Design considerations for massively parallel sequencing studies of complex human disease

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Feng, Bing Jian ^a   Tavtigian, Sean V ^b   Southey, Melissa C ^c   Goldgar, David E ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CHRONIC DISEASE; DISEASE PREDISPOSITION; EXOME; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC PROCEDURES; GENETIC SCREENING; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME; GENOTYPE; MASSIVELY PARALLEL SEQUENCING; PHENOTYPE; PROBABILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY;

ALLELES; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHENOTYPE;

EID: 79961151538     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023221     Document Type: Article

References (23)

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
2. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB, (2010) Rare variants create synthetic genome-wide associations. PLoS Biol 8: e1000294.
3. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42: 30-35.
4. Lalonde E, Albrecht S, Ha KC, Jacob K, Bolduc N, et al. (2010) Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing. Hum Mutat 31: 918-923.
5. Ng SB, Nickerson DA, Bamshad MJ, Shendure J, (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19: R119-124.
6. Stratton MR, Rahman N, (2008) The emerging landscape of breast cancer susceptibility. Nat Genet 40: 17-22.
7. McClellan J, King MC, (2010) Genetic heterogeneity in human disease. Cell 141: 210-217.
8. Breast Cancer Information Core (BIC) website (2009) Available: http://research.nhgri.nih.gov/bic/. Accessed 2009 Oct 30.
9. Bansal V, Libiger O, Torkamani A, Schork NJ, (2010) Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11: 773-785.
10. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832-838.
11. 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.
12. Madsen BE, Browning SR, (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5: e1000384.
13. Tavtigian SV, Byrnes GB, Goldgar DE, Thomas A, (2008) Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications. Hum Mutat 29: 1342-1354.
14. Cirulli ET, Goldstein DB, (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11: 415-425.
15. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276.
16. Skol AD, Scott LJ, Abecasis GR, Boehnke M, (2006) Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38: 209-213.
17. Lathrop GM, Lalouel JM, Julier C, Ott J, (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci U S A 81: 3443-3446.
18. Lathrop GM, Lalouel JM, (1984) Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 36: 460-465.
19. Ott J, (1989) Computer-simulation methods in human linkage analysis. Proc Natl Acad Sci U S A 86: 4175-4178.
20. Weeks DE, Ott J, Lathrop GM, (1990) SLINK: a general simulation program for linkage analysis. Am J Hum Genet 47: A204.
21. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
22. Liu DJ, Leal SM, (2010) Replication strategies for rare variant complex trait association studies via next-generation sequencing. Am J Hum Genet 87: 790-801.
23. Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR, (2009) Power of deep, all-exon resequencing for discovery of human trait genes. Proc Natl Acad Sci U S A 106: 3871-3876.