Evaluation of quality of DNA extracted from buccal swabs for microarray based genotyping

Indian Journal of Clinical Biochemistry

Volumn 27, Issue 1, 2012, Pages 28-33

  Livy, Alex ^a   Lye, Sayhean ^a   Jagdish, Chahil K ^a   Hanis, Nurul ^a   Sharmila, Velapasamy ^a   Ler, Lian Wee ^a   Pramod, Bagali ^a  

^a INFOVALLEY Life Sciences Sdn Bhd   (Malaysia)

Author keywords

Blood; Buccal cells; Concordance; DNA; Genotyping; Microarray; Quality; SNP

Indexed keywords

DNA;

AGAR GEL ELECTROPHORESIS; ARTICLE; BLOOD; BLOOD SAMPLING; CHEEK; CONTROLLED STUDY; DNA DEGRADATION; DNA EXTRACTION; DNA HYBRIDIZATION; GENOTYPING TECHNIQUE; HUMAN; MICROARRAY ANALYSIS; MOUTH; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; TEST RETEST RELIABILITY;

GOSSYPIUM HIRSUTUM;

EID: 84857782409     PISSN: 09701915     EISSN: 09740422     Source Type: Journal    
DOI: 10.1007/s12291-011-0154-y     Document Type: Article

References (22)

