Discovering single nucleotide polymorphisms regulating human gene expression using allele specific expression from RNA-seq data

Genetics

Volumn 204, Issue 3, 2016, Pages 1057-1064

  Kang, Eun Yong ^a   Martin, Lisa J ^b   Mangul, Serghei ^a   Isvilanonda, Warin ^a   Zou, Jennifer ^a   Ben David, Eyal ^c   Han, Buhm ^d,e   Lusis, Aldons J ^b   Shifman, Sagiv ^c   Eskin, Eleazar ^a,b  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

^e BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Allele specific expression; Causal variants; Expression quantitative trait loci

Indexed keywords

ALLELE; ANALYTIC METHOD; ARTICLE; DATA ANALYSIS; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC VARIATION; GENOME ANALYSIS; HAPLOTYPE MAP; HUMAN; HUMAN CELL; LYMPHOBLASTOID CELL LINE; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; RNA SEQUENCE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; WESTERN EUROPEAN; ALGORITHM; CAUCASIAN; EUROPE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; IMMUNOPATHOLOGY; PROCEDURES; TUMOR CELL LINE;

TRANSCRIPTOME;

ALGORITHMS; ALLELES; CELL LINE, TUMOR; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENOME-WIDE ASSOCIATION STUDY; HAPMAP PROJECT; HUMANS; IMMUNE SYSTEM DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; QUANTITATIVE TRAIT LOCI; TRANSCRIPTOME;

EID: 84994881321     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.177246     Document Type: Article

References (37)

