Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: Performance and agreement with genotyping results from genomic DNA from buccal cells

Clinical Chemistry and Laboratory Medicine

Volumn 47, Issue 5, 2009, Pages 516-522

  Agalliu, Ilir ^a   Schweitzer, Peter A ^b   Leanza, Suzanne M ^a   Burk, Robert D ^a   Rohan, Thomas E ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

DNA test panel; GoldenGate assay; Hair; SNP concordance; Whole genome amplification

Indexed keywords

GENOMIC DNA;

ADULT; ARTICLE; CHEEK; COMPARATIVE STUDY; CONTROLLED STUDY; DNA EXTRACTION; FEMALE; GENE AMPLIFICATION; GENETIC LINKAGE; GENOMICS; GENOTYPE; HAIR; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; MALE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

COHORT STUDIES; DNA; FEMALE; GENOME, HUMAN; GENOTYPE; HAIR; HUMANS; MALE; MIDDLE AGED; MOUTH MUCOSA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PILOT PROJECTS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROSPECTIVE STUDIES; SENSITIVITY AND SPECIFICITY; SPECIMEN HANDLING;

EID: 67649201276     PISSN: 14346621     EISSN: 14374331     Source Type: Journal    
DOI: 10.1515/CCLM.2009.106     Document Type: Article

References (23)

1. Ioannidis JP, Trikalinos TA, Ntzani EE, Contopoulos-Ioannidis DG. Genetic associations in large versus small studies: an empirical assessment. Lancet 2003;361:567-71.
2. Nannya Y, Taura K, Kurokawa M, Chiba S, Ogawa S. Evaluation of genome-wide power of genetic association studies based on empirical data from the HapMap project. Hum Mol Genet 2007;16:2494-505.
3. Eberle MA, Ng PC, Kuhn K, Zhou L, Peiffer DA, Galver L, et al. Power to detect risk alleles using genome-wide tag SNP panels. PLoS Genet 2007;3:1827-37.
4. Li C, Li M, Long JR, Cai Q, Zheng W. Evaluating cost efficiency of SNP chips in genome-wide association studies. Genet Epidemiol 2008;32:387-95.
5. Murray SS, Oliphant A, Shen R, McBride C, Steeke RJ, Shannon SG, et al. A highly informative SNP linkage panel for human genetic studies. Nat Methods 2004; 1:113-7.
6. Steinberg K, Beck J, Nickerson D, Garcia-Closas M, Gallagher M, Caggana M, et al. DNA banking for epidemiologic studies: a review of current practices. Epidemiology 2002;13:246-54.
7. Barker DL, Hansen MS, Faruqi AF, Giannola D, Irsula OR, Lasken RS, et al. Two methods of whole-genome amplification enable accurate genotyping across a 2320-SNP linkage panel. Genome Res 2004;14:901-7.
8. Pask R, Rance HE, Barratt BJ, Nutland S, Smyth DJ, Sebastian M, et al. Investigating the utility of combining phi29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping. BMC Biotechnol 2004;4:15.
9. Park JW, Beaty TH, Boyce P, Scott AF, McIntosh I. Comparing whole-genome amplification methods and sources of biological samples for single-nucleotide polymorphism genotyping. Clin Chem 2005;51:1520-3.
10. Paynter RA, Skibola DR, Skibola CF, Buffler PA, Wiemels JL, Smith MT. Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources. Cancer Epidemiol Biomarkers Prev 2006;15:2533-6.
11. Berthier-Schaad Y, Kao WH, Coresh J, Zhang L, Ingersoll RG, Stephens R, et al. Reliability of high-throughput genotyping of whole genome amplified DNA in SNP genotyping studies. Electrophoresis 2007;28:2812-7.
12. Hansen HM, Wiemels JL, Wrensch M, Wiencke JK. DNA quantification of whole genome amplified samples for genotyping on a multiplexed bead array platform. Cancer Epidemiol Biomarkers Prev 2007;16:1686-90.
13. Feigelson HS, Rodriguez C, Welch R, Hutchinson A, Shao W, Jacobs K, et al. Successful genome-wide scan in paired blood and buccal samples. Cancer Epidemiol Biomarkers Prev 2007;16:1023-5.
14. Mead S, Poulter M, Beck J, Uphill J, Jones C, Ang CE, et al. Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms. Hum Mutat 2008;29:1452-8.
15. Cunningham JM, Sellers TA, Schildkraut JM, Fredericksen ZS, Vierkant RA, Kelemen LE, et al. Performance of amplified DNA in an Illumina GoldenGate BeadArray assay. Cancer Epidemiol Biomarkers Prev 2008;17:1781-9.
16. Roon DA, Waits LP, Kendall KC. A quantitative evaluation of two methods for preserving hair samples. Mol Ecol Notes 2003;3:163-6.
17. Leanza SM, Burk RD, Rohan TE. Whole genome amplification of DNA extracted from hair samples: potential for use in molecular epidemiologic studies. Cancer Detect Prev 2007;31:480-8.
18. Rohan TE, Soskolne CL, Carroll KK, Kreiger N. The Canadian Study of Diet, Lifestyle, and Health: design and characteristics of a new cohort study of cancer risk. Cancer Detect Prev 2007;31:12-7.
19. Thompson MD, Bowen RA, Wong BY, 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 2005;43: 157-62.
20. Arinami T, Ohtsuki T, Ishiguro H, Ujike H, Tanaka Y, Morita Y, et al. Genome wide high-density SNP linkage analysis of 236 Japanese families supports the existence of schizophrenia susceptibility loci on chromosomes 1p, 14q, and 20p. Am J Hum Genet 2005;77:937-44.
21. Amos CI, Chen WV, Lee A, Li W, Kern M, Lundsten R, et al. High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33. Genes Immun 2006;7:277-86.
22. Ballantyne KN, van Oorschot RA, Mitchell RJ. Comparison of two whole genome amplification methods for STR genotyping of LCN and degraded DNA samples. Forensic Sci Int 2007;166:35-41.
23. Butler H, Ragoussis J. BeadArray-based genotyping. In: Starkey M, Elaswarapu R. Genomics protocols, Vol. 439, 2nd ed. Totowa, NJ: Humana Press Inc., 2008:53-74.