Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies

Nucleic Acids Research

Volumn 41, Issue 7, 2013, Pages

  Ramasamy, Adaikalavan ^a   Trabzuni, Daniah ^b,c   Raphael Gibbs, J ^b,d   Dillman, Allissa ^d   Hernandez, Dena G ^b,d   Arepalli, Sampath ^d   Walker, Robert ^e   Smith, Colin ^e   Ilori, Gigaloluwa Peter ^a   Shabalin, Andrey A ^f   Li, Yun ^f,g   Singleton, Andrew B ^d   Cookson, Mark R ^d   Hardy, John ^b   Ryten, Mina ^b   Weale, Michael E ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c KING FAISAL SPECIALIST HOSPITAL AND RESEARCH CENTER   (Saudi Arabia)

^d NATIONAL INSTITUTE ON AGING   (United States)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

^f IL   (United States)

^g UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CEREBELLUM; CONTROLLED STUDY; EUROPE; EXOME; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FRONTAL CORTEX; GENE SEQUENCE; GENETIC DATABASE; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; MOLECULAR PROBE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84876555533     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt069     Document Type: Article

References (39)

1. Cookson, W., Liang, L., Abecasis, G., Moffatt, M. and Lathrop, M. (2009) Mapping complex disease traits with global gene expression. Nat. Rev. Genet., 10, 184-194.
2. Cheung, V.G. and Spielman, R.S. (2009) Genetics of human gene expression: mapping DNA variants that influence gene expression. Nat. Rev. Genet., 10, 595-604.
3. Gilad, Y., Rifkin, S.A. and Pritchard, J.K. (2008) Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet., 24, 408-415.
4. Naiser, T., Ehler, O., Kayser, J., Mai, T., Michel, W. and Ott, A. (2008) Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges. BMC Biotechnol., 8, 48.
5. Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N. et al. (2011) AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol. Syst. Biol., 7, 522.
6. Vijaya Satya, R., Zavaljevski, N. and Reifman, J. (2012) A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Res, 40, e127.
7. Degner, J.F., Marioni, J.C., Pai, A.A., Pickrell, J.K., Nkadori, E., Gilad, Y. and Pritchard, J.K. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
8. Walter, N.A., McWeeney, S.K., Peters, S.T., Belknap, J.K., Hitzemann, R. and Buck, K.J. (2007) SNPs matter: impact on detection of differential expression. Nat. Methods, 4, 679-680. (Pubitemid 47338152)
9. Myers, A.J., Gibbs, J.R., Webster, J.A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P. et al. (2007) A survey of genetic human cortical gene expression. Nat. Genet., 39, 1494-1499. (Pubitemid 350191339)
10. Benovoy, D., Kwan, T. and Majewski, J. (2008) Effect of polymorphisms within probe-target sequences on olignonucleotide microarray experiments. Nucleic Acids Res., 36, 4417-4423.
11. Heinzen, E.L., Ge, D., Cronin, K.D., Maia, J.M., Shianna, K.V., Gabriel, W.N., Welsh-Bohmer, K.A., Hulette, C.M., Denny, T.N. and Goldstein, D.B. (2008) Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol., 6, e1.
12. Alberts, R., Terpstra, P., Li, Y., Breitling, R., Nap, J.P. and Jansen, R.C. (2007) Sequence polymorphisms cause many false cis eQTLs. PLoS One, 2, e622.
13. Gamazon, E.R., Zhang, W., Dolan, M.E. and Cox, N.J. (2010) Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset. PLoS One, 5, e9366.
14. Stranger, B.E., Montgomery, S.B., Dimas, A.S., Parts, L., Stegle, O., Ingle, C.E., Sekowska, M., Smith, G.D., Evans, D., Gutierrez-Arcelus, M. et al. (2012) Patterns of cis regulatory variation in diverse human populations. PLoS Genet., 8, e1002639.
15. (IPDGC), I.P.s.D.G.C. and (WTCCC2), W.T.C.C.C. (2011) A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genet, 7, e1002142.
16. Gibbs, J.R., van der Brug, M.P., Hernandez, D.G., Traynor, B.J., Nalls, M.A., Lai, S.L., Arepalli, S., Dillman, A., Rafferty, I.P., Troncoso, J. et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet., 6, e1000952.
17. Hernandez, D.G., Nalls, M.A., Moore, M., Chong, S., Dillman, A., Trabzuni, D., Gibbs, J.R., Ryten, M., Arepalli, S., Weale, M.E. et al. (2012) Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain. Neurobiol. Dis., 47, 20-28.
18. Trabzuni, D., Ryten, M., Walker, R., Smith, C., Imran, S., Ramasamy, A., Weale, M.E. and Hardy, J. (2011) Quality control parameters on a large dataset of regionally dissected human control brains for whole genome expression studies. J. Neurochem., 119, 275-282.
