Hierarchical bayesian model for rare variant association analysis integrating genotype uncertainty in human sequence data

Genetic Epidemiology

Volumn 39, Issue 2, 2015, Pages 89-100

  He, Liang ^a   Pitkäniemi, Janne ^a,b   Sarin, Antti Pekka ^a,c   Salomaa, Veikko ^c   Sillanpää, Mikko J ^d   Ripatti, Samuli ^a,e  

^a UNIVERSITY OF HELSINKI   (Finland)

^b FINNISH CANCER REGISTRY   (Finland)

^c NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

^d UNIVERSITY OF OULU   (Finland)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Classification error; LDL C; Rare variant; Shrinkage based bayesian variable selection

Indexed keywords

ALLELE; ARTICLE; BAYES THEOREM; GENE FREQUENCY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; MATHEMATICAL ANALYSIS; MEASUREMENT ERROR; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE ANALYSIS; BIOLOGICAL MODEL; COMPUTER PROGRAM; FINLAND; GENETIC PREDISPOSITION; GENETICS; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HUMAN; NUCLEOTIDE SEQUENCE; UNCERTAINTY;

LDLR PROTEIN, HUMAN; LOW DENSITY LIPOPROTEIN CHOLESTEROL; LOW DENSITY LIPOPROTEIN RECEPTOR;

ALLELES; BASE SEQUENCE; BAYES THEOREM; CHOLESTEROL, LDL; FINLAND; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOTYPE; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MODELS, GENETIC; RECEPTORS, LDL; SOFTWARE; UNCERTAINTY;

EID: 84920971068     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21871     Document Type: Article

References (58)

