Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies

BMC Medical Genomics

Volumn 4, Issue , 2011, Pages

  Earp, Madalene A ^a,b   Rahmani, Maziar ^a   Chew, Kevin ^a   Brooks Wilson, Angela ^a,c  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA DETERMINATION; DNA MICROARRAY; DNA REPLICATION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HUMAN; MOLECULAR SIZE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; VARIANCE; ANALYSIS OF VARIANCE; BIOLOGY; GENETICS; METHODOLOGY; SAMPLE SIZE;

DNA;

ANALYSIS OF VARIANCE; COMPUTATIONAL BIOLOGY; DNA; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SAMPLE SIZE;

EID: 82155203003     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-4-81     Document Type: Article

References (26)

1. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA, Proc Natl Acad Sci USA 2009 106 23 9362 9367
2. Genomewide association studies - illuminating biologic pathways. Hirschhorn JN, N Engl J Med 2009 360 17 1699 1701
3. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN, Nat Rev Genet 2008 9 5 356 369 (Pubitemid 351556063)
4. Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies. Pearson JV, Huentelman MJ, Halperin RF, Tembe WD, Melquist S, Homer N, Brun M, Szelinger S, Coon KD, Zismann VL, Webster JA, Beach T, Sando SB, Aasly JO, Heun R, Jessen F, Kolsch H, Tsolaki M, Daniilidou M, Reiman EM, Papassotiropoulos A, Hutton ML, Stephan DA, Craig DW, Am J Hum Genet 2007 80 1 126 139 (Pubitemid 46047656)
5. Rapid inexpensive genome-wide association using pooled whole blood. Craig JE, Hewitt AW, McMellon AE, Henders AK, Ma L, Wallace L, Sharma S, Burdon KP, Visscher PM, Montgomery GW, MacGregor S, Genome Res 2009 19 11 2075 2080
6. Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. Skibola CF, Bracci PM, Halperin E, Conde L, Craig DW, Agana L, Iyadurai K, Becker N, Brooks-Wilson A, Curry JD, Spinelli JJ, Holly EA, Riby J, Zhang L, Nieters A, Smith MT, Brown KM, Nat Genet 2009 41 8 873 875
7. A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis. Schrauwen I, Ealy M, Huentelman MJ, Thys M, Homer N, Vanderstraeten K, Fransen E, Corneveaux JJ, Craig DW, Claustres M, Cremers CW, Dhooge I, Van de Heyning P, Vincent R, Offeciers E, Smith RJ, Van Camp G, Am J Hum Genet 2009 84 3 328 338
8. Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. Comabella M, Craig DW, Camina-Tato M, Morcillo C, Lopez C, Navarro A, Rio J, BiomarkerMS Study Group, Montalban X, Martin R, PLoS One 2008 3 10 3490
9. A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G, BMC Med Genomics 2008 1 44
10. Common sequence variants on 20q11.22 confer melanoma susceptibility. Brown KM, Macgregor S, Montgomery GW, Craig DW, Zhao ZZ, Iyadurai K, Henders AK, Homer N, Campbell MJ, Stark M, Thomas S, Schmid H, Holland EA, Gillanders EM, Duffy DL, Maskiell JA, Jetann J, Ferguson M, Stephan DA, Cust AE, Whiteman D, Green A, Olsson H, Puig S, Ghiorzo P, Hansson J, Demenais F, Goldstein AM, Gruis NA, Elder DE, Bishop JN, Kefford RF, Giles GG, Armstrong BK, Aitken JF, Hopper JL, Martin NG, Trent JM, Mann GJ, Hayward NK, Nat Genet 2008 40 7 838 840 (Pubitemid 351913651)
11. Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene. Capon F, Bijlmakers MJ, Wolf N, Quaranta M, Huffmeier U, Allen M, Timms K, Abkevich V, Gutin A, Smith R, Warren RB, Young HS, Worthington J, Burden AD, Griffiths CE, Hayday A, Nestle FO, Reis A, Lanchbury J, Barker JN, Trembath RC, Hum Mol Genet 2008 17 13 1938 1945 (Pubitemid 351865842)
12. A genomewide association study of skin pigmentation in a South Asian population. Stokowski RP, Pant PV, Dadd T, Fereday A, Hinds DA, Jarman C, Filsell W, Ginger RS, Green MR, van der Ouderaa FJ, Cox DR, Am J Hum Genet 2007 81 6 1119 1132 (Pubitemid 350211444)
13. DNA Pooling: a tool for large-scale association studies. Sham P, Bader JS, Craig I, O'Donovan M, Owen M, Nat Rev Genet 2002 3 11 862 87
14. How to interpret a genome-wide association study. Pearson TA, Manolio TA, JAMA 2008 299 11 1335 1344 (Pubitemid 351439079)
15. Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Macgregor S, Visscher PM, Montgomery G, Nucleic Acids Res 2006 34 7 55
16. Simple method to analyze SNP-based association studies using DNA pools. Visscher PM, Le Hellard S, Genet Epidemiol 2003 24 4 291 296 (Pubitemid 36534996)
17. Most pooling variation in array-based DNA pooling is attributable to array error rather than pool construction error. Macgregor S, Eur J Hum Genet 2007 15 4 501 504
18. Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays. Macgregor S, Zhao ZZ, Henders A, Nicholas MG, Montgomery GW, Visscher PM, Nucleic Acids Res 2008 36 6 35
19. Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Barratt BJ, Payne F, Rance HE, Nutland S, Todd JA, Clayton DG, Ann Hum Genet 2002 66 Pt 5-6 393 405 (Pubitemid 36004229)
20. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Skol AD, Scott LJ, Abecasis GR, Boehnke M, Nat Genet 2006 38 2 209 213 (Pubitemid 43177235)
21. Gene × Environment, Gene × Gene Interaction Home page. http://hydra.usc.edu/gxe/
22. Whole genome genotyping technologies on the BeadArray platform. Steemers FJ, Gunderson KL, Biotechnol J 2007 2 1 41 49 (Pubitemid 46738887)
23. A novel, high-performance random array platform for quantitative gene expression profiling. Kuhn K, Baker SC, Chudin E, Lieu MH, Oeser S, Bennett H, Rigault P, Barker D, McDaniel TK, Chee MS, Genome Res 2004 14 11 2347 2356 (Pubitemid 39517342)
24. Candidate genes for non-diabetic ESRD in African Americans: a genome-wide association study using pooled DNA. Bostrom MA, Lu L, Chou J, Hicks PJ, Xu J, Langefeld CD, Bowden DW, Freedman BI, Hum Genet 2010 128 2 195 204
25. Impact and quantification of the sources of error in DNA pooling designs. Jawaid A, Sham P, Ann Hum Genet 2009 73 1 118 24
26. Tackling the widespread and critical impact of batch effects in high-throughput data. Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry R, Nat Rev Genet 2010 11 10 733 739