19. Shabalin, A.A. (2012) Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics, 28, 1353-1358.
20. Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
21. Rennie, C., Noyes, H.A., Kemp, S.J., Hulme, H., Brass, A. and Hoyle, D.C. (2008) Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays. BMC Genomics, 9, 317.
22. Vandrovcova, J., Anaya, F., Kay, V., Lees, A., Hardy, J. and de Silva, R. (2010) Disentangling the role of the tau gene locus in sporadic tauopathies. Curr. Alzheimer Res., 7, 726-734.
23. Bassuk, A.G., Wallace, R.H., Buhr, A., Buller, A.R., Afawi, Z., Shimojo, M., Miyata, S., Chen, S., Gonzalez-Alegre, P., Griesbach, H.L. et al. (2008) A homozygous mutation in human PRICKLE1 causes an autosomal-recessive progressive myoclonus epilepsy-ataxia syndrome. Am. J. Hum. Genet., 83, 572-581.
24. Nalls, M.A., Plagnol, V., Hernandez, D.G., Sharma, M., Sheerin, U.M., Saad, M., Simon-Sanchez, J., Schulte, C., Lesage, S., Sveinbjornsdottir, S. et al. (2011) Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet, 377, 641-649.
25. Trabzuni, D., Wray, S., Vandrovcova, J., Ramasamy, A., Walker, R., Smith, C., Luk, C., Gibbs, J.R., Dillman, A., Hernandez, D.G. et al. (2012) MAPT expression and splicing is differentially regulated by brain region: relation to genotype and implication for tauopathies. Hum. Mol. Genet., 21, 4094-4103.
26. Naiser, T., Kayser, J., Mai, T., Michel, W. and Ott, A. (2008) Position dependent mismatch discrimination on DNA microarrays-experiments and model. BMC Bioinformatics, 9, 509.
27. Pickrell, J.K., Marioni, J.C., Pai, A.A., Degner, J.F., Engelhardt, B.E., Nkadori, E., Veyrieras, J.B., Stephens, M., Gilad, Y. and Pritchard, J.K. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768-772.
28. Montgomery, S.B., Sammeth, M., Gutierrez-Arcelus, M., Lach, R.P., Ingle, C., Nisbett, J., Guigo, R. and Dermitzakis, E.T. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 464, 773-777.
29. Grundberg, E., Small, K.S., Hedman, A.K., Nica, A.C., Buil, A., Keildson, S., Bell, J.T., Yang, T.P., Meduri, E., Barrett, A. et al. (2012) Mapping cis-and trans-regulatory effects across multiple tissues in twins. Nat. Genet., 44, 1084-1089.
30. Zeller, T., Wild, P., Szymczak, S., Rotival, M., Schillert, A., Castagne, R., Maouche, S., Germain, M., Lackner, K., Rossmann, H. et al. (2010) Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One, 5, e10693.
31. Xia, K., Shabalin, A.A., Huang, S., Madar, V., Zhou, Y.H., Wang, W., Zou, F., Sun, W., Sullivan, P.F. and Wright, F.A. (2012) seeQTL: a searchable database for human eQTLs. Bioinformatics, 28, 451-452.
32. Yang, T.P., Beazley, C., Montgomery, S.B., Dimas, A.S., Gutierrez-Arcelus, M., Stranger, B.E., Deloukas, P. and Dermitzakis, E.T. (2010) Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics, 26, 2474-2476.
33. Zou, F., Chai, H.S., Younkin, C.S., Allen, M., Crook, J., Pankratz, V.S., Carrasquillo, M.M., Rowley, C.N., Nair, A.A., Middha, S. et al. (2012) Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. PLoS Genet., 8, e1002707.
34. Millar, T., Walker, R., Arango, J.C., Ironside, J.W., Harrison, D.J., MacIntyre, D.J., Blackwood, D., Smith, C. and Bell, J.E. (2007) Tissue and organ donation for research in forensic pathology: the MRC Sudden Death Brain and Tissue Bank. J. Pathol., 213, 369-375. (Pubitemid 350206508)
35. Beach, T.G., Sue, L.I., Walker, D.G., Roher, A.E., Lue, L., Vedders, L., Connor, D.J., Sabbagh, M.N. and Rogers, J. (2008) The Sun Health Research Institute Brain Donation Program: description and experience, 1987-2007. Cell Tissue Bank, 9, 229-245.
36. Wu, Z.J., Irizarry, R.A., Gentleman, R., Martinez-Murillo, F. and Spencer, F. (2004) A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc., 99, 909-917. (Pubitemid 39665934)
37. Li, Y., Willer, C., Sanna, S. and Abecasis, G. (2009) Genotype imputation. Annu. Rev. Genomics Hum. Genet., 10, 387-406.
38. Li, Y., Willer, C.J., Ding, J., Scheet, P. and Abecasis, G.R. (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol., 34, 816-834.
39. Barbosa-Morais, N.L., Dunning, M.J., Samarajiwa, S.A., Darot, J.F., Ritchie, M.E., Lynch, A.G. and Tavare, S. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res., 38, e17.