Whole genome amplification of DNA extracted from hair samples

Potential for use in molecular epidemiologic studies

Suzanne M. Leanza, Robert D. Burk, Thomas E. Rohan

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Because of concerns regarding the quality and quantity of DNA isolated from human hair, such samples are often overlooked as a source of DNA for molecular epidemiological studies. Nevertheless, there are many potential benefits to using hair: it is easily self-collected; it does not require costly collection kits; it can be mailed for a nominal fee; and the hair specimens can be stored at room temperature. However, the amount of DNA that can be extracted from hair samples is somewhat limited. Therefore, we assessed the feasibility of using whole genome amplification (WGA) on genomic DNA extracted from archived human hairs (stored for 7 to 11 years) to increase the quantity of DNA available for genotyping analysis. Methods: We evaluated two methods of WGA, multiple displacement amplification and the Genomeplex® method. Both WGA methods were performed on each of 44 DNA samples isolated from archived human hair specimens. The resulting WGA products where then screened for the presence of three single nucleotide polymorphisms. The genotyping results were compared to genotyping data obtained from DNA isolated from mouthwash samples collected from the same individuals. Results: When we focused on DNA extracted from the hair root, we observed excellent agreement between the genotypes determined from both the hair (pre-WGA) samples and Genomeplex® WGA when compared to their corresponding mouthwash DNA samples (kappa = 0.83-0.91 and 0.79-0.92, respectively); whereas the agreement between the MDA samples and mouthwash DNA samples was poor (kappa = 0.27-0.51). Conclusions: Our data suggest that, when combined with Genomeplex® WGA, hair specimens containing the root portion can serve as a reliable and renewable source of DNA.

Original languageEnglish (US)
Pages (from-to)480-488
Number of pages9
JournalCancer Detection and Prevention
Volume31
Issue number6
DOIs
StatePublished - 2007

Fingerprint

Hair
Epidemiologic Studies
Genome
DNA
Mouthwashes
Fees and Charges
Single Nucleotide Polymorphism
Genotype
Temperature

Keywords

  • Amplification techniques
  • Epidemiology
  • Genomic DNA
  • Genotype
  • Hair follicle
  • Molecular biology
  • Nucleic acid
  • Phage phi 29
  • Polymorphism
  • Single nucleotide
  • Specimen collection
  • Specimen handling

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

@article{6c4d14899232468f8da9f76cd350ed7b,
title = "Whole genome amplification of DNA extracted from hair samples: Potential for use in molecular epidemiologic studies",
abstract = "Background: Because of concerns regarding the quality and quantity of DNA isolated from human hair, such samples are often overlooked as a source of DNA for molecular epidemiological studies. Nevertheless, there are many potential benefits to using hair: it is easily self-collected; it does not require costly collection kits; it can be mailed for a nominal fee; and the hair specimens can be stored at room temperature. However, the amount of DNA that can be extracted from hair samples is somewhat limited. Therefore, we assessed the feasibility of using whole genome amplification (WGA) on genomic DNA extracted from archived human hairs (stored for 7 to 11 years) to increase the quantity of DNA available for genotyping analysis. Methods: We evaluated two methods of WGA, multiple displacement amplification and the Genomeplex{\circledR} method. Both WGA methods were performed on each of 44 DNA samples isolated from archived human hair specimens. The resulting WGA products where then screened for the presence of three single nucleotide polymorphisms. The genotyping results were compared to genotyping data obtained from DNA isolated from mouthwash samples collected from the same individuals. Results: When we focused on DNA extracted from the hair root, we observed excellent agreement between the genotypes determined from both the hair (pre-WGA) samples and Genomeplex{\circledR} WGA when compared to their corresponding mouthwash DNA samples (kappa = 0.83-0.91 and 0.79-0.92, respectively); whereas the agreement between the MDA samples and mouthwash DNA samples was poor (kappa = 0.27-0.51). Conclusions: Our data suggest that, when combined with Genomeplex{\circledR} WGA, hair specimens containing the root portion can serve as a reliable and renewable source of DNA.",
keywords = "Amplification techniques, Epidemiology, Genomic DNA, Genotype, Hair follicle, Molecular biology, Nucleic acid, Phage phi 29, Polymorphism, Single nucleotide, Specimen collection, Specimen handling",
author = "Leanza, {Suzanne M.} and Burk, {Robert D.} and Rohan, {Thomas E.}",
year = "2007",
doi = "10.1016/j.cdp.2007.10.009",
language = "English (US)",
volume = "31",
pages = "480--488",
journal = "Cancer Epidemiology",
issn = "1877-7821",
publisher = "Elsevier BV",
number = "6",

}

TY - JOUR

T1 - Whole genome amplification of DNA extracted from hair samples

T2 - Potential for use in molecular epidemiologic studies

AU - Leanza, Suzanne M.

