Analysis and Optimal Design for Association Studies Using Next-Generation Sequencing With Case-Control Pools

Genetic Epidemiology

Volumn 36, Issue 8, 2012, Pages 870-881

  Liang, Wei E ^a   Thomas, Duncan C ^a   Conti, David V ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Genetic association studies; Rare variants; Sequencing

Indexed keywords

ARTICLE; BAYES THEOREM; COST EFFECTIVENESS ANALYSIS; EFFECT SIZE; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOTYPE; HUMAN; NEXT GENERATION SEQUENCE; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; CASE CONTROL STUDY; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; METHODOLOGY; PROCEDURES; REPRODUCIBILITY;

BAYES THEOREM; CASE-CONTROL STUDIES; GENE FREQUENCY; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SAMPLE SIZE; SEQUENCE ANALYSIS, DNA;

EID: 84869112617     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21681     Document Type: Article

References (21)

1. Druley TE, Vallania FLM, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. 2009. Quantification of rare allelic variants from pooled genomic DNA. Nat Meth 6:263-265.
2. Erlich Y, Chang K, Gordon A, Ronen R, Navon O, Rooks M, Hannon GJ. 2009. DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 19:1243-1253.
3. Frazer KA, Murray SS, Schork NJ, Topol EJ. 2009. Human genetic variation and its contribution to complex traits. Nat Rev Genet 10:241-251.
4. Futschik A, Schlotterer C. 2010. Massively parallel sequencing of pooled DNA samples-the next generation of molecular markers. Genetics 186(1):207-218.
5. Gauderman W. 2002. Sample size requirements for association studies of gene-gene interaction. Am J Epidemiol 25(4):327-338.
6. Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R. 2010. Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol 34:479-491.
7. Lee JS, Choi M, Yan X, Lifton RP, Zhao H. 2011. On optimal pooling designs to identify rare variants through massive resequencing. Genet Epidemiol 35:139-147.
8. Li B, Leal SM. 2008. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321.
9. Lupton MK, Proitsi P, Danillidou M, Tsolaki M, Hamilton G, Wroe R, Pritchard M, Lord K, Martin BM, Kloszewska I, Soininen H, Mecocci P, Vellas B, Harold D, Hollingworth P, Lovestone S, Powell JF. 2011. Deep sequencing of the nicastrin gene in pooled DNA, the identification of genetic variants that affect risk of Alzheimer's disease. PLoS ONE 6:e17298.
10. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
11. Morris AP, Zeggini E. 2009. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193.
12. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ. 2011. Testing for an unusual distribution of rare variants. PLoS Genet 7:e1001322.
13. Out AA, van Minderhout IJHM, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PEM, Tops CMJ, Breuning MH, van Ommen G-JB, Dunnen den JT, Devilee P, Hes FJ. 2009. Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 30:1703-1712.
14. Prabhu S, Pe'er I. 2009. Overlapping pools for high-throughput targeted resequencing. Genome Res 19:1254-1261.
15. Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, Wei L-J, Sunyaev SR. 2010. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86:832-838.
16. Quintana MA, Berstein JL, Thomas DC, Conti DV. 2011. Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol 35:638-649.
17. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145.
18. Shental N, Amir A, Zuk O. 2010. Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Research 38(19):e179.
19. Smith AM, Heisler LE, St Onge RP, Farias-Hesson E, Wallace IM, Bodeau J, Harris AN, Perry KM, Giaever G, Pourmand N, Nislow C. 2010. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38:e142-e142.
20. Wang T, Pradhan K, Ye K, Wong L-J, Rohan TE. 2011. Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples. Front Genet 2:51.
21. Zhao Y, Wang S. 2009. Optimal DNA pooling-based two-stage designs in case-control association studies. Hum Hered 67:46-56.