1. M Garcia-Closas KM Egan J Abruzzo PA Newcomb L Titus-Ernstoff T Franklin, et al. 2001 Collection of genomic DNA from adults in epidemiological studies by buccal cytobrush and mouthwash Cancer Epidemiol Biomarkers Prev 10 6 687 696 11401920 1:CAS:528:DC%2BD3MXlt1SrtL8%3D (Pubitemid 32703204)
2. B Freeman J Powell D Ball L Hill I Craig R Plomin 1997 DNA by mail: an inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations Behav Genet 27 3 251 257 9210796 1:STN:280: DyaK2szlsVGgsg%3D%3D 10.1023/A:1025614231190 (Pubitemid 27278642)
3. LC Harty M Garcia-Closas N Rothman YA Reid MA Tucker P Hartge 2000 Collection of buccal cell DNA using treated cards Cancer Epidemiol Biomarkers Prev 9 5 501 506 10815695 1:CAS:528:DC%2BD3cXjslKgs78%3D (Pubitemid 30313893)
4. L Le Marchand A Lum-Jones B Saltzman V Visaya AM Nomura LN Kolonel 2001 Feasibility of collecting buccal cell DNA by mail in a cohort study Cancer Epidemiol Biomarkers Prev 10 6 701 703 11401922 1:CAS:528:DC%2BD3MXlt1SrtL0%3D (Pubitemid 32703206)
5. DL Herraez M Stoneking 2008 High fractions of exogenous DNA in human buccal samples reduce the quality of large-scale genotyping Anal Biochem 383 2 329 331 18804445 1:CAS:528:DC%2BD1cXht12rsr3M 10.1016/j.ab.2008.08.015
6. HS Feigelson C Rodriguez AS Robertson EJ Jacobs EE Calle YA Reid, et al. 2001 Determinants of DNA yield and quality from buccal cell samples collected with mouthwash Cancer Epidemiol Biomarkers Prev 10 9 1005 1008 11535555 1:CAS:528:DC%2BD3MXnt1GisL0%3D (Pubitemid 32844910)
7. D Quinque R Kittler M Kayser M Stoneking I Nasidze 2006 Evaluation of saliva as a source of human DNA for population and association studies Anal Biochem 353 2 272 277 16620753 1:CAS:528:DC%2BD28XltFCrs74%3D 10.1016/j.ab.2006.03.021 (Pubitemid 43775441)
8. AW Bergen KA Haque Y Qi MB Beerman M Garcia-Closas N Rothman, et al. 2005 Comparison of yield and genotyping performance of multiple displacement amplification and OmniPlex whole genome amplified DNA generated from multiple DNA sources Hum Mutat 26 3 262 270 16086324 1:CAS:528:DC%2BD2MXhtFSktrfP 10.1002/humu.20213 (Pubitemid 41254381)
9. G Kirov I Nikolov L Georgieva V Moskvina MJ Owen MC O'Donovan 2006 Pooled DNA genotyping on Affymetrix SNP genotyping arrays BMC Genomics 7 27 16480507 10.1186/1471-2164-7-27
10. ML Chang RL Terrill MM Bautista EJ Carlson DJ Dyer KL Overall, et al. 2007 Large-scale SNP genotyping with canine buccal swab DNA J Hered 98 5 428 437 17602178 1:CAS:528:DC%2BD2sXhtVSgt7%2FN 10.1093/jhered/esm044 (Pubitemid 47357587)
11. JG Woo G Sun M Haverbusch S Indugula LJ Martin JP Broderick, et al. 2007 Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500K GeneChip BMC Genet 8 79 17996058 10.1186/1471-2156-8-79
12. A Brazma P Hingamp J Quackenbush G Sherlock P Spellman C Stoeckert, et al. 2001 Minimum information about a microarray experiment (MIAME)-toward standards for microarray data Nat Genet 29 4 365 371 11726920 1:CAS:528:DC%2BD3MXovFamurw%3D 10.1038/ng1201-365 (Pubitemid 34326681)
13. JB Fan KL Gunderson M Bibikova JM Yeakley J Chen E Wickham Garcia, et al. 2006 Illumina universal bead arrays Methods Enzymol 410 57 73 16938546 1:CAS:528:DC%2BD2sXmtV2nu7Y%3D 10.1016/S0076-6879(06)10003-8 (Pubitemid 44287000)
14. T Zayats TL Young DA Mackey F Malecaze P Calvas JA Guggenheim 2009 Quality of DNA extracted from mouthwashes PLoS One 4 7 e6165 19582144 10.1371/journal.pone.0006165
15. JD Rudney R Chen 2006 The vital status of human buccal epithelial cells and the bacteria associated with them Arch Oral Biol 51 4 291 298 16239000 1:CAS:528:DC%2BD28Xit1Ojtbw%3D 10.1016/j.archoralbio.2005.09.003 (Pubitemid 43363505)
16. IB King J Satia-Abouta MD Thornquist J Bigler RE Patterson AR Kristal, et al. 2002 Buccal cell DNA yield, quality, and collection costs: comparison of methods for large-scale studies Cancer Epidemiol Biomarkers Prev 11 10 Pt 1 1130 1133 12376522 (Pubitemid 35192672)
17. JA Aas BJ Paster LN Stokes I Olsen FE Dewhirst 2005 Defining the normal bacterial flora of the oral cavity J Clin Microbiol 43 11 5721 5732 16272510 10.1128/JCM.43.11.5721-5732.2005 (Pubitemid 41612354)
18. BJ Paster SK Boches JL Galvin RE Ericson CN Lau VA Levanos, et al. 2001 Bacterial diversity in human subgingival plaque J Bacteriol 183 12 3770 3783 11371542 1:CAS:528:DC%2BD3MXktlSguro%3D 10.1128/JB.183.12.3770-3783.2001 (Pubitemid 32510445)
19. AD Haffajee SS Socransky 2001 Relationship of cigarette smoking to the subgingival microbiota J Clin Periodontol 28 5 377 388 11350499 1:STN:280:DC%2BD38%2FgvF2itQ%3D%3D 10.1034/j.1600-051x.2001.028005377.x (Pubitemid 33755454)
20. J Shiloah MR Patters MB Waring 2000 The prevalence of pathogenic periodontal microflora in healthy young adult smokers J Periodontol 71 4 562 567 10807119 1:STN:280:DC%2BD3c3msFequw%3D%3D 10.1902/jop.2000.71.4.562
21. M Glei N Habermann K Osswald C Seidel C Persin G Jahreis, et al. 2005 Assessment of DNA damage and its modulation by dietary and genetic factors in smokers using the Comet assay: a biomarker model Biomarkers 10 2-3 203 217 16076733 1:CAS:528:DC%2BD2MXlslOms78%3D 10.1080/13547500500138963 (Pubitemid 40916676)
22. KG Konig 2000 Diet and oral health Int Dent J 50 3 162 174 10967767 1:STN:280:DC%2BD3M%2Fls1ajtQ%3D%3D 10.1111/j.1875-595X.2000.tb00555.x