AU - Burk, Robert D.

AU - Rohan, Thomas E.

PY - 2007

Y1 - 2007

N2 - Background: Because of concerns regarding the quality and quantity of DNA isolated from human hair, such samples are often overlooked as a source of DNA for molecular epidemiological studies. Nevertheless, there are many potential benefits to using hair: it is easily self-collected; it does not require costly collection kits; it can be mailed for a nominal fee; and the hair specimens can be stored at room temperature. However, the amount of DNA that can be extracted from hair samples is somewhat limited. Therefore, we assessed the feasibility of using whole genome amplification (WGA) on genomic DNA extracted from archived human hairs (stored for 7 to 11 years) to increase the quantity of DNA available for genotyping analysis. Methods: We evaluated two methods of WGA, multiple displacement amplification and the Genomeplex® method. Both WGA methods were performed on each of 44 DNA samples isolated from archived human hair specimens. The resulting WGA products where then screened for the presence of three single nucleotide polymorphisms. The genotyping results were compared to genotyping data obtained from DNA isolated from mouthwash samples collected from the same individuals. Results: When we focused on DNA extracted from the hair root, we observed excellent agreement between the genotypes determined from both the hair (pre-WGA) samples and Genomeplex® WGA when compared to their corresponding mouthwash DNA samples (kappa = 0.83-0.91 and 0.79-0.92, respectively); whereas the agreement between the MDA samples and mouthwash DNA samples was poor (kappa = 0.27-0.51). Conclusions: Our data suggest that, when combined with Genomeplex® WGA, hair specimens containing the root portion can serve as a reliable and renewable source of DNA.

AB - Background: Because of concerns regarding the quality and quantity of DNA isolated from human hair, such samples are often overlooked as a source of DNA for molecular epidemiological studies. Nevertheless, there are many potential benefits to using hair: it is easily self-collected; it does not require costly collection kits; it can be mailed for a nominal fee; and the hair specimens can be stored at room temperature. However, the amount of DNA that can be extracted from hair samples is somewhat limited. Therefore, we assessed the feasibility of using whole genome amplification (WGA) on genomic DNA extracted from archived human hairs (stored for 7 to 11 years) to increase the quantity of DNA available for genotyping analysis. Methods: We evaluated two methods of WGA, multiple displacement amplification and the Genomeplex® method. Both WGA methods were performed on each of 44 DNA samples isolated from archived human hair specimens. The resulting WGA products where then screened for the presence of three single nucleotide polymorphisms. The genotyping results were compared to genotyping data obtained from DNA isolated from mouthwash samples collected from the same individuals. Results: When we focused on DNA extracted from the hair root, we observed excellent agreement between the genotypes determined from both the hair (pre-WGA) samples and Genomeplex® WGA when compared to their corresponding mouthwash DNA samples (kappa = 0.83-0.91 and 0.79-0.92, respectively); whereas the agreement between the MDA samples and mouthwash DNA samples was poor (kappa = 0.27-0.51). Conclusions: Our data suggest that, when combined with Genomeplex® WGA, hair specimens containing the root portion can serve as a reliable and renewable source of DNA.

KW - Amplification techniques

KW - Epidemiology

KW - Genomic DNA

KW - Genotype

KW - Hair follicle

KW - Molecular biology

KW - Nucleic acid

KW - Phage phi 29

KW - Polymorphism

KW - Single nucleotide

KW - Specimen collection

KW - Specimen handling

UR - http://www.scopus.com/inward/record.url?scp=36549004450&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=36549004450&partnerID=8YFLogxK

U2 - 10.1016/j.cdp.2007.10.009

DO - 10.1016/j.cdp.2007.10.009

M3 - Article

VL - 31

SP - 480

EP - 488

JO - Cancer Epidemiology

JF - Cancer Epidemiology

SN - 1877-7821

IS - 6

ER -