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Volumn 31, Issue 8, 2015, Pages 1235-1242

QuASAR: Quantitative allele-specific analysis of reads

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84927739680     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu802     Document Type: Article
Times cited : (59)

References (41)
  • 1
    • 84856387609 scopus 로고    scopus 로고
    • Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection
    • Barreiro, L. B. et al. (2012) Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc. Natl Acad. Sci. USA, 109, 1204-1209.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 1204-1209
    • Barreiro, L.B.1
  • 2
    • 84868198825 scopus 로고    scopus 로고
    • Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression
    • Cowper-Sal lari, R. et al. (2012) Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat. Genet., 44, 1191-1198.
    • (2012) Nat. Genet. , vol.44 , pp. 1191-1198
    • Cowper-Sallari, R.1
  • 3
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allelespecific expression from RNA-sequencing data
    • Degner, J. F. et al. (2009) Effect of read-mapping biases on detecting allelespecific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
    • (2009) Bioinformatics , vol.25 , pp. 3207-3212
    • Degner, J.F.1
  • 4
    • 84857111200 scopus 로고    scopus 로고
    • DNaseI sensitivity QTLs are a major determinant of human expression variation
    • Degner, J. F. et al. (2012) DNaseI sensitivity QTLs are a major determinant of human expression variation. Nature, 482, 390-394.
    • (2012) Nature , vol.482 , pp. 390-394
    • Degner, J.F.1
  • 5
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M. A. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • Depristo, M.A.1
  • 7
    • 69949176863 scopus 로고    scopus 로고
    • Common regulatory variation impacts gene expression in a cell type-dependent manner
    • Dimas, A. S. et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science, 325, 1246-1250.
    • (2009) Science , vol.325 , pp. 1246-1250
    • Dimas, A.S.1
  • 8
    • 78649783848 scopus 로고    scopus 로고
    • Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals
    • Ding, J. et al. (2010) Gene expression in skin and lymphoblastoid cells: refined statistical method reveals extensive overlap in cis-eQTL signals. Am. J. Hum. Genet., 87, 779-789.
    • (2010) Am. J. Hum. Genet. , vol.87 , pp. 779-789
    • Ding, J.1
  • 9
    • 84860505950 scopus 로고    scopus 로고
    • Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data
    • Duitama, J. et al. (2012) Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. BMC Genomics, 13(Suppl. 2), S6.
    • (2012) BMC Genomics , vol.13 , pp. S6
    • Duitama, J.1
  • 10
    • 84896742056 scopus 로고    scopus 로고
    • Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression
    • Fairfax, B. P. et al. (2014) Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science, 343, 1246949.
    • (2014) Science , vol.343 , pp. 1246949
    • Fairfax, B.P.1
  • 11
    • 77953223693 scopus 로고    scopus 로고
    • Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain
    • Gibbs, J. R. et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet., 6, e1000952.
    • (2010) PLoS Genet. , vol.6 , pp. e1000952
    • Gibbs, J.R.1
  • 12
    • 57149114936 scopus 로고    scopus 로고
    • Genetics meets metabolomics: A genome-wide association study of metabolite profiles in human serum
    • Gieger, C. et al. (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet., 4, e1000282.
    • (2008) PLoS Genet. , vol.4 , pp. e1000282
    • Gieger, C.1
  • 13
    • 79851479498 scopus 로고    scopus 로고
    • Global analysis of the impact of environmental perturbation on cis-regulation of gene expression
    • Grundberg, E. et al. (2011) Global analysis of the impact of environmental perturbation on cis-regulation of gene expression. PLoS Genet., 7, e1001279.
    • (2011) PLoS Genet. , vol.7 , pp. e1001279
    • Grundberg, E.1
  • 14
    • 84902068590 scopus 로고    scopus 로고
    • Allele-specific expression and eQTL analysis in mouse adipose tissue
    • Hasin-Brumshtein, Y. et al. (2014) Allele-specific expression and eQTL analysis in mouse adipose tissue. BMC Genomics, 15, 471.
    • (2014) BMC Genomics , vol.15 , pp. 471
    • Hasin-Brumshtein, Y.1
  • 15
    • 77950833803 scopus 로고    scopus 로고
    • Variation in transcription factor binding among humans
    • Kasowski, M. et al. (2010) Variation in transcription factor binding among humans. Science, 328, 232-235.
    • (2010) Science , vol.328 , pp. 232-235
    • Kasowski, M.1
  • 16
    • 78649714014 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying isoform regulation
    • Katz, Y. et al. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
    • (2010) Nat. Methods , vol.7 , pp. 1009-1015
    • Katz, Y.1
  • 17
    • 84901624486 scopus 로고    scopus 로고
    • Allelic expression of deleterious protein-coding variants across human tissues
    • Kukurba, K. R. et al. (2014) Allelic expression of deleterious protein-coding variants across human tissues. PLoS Genet., 10, e1004304.
    • (2014) PLoS Genet. , vol.10 , pp. e1004304
    • Kukurba, K.R.1
  • 18
    • 84885645853 scopus 로고    scopus 로고
    • Transcriptome and genome sequencing uncovers functional variation in humans
    • Lappalainen, T. et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501, 506-511.
    • (2013) Nature , vol.501 , pp. 506-511
    • Lappalainen, T.1
  • 19
    • 84896759364 scopus 로고    scopus 로고
    • Common genetic variants modulate pathogen-sensing responses in human dendritic cells
