Mark Abney, Ph.D.

Research Associate (Associate Professor)

Research Description

My research focus is on developing both new statistical methods and computational techniques to overcome the difficult problems in the analysis of genetic data, with the objective of the methods being to find genes that influence complex traits. A primary interest is on developing models and approximations that are highly computationally efficient while leveraging as much of the information in the data as possible. Ultimately, application of these methods help us to discover the regions of the genome that contribute to a trait's variability.

Some specific interests include:

  • Development of linear mixed model and generalized linear mixed model approaches to the analysis of genomic data.
  • Identification of shared genomic regions between individuals who are members of an isolated population and may be either cryptically related or related through a known genealogy.
  • Application of our complex trait mapping methods to human and model organism (e.g. mouse) data sets.

Selected Publications

Directional dominance on stature and cognition in diverse human populations.
Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W, Okada Y, Stancakova A, Faul JD, Zhao W, Bartz TM, Concas MP, Franceschini N, Enroth S, Vitart V, Trompet S, Guo X, Chasman DI, O'Connel JR, Corre T, Nongmaithem SS, Chen Y, Mangino M, Ruggiero D, Traglia M, Farmaki AE, Kacprowski T, Bjonnes A, van der Spek A, Wu Y, Giri AK, Yanek LR, Wang L, Hofer E, Rietveld CA, McLeod O, Cornelis MC, Pattaro C, Verweij N, Baumbach C, Abdellaoui A, Warren HR, Vuckovic D, Mei H, Bouchard C, Perry JR, Cappellani S, Mirza SS, Benton MC, Broeckel U, Medland SE, Lind PA, Malerba G, Drong A, Yengo L, Bielak LF, Zhi D, van der Most PJ, Shriner D, Magi R, Hemani G, Karaderi T, Wang Z, Liu T, Demuth I, Zhao JH, Meng W, Lataniotis L, van der Laan SW, Bradfield JP, Wood AR, Bonnefond A, Ahluwalia TS, Hall LM, Salvi E, Yazar S, Carstensen L, de Haan HG, Abney M, Afzal U, Allison MA, Amin N, et al.
(2015 Jul) Nature. 2015 Jul 23;523(7561):459-62. doi: 10.1038/nature14618. Epub 2015 Jul 1. 26131930 (Full Text)

Permutation testing in the presence of polygenic variation.
Abney M
(2015 May) Genet Epidemiol. 2015 May;39(4):249-58. doi: 10.1002/gepi.21893. Epub 2015 Mar 10. 25758362 (Full Text)

High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice.
Parker CC, Carbonetto P, Sokoloff G, Park YJ, Abney M, Palmer AA
(2014 Sep) Genetics. 2014 Sep;198(1):103-16. doi: 10.1534/genetics.114.167056. 25236452 (Full Text)

Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.
Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF Jr, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE
(2014) PLoS One. 2014 Aug 12;9(8):e104396. doi: 10.1371/journal.pone.0104396. eCollection 2014. 25116239 (Full Text)

Genome-wide association study of lung function phenotypes in a founder population.
Yao TC, Du G, Han L, Sun Y, Hu D, Yang JJ, Mathias R, Roth LA, Rafaels N, Thompson EE, Loisel DA, Anderson R, Eng C, Arruabarrena Orbegozo M, Young M, Klocksieben JM, Anderson E, Shanovich K, Lester LA, Williams LK, Barnes KC, Burchard EG, Nicolae DL, Abney M, Ober C
(2014 Jan) J Allergy Clin Immunol. 2014 Jan;133(1):248-55.e1-10. doi: 10.1016/j.jaci.2013.06.018. Epub 2013 Aug 6. 23932459 (Full Text)

Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies.
Cheng R, Parker CC, Abney M, Palmer AA
(2013 Oct) G3 (Bethesda). 2013 Oct 3;3(10):1861-7. doi: 10.1534/g3.113.007948. 23979941 (Full Text)

Using identity by descent estimation with dense genotype data to detect positive selection.
Han L, Abney M
(2013 Feb) Eur J Hum Genet. 2013 Feb;21(2):205-11. doi: 10.1038/ejhg.2012.148. Epub 2012 Jul 11. 22781100 (Full Text)