1. Albert JH, Chib S. 1993. Bayesian analysis of binary and polychotomous response data. J Am Stat Assoc 88:669-679.
2. Andrews DF, Mallows CL. 1974. Scale mixtures of normal distributions. J R Stat Soc Ser B 36:99-102.
3. Ayers KL, Cordell HJ. 2013. Identification of grouped rare and common variants via penalized logistic regression. Genet Epidemiol 37:592-602.
4. Basu S, Pan W. 2011. Comparison of statistical tests for disease association with rare variants. Genet Epidemiol 35:606-619.
5. Browning BL, Browning SR. 2013. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194:459-471.
6. Che X, Xu S. 2010. Significance test and genome selection in Bayesian shrinkage analysis. Int J Plant Genomics 2010:893206.
7. Daye ZJ, Li H, Wei Z. 2012. A powerful test for multiple rare variants association studies that incorporates sequencing qualities. Nucleic Acids Res 40:e60.
8. Duane S, Kennedy AD, Pendleton BJ, Roweth D. 1987. Hybrid Monte Carlo. Phys Lett B 195:216-222.
9. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186-194.
10. Fawcett T. 2006. An introduction to ROC analysis. Pattern Recognit Lett 27:861-874.
11. Friedewald WT, Levy RI, Fredrickson DS. 1972. Estimation of the concentration of low-density lipoprotein cholesterol in plasma, without use of the preparative ultracentrifuge. Clin Chem 18:499-502.
12. Good IJ. 1992. The Bayes/non-Bayes compromise: a brief review. J Am Stat Assoc 87:597-606.
13. Gustafson P. 2003. Measurement Error and Misclassification in Statistics and Epidemiology: Impacts and Bayesian Adjustments. Boca Raton, FL: CRC Press.
14. He L, Sillanpää MJ, Ripatti S, Pitkäniemi J. 2014. Bayesian latent variable collapsing model for detecting rare variant interaction effect in twin study. Genet Epidemiol 38:310-324.
15. Hoerl AE, Kennard RW. 1970. Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12:55-67.
16. Holmes CC, Held L. 2006. Bayesian auxiliary variable models for binary and multinomial regression. Bayesian Anal 1:145-168.
17. Kärkkäinen HP, Sillanpää MJ. 2012. Back to basics for Bayesian model building in genomic selection. Genetics 191:969-987.
18. Kass RE, Raftery AE. 1995. Bayes factors. J Am Stat Assoc 90:773-795.
19. Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D and others. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 12:231.
20. Kinnamon DD, Hershberger RE, Martin ER. 2012. Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants. PLoS One 7:e30238.
21. Koivisto UM, Turtola H, Aalto-Setälä K, Top B, Frants RR, Kovanen PT, Syvänen AC, Kontula K. 1992. The familial hypercholesterolemia (FH)-North Karelia mutation of the low density lipoprotein receptor gene deletes seven nucleotides of exon 6 and is a common cause of FH in Finland. J Clin Invest 90:219.
22. Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CMT, Richards JB. 2012. The empirical power of rare variant association methods: results from Sanger sequencing in 1998 individuals. PLoS Genet 8:e1002496.
23. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang Z-Z, Bizon C, Lange EM, Smith JD, Turner EH and others. 2014. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet 94:233-245.
24. Ledergerber C, Dessimoz C. 2011. Base-calling for next-generation sequencing platforms. Brief Bioinform 12:489-497.
25. Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987-2993.
26. 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.
27. Li B, Leal SM. 2009. Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet 5:e1000481.
28. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
29. Liu DJ, Leal SM. 2010. A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet 6:e1001156.
30. MacKay DJ. 1992. Bayesian methods for adaptive models. Technical report. Pasadena, CA: California Institute of Technology.
31. MacKay DJ. 1994. Bayesian nonlinear modeling for the prediction competition. ASHRAE Trans 100:1053-1062.
32. Madsen BE, Browning SR. 2009. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384.
33. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M and others. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303.
34. Morris AP, Zeggini E. 2010. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193.
35. Neal RM. 1995. Bayesian learning for neural networks. Thesis, University of Toronto.
36. 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.
37. Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443-451.
38. Nummenmaa A, Auranen T, Hämäläinen MS, Jääskeläinen IP, Sams M, Vehtari A, Lampinen J. 2007. Automatic relevance determination based hierarchical Bayesian MEG inversion in practice. Neuroimage 37:876-889.
39. Park T, Casella G. 2008. The Bayesian lasso. J Am Stat Assoc 103:681-686.
40. Price AL, Kryukov GV, de Bakker PI, 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.
41. Qi YA, Minka TP, Picard RW, Ghahramani Z. 2004. Predictive Automatic Relevance Determination by Expectation Propagation. In Proceedings of the Twenty-First International Conference on Machine Learning (p. 85). New York, NY: ACM.
42. 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.
43. Schork NJ, Murray SS, Frazer KA, Topol EJ. 2009. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 19:212-219.
44. Sellke T, Bayarri MJ, Berger JO. 2001. Calibration of ρ values for testing precise null hypotheses. Am Stat 55:62-71.
45. Sham PC, Purcell SM. 2014. Statistical power and significance testing in large-scale genetic studies. Nat Rev Genet 15:335-346.
46. 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.
47. Tibshirani R. 1996. Regression shrinkage and selection via the lasso. J R Stat Soc Ser B 267-288.
48. Tipping ME. 2001. Sparse Bayesian learning and the relevance vector machine. J Mach Learn Res 1:211-244.
49. Vartiainen E, Laatikainen T, Peltonen M, Juolevi A, Männistö S, Sundvall J, Jousilahti P, Salomaa V, Valsta L, Puska P. 2010. Thirty-five-year trends in cardiovascular risk factors in Finland. Int J Epidemiol 39:504-518.
50. Vuorio AF, Turtola H, Piilahti K-M, Repo P, Kanninen T, Kontula K. 1997. Familial hypercholesterolemia in the Finnish north Karelia. A molecular, clinical, and genealogical Study. Arterioscler Thromb Vasc Biol 17:3127-3138.
51. Wen X. 2013. Robust Bayesian FDR control with Bayes factors. arXiv preprint. arXiv:13113981.
52. Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X. 2011. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89:82-93.
53. Xu C, Ladouceur M, Dastani Z, Richards JB, Ciampi A, Greenwood CMT. 2012. Multiple regression methods show great potential for rare variant association tests. PLoS One 7:e41694.
54. Yang X, Chockalingam SP, Aluru S. 2013. A survey of error-correction methods for next-generation sequencing. Brief Bioinform 14:56-66.
55. Yi N, Zhi D. 2011. Bayesian analysis of rare variants in genetic association studies. Genet Epidemiol 35:57-69.
56. Yi N, Liu N, Zhi D, Li J. 2011. Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects. PLoS Genet 7:e1002382.
57. Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zöllner S. 2010. Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am J Hum Genet 87:604-617.
58. Zuk O, Schaffner SF, Samocha K, Do R, Hechter RDE, Kathiresan S, Daly MJ, Neale BM, Sunyaev SR, Lander ES. 2014. Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci USA 111:E455-E464.