1. Bell, C. G., and S. Beck, 2009 Advances in the identification and analysis of allele-specific expression. Genome Med. 1: 56.
2. Bjornsson, H. T., T. J. Albert, C. M. Ladd-Acosta, R. D. Green, M. A. Rongione et al., 2008 Snp-specific array-based allele-specific expression analysis. Genome Res. 18: 771-779.
3. Boyle, A. P., E. L. Hong, M. Hariharan, Y. Cheng, M. A. Schaub et al., 2012 Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22: 1790-1797.
4. Castel, S. E., A. Levy-Moonshine, P. Mohammadi, E. Banks, and T. Lappalainen, 2015 Tools and best practices for data processing in allelic expression analysis. Genome Biol. 16: 1.
5. Cookson, W., L. Liang, G. Abecasis, M. Moffatt, and M. Lathrop, 2009 Mapping complex disease traits with global gene expression. Nat. Rev. Genet. 10: 184-194.
6. Daelemans, C., M. E. Ritchie, G. Smits, S. Abu-Amero, I. M. Sudbery et al., 2010 High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet. 11: 25.
7. Degner, J. F., J. C. Marioni, A. A. Pai, J. K. Pickrell, E. Nkadori et al., 2009 Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25: 3207-3212.
8. Eckersley-Maslin, M. A., and D. L. Spector, 2014 Random mono-allelic expression: regulating gene expression one allele at a time. Trends Genet. 30: 237-244.
9. Farber, C. R., J. E. Aten, E. A. Farber, V. de Vera, R. Gularte et al., 2009 Genetic dissection of a major mouse obesity QTL (Carfhg2): integration of gene expression and causality modeling. Physiol. Genomics 37: 294-302.
10. Francesconi, M., and B. Lehner, 2014 The effects of genetic variation on gene expression dynamics during development. Nature 505: 208-211.
11. Gaffney, D. J., J.-B. B. Veyrieras, J. F. Degner, R. Pique-Regi, A. A. Pai et al., 2012 Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 13: R7.
12. Ge, B., D. K. Pokholok, T. Kwan, E. Grundberg, L. Morcos et al., 2009 Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat. Genet. 41: 1216-1222.
13. Ghazalpour, A., S. Doss, H. Kang, C. Farber, P.-Z. Z. Wen et al., 2008 High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet. 4: e1000149.
14. Gregg, C., J. Zhang, J. E. Butler, D. Haig, and C. Dulac, 2010 Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329: 682-685.
15. Hayes, K. R., B. M. Young, and M. T. Pletcher, 2009 Expression quantitative trait loci mapping identifies new genetic models of glutathione S-transferase variation. Drug Metab. Dispos. 37: 1269-1276.
16. Heap, G. A., J. H. M. Yang, K. Downes, B. C. Healy, K. A. Hunt et al., 2010 Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum. Mol. Genet. 19: 122-134.
17. Hill, M. J., E. Kenny, S. Roche, D. W. Morris, A. Corvin et al., 2011 Allelic expression imbalance of the schizophrenia susceptibility gene CHI311: evidence of cis-acting variation and tissue specific regulation. Psychiatr. Genet. 21: 281-286.
18. Jiménez-Gómez, J. M., A. D. Wallace, and J. N. Maloof, 2010 Network analysis identifies ELF3 as a QTL for the shade avoidance response in arabidopsis. PLoS Genet. 6: e1001100.
19. Kabakchiev, B., and M. S. Silverberg, 2013 Expression quantitative trait loci analysis identifies associations between genotype and gene expression in human intestine. Gastroenterology 144: 1488-1496, 1496.e1-3.
20. Lappalainen, T., M. Sammeth, M. R. Friedländer, P. A. C. ’t Hoen, J. Monlong et al., 2013 Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501: 506-511.
21. Montgomery, S. B., M. Sammeth, M. Gutierrez-Arcelus, R. P. Lach, C. Ingle et al., 2010 Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
22. Montgomery, S. B., T. Lappalainen, M. Gutierrez-Arcelus, and E. T. Dermitzakis, 2011 Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet. 7: e1002144.
23. Palacios, R., E. Gazave, J. Goñi, G. Piedrafita, O. Fernando et al., 2009 Allele-specific gene expression is widespread across the genome and biological processes. PLoS One 4: e4150.
24. Pastinen, T., 2010 Genome-wide allele-specific analysis: insights into regulatory variation. Nat. Rev. Genet. 11: 533-538.
25. Ritchie, M. E., M. S. Forrest, A. S. Dimas, C. Daelemans, E. T. Dermitzakis et al., 2010 Data analysis issues for allele-specific expression using Illumina’s GoldenGate assay. BMC Bioinformatics 11: 280.
26. Serre, D., S. Gurd, B. Ge, R. Sladek, D. Sinnett et al., 2008 Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet. 4: e1000006.
27. Steibel, J. P., R. O. Bates, G. J. Rosa, R. J. Tempelman, V. D. Rilington et al., 2011 Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS One 6: e16766.
28. Stevenson, K. R., J. D. Coolon, and P. J. Wittkopp, 2013 Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome. BMC Genomics 14: 536.
29. Sun, C., C. Southard, D. B. Witonsky, O. I. Olopade, and A. Di Rienzo, 2010 Allelic imbalance (AI) identifies novel tissue-specific cisregulatory variation for human UGT2B15. Hum. Mutat. 31: 99-107.
30. Sun, W., 2011 A statistical framework for eQTL mapping using RNA-seq data. Biometrics 68: 1-11.
31. Tao, H., D. R. Cox, and K. A. Frazer, 2006 Allele-specific KRT1 expression is a complex trait. PLoS Genet. 2(6): e93.
32. van de Geijn, B., G. McVicker, Y. Gilad, and J. K. Pritchard, 2015 Wasp: allele-specific software for robust molecular quantitative trait locus discovery. Nat. Methods 12: 1061-1063.
33. van Nas, A., L. Ingram-Drake, J. S. Sinsheimer, S. S. Wang, E. E. Schadt et al., 2010 Expression quantitative trait loci: replication, tissue- and sex-specificity in mice. Genetics 185: 1059-1068.
34. Veyrieras, J.-B., S. Kudaravalli, S. Y. Kim, E. T. Dermitzakis, Y. Gilad et al., 2008 High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4: e1000214.
35. Wagner, J. R., B. Ge, D. Pokholok, K. L. Gunderson, T. Pastinen et al., 2010 Computational analysis of whole-genome differential allelic expression data in human. PLOS Comput. Biol. 6: e1000849.
36. Wolff, P., I. Weinhofer, J. Seguin, P. Roszak, C. Beisel et al., 2011 High-resolution analysis of parent-of-origin allelic expression in the arabidopsis endosperm. PLoS Genet. 7: e1002126.
37. Yan, H., W. Yuan, V. E. Velculescu, B. Vogelstein, and K. W. Kinzler, 2002 Allelic variation in human gene expression. Science 297: 1143.