    • Lee, M. N. et al. (2014) Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science, 343, 1246980.
    • (2014) Science , vol.343 , pp. 1246980
    • Lee, M.N.1
  • 20
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 21
    • 79960967243 scopus 로고    scopus 로고
    • Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes
    • Maranville, J. C. et al. (2011) Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet., 7, e1002162.
    • (2011) PLoS Genet. , vol.7 , pp. e1002162
    • Maranville, J.C.1
  • 22
    • 77950854479 scopus 로고    scopus 로고
    • Heritable individual-specific and allele-specific chromatin signatures in humans
    • McDaniell, R. et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science, 328, 235-239.
    • (2010) Science , vol.328 , pp. 235-239
    • McDaniell, R.1
  • 24
    • 84887322043 scopus 로고    scopus 로고
    • Identification of genetic variants that affect histone modifications in human cells
    • McVicker, G. et al. (2013) Identification of genetic variants that affect histone modifications in human cells. Science, 342, 747-749.
    • (2013) Science , vol.342 , pp. 747-749
    • McVicker, G.1
  • 25
    • 44949201115 scopus 로고    scopus 로고
    • A genome-wide association study identifies protein quantitative trait loci (pQTLs)
    • Melzer, D. et al. (2008) A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet., 4, e1000072.
    • (2008) PLoS Genet. , vol.4 , pp. e1000072
    • Melzer, D.1
  • 26
    • 77952367694 scopus 로고    scopus 로고
    • Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations
    • Nica, A. C. et al. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet., 6, e1000895.
    • (2010) PLoS Genet. , vol.6 , pp. e1000895
    • Nica, A.C.1
  • 27
    • 79952256739 scopus 로고    scopus 로고
    • The architecture of gene regulatory variation across multiple human tissues: The MuTHER study
    • Nica, A. C. et al. (2011) The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet., 7, e1002003.
    • (2011) PLoS Genet. , vol.7 , pp. e1002003
    • Nica, A.C.1
  • 28
    • 77951439152 scopus 로고    scopus 로고
    • Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery fromGWAS
    • Nicolae, D. L. et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery fromGWAS. PLoS Genet., 6, e1000888.
    • (2010) PLoS Genet. , vol.6 , pp. e1000888
    • Nicolae, D.L.1
  • 29
    • 77954763156 scopus 로고    scopus 로고
    • Genome-wide allele-specific analysis: Insights into regulatory variation
    • Pastinen, T. (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nat. Rev. Genet., 11, 533-538.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 533-538
    • Pastinen, T.1
  • 30
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • Pickrell, J. K. et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768-772.
    • (2010) Nature , vol.464 , pp. 768-772
    • Pickrell, J.K.1
  • 31
    • 84885300845 scopus 로고    scopus 로고
    • Reliable identification of genomic variants from RNAseq data
    • Piskol, R. et al. (2013) Reliable identification of genomic variants from RNAseq data. Am. J. Hum. Genet., 93, 641-651.
    • (2013) Am. J. Hum. Genet. , vol.93 , pp. 641-651
    • Piskol, R.1
  • 32
    • 84859916280 scopus 로고    scopus 로고
    • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
    • Reddy, T. E. et al. (2012) Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res., 22, 860-869.
    • (2012) Genome Res. , vol.22 , pp. 860-869
    • Reddy, T.E.1
  • 33
    • 33845365768 scopus 로고    scopus 로고
    • Maximum likelihood inference of imprinting and allele-specific expression from EST data
    • Seoighe, C. et al. (2006) Maximum likelihood inference of imprinting and allele-specific expression from EST data. Bioinformatics, 22, 3032-3039.
    • (2006) Bioinformatics , vol.22 , pp. 3032-3039
    • Seoighe, C.1
  • 34
    • 70349969478 scopus 로고    scopus 로고
    • Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
    • Shah, S. P. et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809-813.
    • (2009) Nature , vol.461 , pp. 809-813
    • Shah, S.P.1
  • 35
    • 80053522581 scopus 로고    scopus 로고
    • A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Skelly, D. A. et al. (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res., 21, 1728-1737.
    • (2011) Genome Res. , vol.21 , pp. 1728-1737
    • Skelly, D.A.1
  • 36
    • 65249170333 scopus 로고    scopus 로고
    • Genetic analysis of radiation-induced changes in human gene expression
    • Smirnov, D. A. et al. (2009) Genetic analysis of radiation-induced changes in human gene expression. Nature, 459, 587-591.
    • (2009) Nature , vol.459 , pp. 587-591
    • Smirnov, D.A.1
  • 38
    • 34548738566 scopus 로고    scopus 로고
    • Population genomics of human gene expression
    • Stranger, B. E. et al. (2007) Population genomics of human gene expression. Nat. Genet., 39, 1217-1224.
    • (2007) Nat. Genet. , vol.39 , pp. 1217-1224
    • Stranger, B.E.1
  • 39
    • 84856753476 scopus 로고    scopus 로고
    • A statistical framework for eQTL mapping using RNA-seq data
    • Sun, W. (2012) A statistical framework for eQTL mapping using RNA-seq data. Biometrics, 68, 1-11.
    • (2012) Biometrics , vol.68 , pp. 1-11
    • Sun, W.1
  • 40
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 41
    • 84930450065 scopus 로고    scopus 로고
    • Cross-population meta-analysis of eQTLs: Fine mapping and functional study
    • Wen, X. et al. (2014) Cross-population meta-analysis of eQTLs: fine mapping and functional study. bioRxiv. doi 10. 1101/008797.
    • (2014) BioRxiv.
    • Wen, X.1


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