Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data

Overview

Journal Annu Rev Stat Appl

Publisher Annual Reviews

Specialty Public Health

Date 2014 Jun 24

PMID 24955378

Citations 16

Authors

Kenneth Lange

Jeanette C Papp

Janet S Sinsheimer

Eric M Sobel

Affiliations

Soon will be listed here.

Abstract

Statistical genetics is undergoing the same transition to big data that all branches of applied statistics are experiencing. With the advent of inexpensive DNA sequencing, the transition is only accelerating. This brief review highlights some modern techniques with recent successes in statistical genetics. These include: (a) lasso penalized regression and association mapping, (b) ethnic admixture estimation, (c) matrix completion for genotype and sequence data, (d) the fused lasso and copy number variation, (e) haplotyping, (f) estimation of relatedness, (g) variance components models, and (h) rare variant testing. For more than a century, genetics has been both a driver and beneficiary of statistical theory and practice. This symbiotic relationship will persist for the foreseeable future.

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References

Browning S, Browning B . Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81(5):1084-97. PMC: 2265661. DOI: 10.1086/521987. View

Morgenthaler S, Thilly W . A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res. 2006; 615(1-2):28-56. DOI: 10.1016/j.mrfmmm.2006.09.003. View

Neale B, Rivas M, Voight B, Altshuler D, Devlin B, Orho-Melander M . Testing for an unusual distribution of rare variants. PLoS Genet. 2011; 7(3):e1001322. PMC: 3048375. DOI: 10.1371/journal.pgen.1001322. View

Asimit J, Day-Williams A, Morris A, Zeggini E . ARIEL and AMELIA: testing for an accumulation of rare variants using next-generation sequencing data. Hum Hered. 2012; 73(2):84-94. PMC: 3477640. DOI: 10.1159/000336982. View

Alexander D, Lange K . Stability selection for genome-wide association. Genet Epidemiol. 2011; 35(7):722-8. DOI: 10.1002/gepi.20623. View

Lee S, Wray N, Goddard M, Visscher P . Estimating missing heritability for disease from genome-wide association studies. Am J Hum Genet. 2011; 88(3):294-305. PMC: 3059431. DOI: 10.1016/j.ajhg.2011.02.002. View

Visscher P, Brown M, McCarthy M, Yang J . Five years of GWAS discovery. Am J Hum Genet. 2012; 90(1):7-24. PMC: 3257326. DOI: 10.1016/j.ajhg.2011.11.029. View

Behar D, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J . The genome-wide structure of the Jewish people. Nature. 2010; 466(7303):238-42. DOI: 10.1038/nature09103. View

Li B, Leal S . Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008; 83(3):311-21. PMC: 2842185. DOI: 10.1016/j.ajhg.2008.06.024. View

10.

Cantor R, Lange K, Sinsheimer J . Prioritizing GWAS results: A review of statistical methods and recommendations for their application. Am J Hum Genet. 2010; 86(1):6-22. PMC: 2801749. DOI: 10.1016/j.ajhg.2009.11.017. View

11.

Liu D, Leal S . A unified framework for detecting rare variant quantitative trait associations in pedigree and unrelated individuals via sequence data. Hum Hered. 2012; 73(2):105-22. PMC: 3369372. DOI: 10.1159/000336293. View

12.

Lange K, Papp J, Sinsheimer J, Sripracha R, Zhou H, Sobel E . Mendel: the Swiss army knife of genetic analysis programs. Bioinformatics. 2013; 29(12):1568-70. PMC: 3673222. DOI: 10.1093/bioinformatics/btt187. View

13.

Friedman J, Hastie T, Tibshirani R . Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010; 33(1):1-22. PMC: 2929880. View

14.

Price A, Kryukov G, de Bakker P, Purcell S, Staples J, Wei L . Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010; 86(6):832-8. PMC: 3032073. DOI: 10.1016/j.ajhg.2010.04.005. View

15.

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

16.

Almasy L, Blangero J . Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998; 62(5):1198-211. PMC: 1377101. DOI: 10.1086/301844. View

17.

Bacanu S, Nelson M, Whittaker J . Comparison of statistical tests for association between rare variants and binary traits. PLoS One. 2012; 7(8):e42530. PMC: 3415421. DOI: 10.1371/journal.pone.0042530. View

18.

Mazumder R, Friedman J, Hastie T . : Coordinate Descent With Nonconvex Penalties. J Am Stat Assoc. 2015; 106(495):1125-1138. PMC: 4286300. DOI: 10.1198/jasa.2011.tm09738. View

19.

Henn B, Gignoux C, Jobin M, Granka J, Macpherson J, Kidd J . Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci U S A. 2011; 108(13):5154-62. PMC: 3069156. DOI: 10.1073/pnas.1017511108. View

20.

Day-Williams A, Blangero J, Dyer T, Lange K, Sobel E . Linkage analysis without defined pedigrees. Genet Epidemiol. 2011; 35(5):360-70. PMC: 3290352. DOI: 10.1002/gepi.20584. View