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61{\%} of the brush extracts. PCR success rates for amplification of β-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100{\%}). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although DNA isolated from either mouthwash or cytobrush samples collected by mail from adults is adequate for a wide range of PCR-based assays, a single mouthwash sample provides substantially larger amounts and higher molecular weight DNA than two cytobrush samples.",
author = "M. Garc{\'i}a-Closas and Egan, {K. M.} and J. Abruzzo and Newcomb, {P. A.} and L. Titus-Ernstoff and T. Franklin and Bender, {P. K.} and Beck, {J. C.} and {Le Marchand}, L. and A. Lum and M. Alavanja and Hayes, {R. B.} and J. Rutter and Kenneth Buetow and Brinton, {L. A.} and N. Rothman",
year = "2001",
language = "English (US)",
volume = "10",
pages = "687--696",
journal = "Cancer Epidemiology Biomarkers and Prevention",
issn = "1055-9965",
publisher = "American Association for Cancer Research Inc.",
number = "6",

}

TY - JOUR

T1 - Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash

AU - García-Closas, M.

AU - Egan, K. M.

AU - Abruzzo, J.

AU - Newcomb, P. A.

AU - Titus-Ernstoff, L.

AU - Franklin, T.

AU - Bender, P. K.

AU - Beck, J. C.

AU - Le Marchand, L.

AU - Lum, A.

AU - Alavanja, M.

AU - Hayes, R. B.

AU - Rutter, J.

AU - Buetow, Kenneth

AU - Brinton, L. A.

AU - Rothman, N.

PY - 2001

Y1 - 2001

N2 - Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 μg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 μg/mouthwash sample for phases 1 and 2, respectively. Most (94-100%) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61% of the brush extracts. PCR success rates for amplification of β-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100%). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although DNA isolated from either mouthwash or cytobrush samples collected by mail from adults is adequate for a wide range of PCR-based assays, a single mouthwash sample provides substantially larger amounts and higher molecular weight DNA than two cytobrush samples.

AB - Blood samples are an excellent source of large amounts of genomic DNA. However, alternative sources are often needed in epidemiological studies because of difficulties in obtaining blood samples. This report evaluates the buccal cytobrush and alcohol-containing mouthwash protocols for collecting DNA by mail. Several DNA extraction techniques are also evaluated. The study was conducted in two phases. In phase 1, we compared cytobrush and mouthwash samples collected by mail in two different epidemiological studies: (a) cytobrush samples (n = 120) from a United States case-control study of breast cancer; and (b) mouthwash samples (n = 40) from a prospective cohort of male United States farmers. Findings from phase 1 were confirmed in phase 2, where we randomized cytobrush (n = 28) and mouthwash (n = 25) samples among participants in the breast cancer study to directly compare both collection methods. The median human DNA yield determined by hybridization with a human DNA probe from phenol-chloroform extracts was 1.0 and 1.6 μg/2 brushes for phases 1 and 2, respectively, and 27.5 and 16.6 μg/mouthwash sample for phases 1 and 2, respectively. Most (94-100%) mouthwash extracts contained high molecular weight DNA (>23 kb), in contrast to 55-61% of the brush extracts. PCR success rates for amplification of β-globin gene fragments (268, 536, and 989 bp) were similar for cytobrush and mouthwash phenol-chloroform extracts (range, 94.4-100%). Also, we obtained high success rates in determining the number of CAG repeats in the androgen receptor gene, characterizing tetranucleotide microsatellites in six gene loci, and screening for mutations in the BRCA1/2 genes in a subset of phenol-chloroform DNA extracts. Relative to DNA extracted by phenol-chloroform from cytobrush samples, DNA extracted by NaOH had lower molecular weight, decreased PCR success rates for most assays performed, and unreliably high spectrophotometer readings for DNA yields. In conclusion, although DNA isolated from either mouthwash or cytobrush samples collected by mail from adults is adequate for a wide range of PCR-based assays, a single mouthwash sample provides substantially larger amounts and higher molecular weight DNA than two cytobrush samples.

UR - http://www.scopus.com/inward/record.url?scp=0034904540&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0034904540&partnerID=8YFLogxK

M3 - Article

C2 - 11401920

AN - SCOPUS:0034904540

VL - 10

SP - 687

EP - 696

JO - Cancer Epidemiology Biomarkers and Prevention

JF - Cancer Epidemiology Biomarkers and Prevention

SN - 1055-9965

IS - 6

ER -