Estimating the human mutation rate using autozygosity in a founder population.
Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O'Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE
(2012 Nov) Nat Genet. 2012 Nov;44(11):1277-81. doi: 10.1038/ng.2418. Epub 2012 Sep 23. 23001126 (Full Text)

GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations.
Stanhope SA, Abney M
(2012 Jun) Bioinformatics. 2012 Jun 1;28(11):1553-4. doi: 10.1093/bioinformatics/bts190. Epub 2012 Apr 19. 22522135 (Full Text)

Fine-mapping alleles for body weight in LG/J x SM/J F(2) and F(34) advanced intercross lines.
Parker CC, Cheng R, Sokoloff G, Lim JE, Skol AD, Abney M, Palmer AA
(2011 Oct) Mamm Genome. 2011 Oct;22(9-10):563-71. doi: 10.1007/s00335-011-9349-z. Epub 2011 Jul 15. 21761260 (Full Text)

Identity by descent estimation with dense genome-wide genotype data.
Han L, Abney M
(2011 Sep) Genet Epidemiol. 2011 Sep;35(6):557-67. doi: 10.1002/gepi.20606. Epub 2011 Jul 18. 21769932 (Full Text)

Genetic variance components estimation for binary traits using multiple related individuals.
Papachristou C, Ober C, Abney M
(2011 Jul) Genet Epidemiol. 2011 Jul;35(5):291-302. doi: 10.1002/gepi.20577. Epub 2011 Apr 4. 21465547 (Full Text)

The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate.
Kosova G, Pickrell JK, Kelley JL, McArdle PF, Shuldiner AR, Abney M, Ober C
(2010 Jun) PLoS Genet. 2010 Jun 3;6(6):e1000974. doi: 10.1371/journal.pgen.1000974. 20532200 (Full Text)

Colloquium papers: Heritability of reproductive fitness traits in a human population.
Kosova G, Abney M, Ober C
(2010 Jan) Proc Natl Acad Sci U S A. 2010 Jan 26;107 Suppl 1:1772-8. doi: 10.1073/pnas.0906196106. Epub 2009 Oct 12. 19822755 (Full Text)

A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients.
Abney M
(2009 Jun) Bioinformatics. 2009 Jun 15;25(12):1561-3. doi: 10.1093/bioinformatics/btp185. Epub 2009 Apr 9. 19359355 (Full Text)

Identity-by-descent estimation and mapping of qualitative traits in large, complex pedigrees.
Abney M
(2008 Jul) Genetics. 2008 Jul;179(3):1577-90. doi: 10.1534/genetics.108.089912. Epub 2008 Jul 13. 18622032 (Full Text)

Heritability estimation of sex-specific effects on human quantitative traits.
Pan L, Ober C, Abney M
(2007 May) Genet Epidemiol. 2007 May;31(4):338-47. 17323368

The sex-specific genetic architecture of quantitative traits in humans.
Weiss LA, Pan L, Abney M, Ober C
(2006 Feb) Nat Genet. 2006 Feb;38(2):218-22. Epub 2006 Jan 22. 16429159

Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites.
Abney M, Ober C, McPeek MS
(2002 Apr) Am J Hum Genet. 2002 Apr;70(4):920-34. Epub 2002 Mar 4. 11880950 (Full Text)

The genetic dissection of complex traits in a founder population.
Ober C, Abney M, McPeek MS
(2001 Nov) Am J Hum Genet. 2001 Nov;69(5):1068-79. Epub 2001 Oct 3. 11590547 (Full Text)

Broad and narrow heritabilities of quantitative traits in a founder population.
Abney M, McPeek MS, Ober C
(2001 May) Am J Hum Genet. 2001 May;68(5):1302-7. Epub 2001 Apr 10. 11309690 (Full Text)

Detection of mis-specified relationships in inbred and outbred pedigrees.
Sun L, Abney M, McPeek MS
(2001) Genet Epidemiol. 2001;21 Suppl 1:S36-41. 11793699

Estimation of variance components of quantitative traits in inbred populations.
Abney M, McPeek MS, Ober C
(2000 Feb) Am J Hum Genet. 2000 Feb;66(2):629-50. 10677322 (Full Text)