Whole genome amplification of DNA extracted from hair samples: Potential for use in molecular epidemiologic studies

Cancer Detection and Prevention

Volumn 31, Issue 6, 2007, Pages 480-488

  Leanza, Suzanne M ^a   Burk, Robert D ^a   Rohan, Thomas E ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

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

Indexed keywords

GENOMIC DNA;

ARTICLE; CHEEK; COMPARATIVE STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA ISOLATION; FEMALE; GENE AMPLIFICATION; GENETIC SCREENING; GENOTYPE; HAIR; HAIR ROOT; HUMAN; HUMAN CELL; MALE; MOLECULAR EPIDEMIOLOGY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; EPIDEMIOLOGIC STUDIES; FEASIBILITY STUDIES; FEMALE; GENOME, HUMAN; GENOTYPE; HAIR; HUMANS; MALE; MOUTH; NUCLEIC ACID AMPLIFICATION TECHNIQUES;

EID: 36549004450     PISSN: 0361090X     EISSN: 15251500     Source Type: Journal    
DOI: 10.1016/j.cdp.2007.10.009     Document Type: Article

References (25)

1. Barrett J.C., and Cardon L.R. Evaluating coverage of genome-wide association studies. Nat Genet 38 6 (2006) 659-662
2. Milne E., van Bockxmeer F.M., Robertson L., Brisbane J.M., Ashton L.J., Scott R.J., et al. Buccal DNA collection: comparison of buccal swabs with FTA cards. Cancer Epidemiol Biomarkers Prev 15 4 (2006) 816-819
3. King I.B., Satia-Abouta J., Thornquist M.D., Bigler J., Patterson R.E., Kristal A.R., et al. Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies. Cancer Epidemiol Biomarkers Prev 11 10 Pt 1 (2002) 1130-1133
4. Roon D.A., Waits L.D., and Kendall K.C. A quantitative evaluation of two methods for preserving hair samples. Mol Ecol Notes 3 (2003) 163-166
5. Vigilant L. An evaluation of techniques for the extraction and amplification of DNA from naturally shed hairs. Biol Chem 380 11 (1999) 1329-1331
6. McNevin D., Wilson-Wilde L., Robertson J., Kyd J., and Lennard C. Short tandem repeat (STR) genotyping of keratinised hair. Part 1. Review of current status and knowledge gaps. Forensic Sci Int 153 2-3 (2005) 237-246
7. Tanigawara Y., Kita T., Hirono M., Sakaeda T., Komada F., and Okumura K. Identification of N-acetyltransferase 2 and CYP2C19 genotypes for hair, buccal cell swabs, or fingernails compared with blood. Ther Drug Monit 23 4 (2001) 341-346
8. Hughes S., Arneson N., Done S., and Squire J. The use of whole genome amplification in the study of human disease. Prog Biophys Mol Biol 88 1 (2005) 173-189
9. Barker D.L., Hansen M.S., Faruqi A.F., Giannola D., Irsula O.R., Lasken R.S., et al. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res 14 5 (2004) 901-907
10. Bergen A.W., Haque K.A., Qi Y., Beerman M.B., Garcia-Closas M., Rothman N., et al. Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources. Hum Mutat 26 3 (2005) 262-270
11. Lovmar L., and Syvanen A.C. Multiple displacement amplification to create a long-lasting source of DNA for genetic studies. Hum Mutat 27 7 (2006) 603-614
12. Park J.W., Beaty T.H., Boyce P., Scott A.F., and McIntosh I. Comparing whole-genome amplification methods and sources of biological samples for single-nucleotide polymorphism genotyping. Clin Chem 51 8 (2005) 1520-1523
13. Thompson M.D., Bowen R.A., Wong B.Y., Antal J., Liu Z., Yu H., et al. Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification. Clin Chem Lab Med 43 2 (2005) 157-162
14. Murthy K.K., Mahboubi V.S., Santiago A., Barragan M.T., Knoll R., Schultheiss H.P., et al. Assessment of multiple displacement amplification for polymorphism discovery and haplotype determination at a highly polymorphic locus, MC1R. Hum Mutat 26 2 (2005) 145-152
15. Rohan T.E., Soskolne C.L., Carroll K.K., and Kreiger N. Design of a Canadian cohort study of diet, lifestyle, and health-related cancer risk. Cancer Detect Prev 31 1 (2007) 12-17
16. Pyrosequencing [Homepage on the Internet]. Uppsala: Biotage AG; 2005. Available at: http://www.pyrosequencing.com [cited June 3, 2007].
17. Wieser F., Fabjani G., Tempfer C., Schneeberger C., Sator M., Huber J., et al. Analysis of an interleukin-6 gene promoter polymorphism in women with endometriosis by pyrosequencing. J Soc Gynecol Invest 10 1 (2003) 32-36
18. Verri A., Focher F., Tettamanti G., and Grazioli V. Two-step genetic screening of thrombophilia by pyrosequencing. Clin Chem 51 7 (2005) 1282-1284
19. Giambernardi T.A., Rodeck U., and Klebe R.J. Bovine serum albumin reverses inhibition of RT-PCR by melanin. Biotechniques 25 4 (1998) 564-566
20. Suenaga E., and Nakamura H. Evaluation of three methods for effective extraction of DNA from human hair. J Chromatogr B: Analyt Technol Biomed Life Sci 820 1 (2005) 137-141
21. Gan S.H., Ismail R., Wan Adnan W.A., and Wan Z. Standard CYP2D6 genotyping procedures fail for the CYP2D6*5 and duplication alleles when hair roots are used as a source of DNA. Clin Chim Acta 329 1-2 (2003) 61-68
22. Chang H.W., Yen C.Y., Liu S.Y., Singer G., and Shih Ie M. Genotype analysis using human hair shaft. Cancer Epidemiol Biomarkers Prev 11 9 (2002) 925-929
23. Taberlet P., Griffin S., Goossens B., Questiau S., Manceau V., Escaravage N., et al. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res 24 16 (1996) 3189-3194
24. Ballantyne K.N., van Oorschot R.A., and Mitchell R.J. Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples. Forensic Sci Int 166 1 (2006) 35-41
25. Bredel M., Bredel C., Juric D., Kim Y., Vogel H., Harsh G.R., et al. Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J Mol Diagn 7 2 (2005) 171-182