Telomere length varies by DNA extraction method: Implications for epidemiologic research

Julie M Cunningham, Ruth A. Johnson, Kristin Litzelman, Halcyon G. Skinner, Songwon Seo, Corinne D. Engelman, Russell J. Vanderboom, Grace W. Kimmel, Ronald E. Gangnon, Douglas L. Riegert-Johnson, John A. Baron, John D. Potter, Robert Haile, Daniel D. Buchanan, Mark A. Jenkins, David N. Rider, Stephen N Thibodeau, Gloria M Petersen, Lisa Allyn Boardman

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

Background: Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from patients with colorectal cancer. Methods: We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 patients with colorectal cancer and 2,952 healthy controls. DNA was extracted with phenol/chloroform, PureGene, or QIAamp. Results: We observed differences in RTL depending on DNA extraction method (P < 0.001). Phenol/chloroform-extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01-6.54) compared with PureGeneextracted DNA (mean RTL of 0.75; range 0.00-12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02-3.69).Wesubsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBLDNAextracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17-0.58) was less than from either PureGene or phenol/chloroform (ranges, 0.04-2.67 and 0.32-2.81, respectively). Conclusions: RTL measured by qPCR from QIAamp-extracted DNA was less than from either PureGene or phenol/chloroform (P < 0.001). Impact: Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL.

Original languageEnglish (US)
Pages (from-to)2047-2054
Number of pages8
JournalCancer Epidemiology Biomarkers and Prevention
Volume22
Issue number11
DOIs
StatePublished - Nov 2013

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Epidemiologic Methods
Telomere
DNA
Research
Chloroform
Phenol
Colorectal Neoplasms
Polymerase Chain Reaction
Leukocytes
Neoplasms

ASJC Scopus subject areas

  • Epidemiology
  • Oncology

Cite this

Telomere length varies by DNA extraction method : Implications for epidemiologic research. / Cunningham, Julie M; Johnson, Ruth A.; Litzelman, Kristin; Skinner, Halcyon G.; Seo, Songwon; Engelman, Corinne D.; Vanderboom, Russell J.; Kimmel, Grace W.; Gangnon, Ronald E.; Riegert-Johnson, Douglas L.; Baron, John A.; Potter, John D.; Haile, Robert; Buchanan, Daniel D.; Jenkins, Mark A.; Rider, David N.; Thibodeau, Stephen N; Petersen, Gloria M; Boardman, Lisa Allyn.

In: Cancer Epidemiology Biomarkers and Prevention, Vol. 22, No. 11, 11.2013, p. 2047-2054.

Research output: Contribution to journalArticle

Cunningham, JM, Johnson, RA, Litzelman, K, Skinner, HG, Seo, S, Engelman, CD, Vanderboom, RJ, Kimmel, GW, Gangnon, RE, Riegert-Johnson, DL, Baron, JA, Potter, JD, Haile, R, Buchanan, DD, Jenkins, MA, Rider, DN, Thibodeau, SN, Petersen, GM & Boardman, LA 2013, 'Telomere length varies by DNA extraction method: Implications for epidemiologic research', Cancer Epidemiology Biomarkers and Prevention, vol. 22, no. 11, pp. 2047-2054. https://doi.org/10.1158/1055-9965.EPI-13-0409
Cunningham, Julie M ; Johnson, Ruth A. ; Litzelman, Kristin ; Skinner, Halcyon G. ; Seo, Songwon ; Engelman, Corinne D. ; Vanderboom, Russell J. ; Kimmel, Grace W. ; Gangnon, Ronald E. ; Riegert-Johnson, Douglas L. ; Baron, John A. ; Potter, John D. ; Haile, Robert ; Buchanan, Daniel D. ; Jenkins, Mark A. ; Rider, David N. ; Thibodeau, Stephen N ; Petersen, Gloria M ; Boardman, Lisa Allyn. / Telomere length varies by DNA extraction method : Implications for epidemiologic research. In: Cancer Epidemiology Biomarkers and Prevention. 2013 ; Vol. 22, No. 11. pp. 2047-2054.
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abstract = "Background: Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from patients with colorectal cancer. Methods: We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 patients with colorectal cancer and 2,952 healthy controls. DNA was extracted with phenol/chloroform, PureGene, or QIAamp. Results: We observed differences in RTL depending on DNA extraction method (P < 0.001). Phenol/chloroform-extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01-6.54) compared with PureGeneextracted DNA (mean RTL of 0.75; range 0.00-12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02-3.69).Wesubsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBLDNAextracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17-0.58) was less than from either PureGene or phenol/chloroform (ranges, 0.04-2.67 and 0.32-2.81, respectively). Conclusions: RTL measured by qPCR from QIAamp-extracted DNA was less than from either PureGene or phenol/chloroform (P < 0.001). Impact: Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL.",
author = "Cunningham, {Julie M} and Johnson, {Ruth A.} and Kristin Litzelman and Skinner, {Halcyon G.} and Songwon Seo and Engelman, {Corinne D.} and Vanderboom, {Russell J.} and Kimmel, {Grace W.} and Gangnon, {Ronald E.} and Riegert-Johnson, {Douglas L.} and Baron, {John A.} and Potter, {John D.} and Robert Haile and Buchanan, {Daniel D.} and Jenkins, {Mark A.} and Rider, {David N.} and Thibodeau, {Stephen N} and Petersen, {Gloria M} and Boardman, {Lisa Allyn}",
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T1 - Telomere length varies by DNA extraction method

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AU - Cunningham, Julie M

AU - Johnson, Ruth A.

AU - Litzelman, Kristin

AU - Skinner, Halcyon G.

AU - Seo, Songwon

AU - Engelman, Corinne D.

AU - Vanderboom, Russell J.

AU - Kimmel, Grace W.

AU - Gangnon, Ronald E.

AU - Riegert-Johnson, Douglas L.

AU - Baron, John A.

AU - Potter, John D.

AU - Haile, Robert

AU - Buchanan, Daniel D.

AU - Jenkins, Mark A.

AU - Rider, David N.

AU - Thibodeau, Stephen N

AU - Petersen, Gloria M

AU - Boardman, Lisa Allyn

PY - 2013/11

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N2 - Background: Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from patients with colorectal cancer. Methods: We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 patients with colorectal cancer and 2,952 healthy controls. DNA was extracted with phenol/chloroform, PureGene, or QIAamp. Results: We observed differences in RTL depending on DNA extraction method (P < 0.001). Phenol/chloroform-extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01-6.54) compared with PureGeneextracted DNA (mean RTL of 0.75; range 0.00-12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02-3.69).Wesubsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBLDNAextracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17-0.58) was less than from either PureGene or phenol/chloroform (ranges, 0.04-2.67 and 0.32-2.81, respectively). Conclusions: RTL measured by qPCR from QIAamp-extracted DNA was less than from either PureGene or phenol/chloroform (P < 0.001). Impact: Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL.

AB - Background: Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from patients with colorectal cancer. Methods: We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 patients with colorectal cancer and 2,952 healthy controls. DNA was extracted with phenol/chloroform, PureGene, or QIAamp. Results: We observed differences in RTL depending on DNA extraction method (P < 0.001). Phenol/chloroform-extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01-6.54) compared with PureGeneextracted DNA (mean RTL of 0.75; range 0.00-12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02-3.69).Wesubsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBLDNAextracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17-0.58) was less than from either PureGene or phenol/chloroform (ranges, 0.04-2.67 and 0.32-2.81, respectively). Conclusions: RTL measured by qPCR from QIAamp-extracted DNA was less than from either PureGene or phenol/chloroform (P < 0.001). Impact: Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL.

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