Transcriptome genetics using second generation sequencing in a Caucasian population (original) (raw)

• Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423–428 (2008)
  Article CAS ADS PubMed Google Scholar
• Göring, H. H. et al. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nature Genet. 39, 1208–1216 (2007)
  Article PubMed Google Scholar
• Moffatt, M. F. et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448, 470–473 (2007)
  Article CAS ADS PubMed Google Scholar
• Morley, M. et al. Genetic analysis of genome-wide variation in human gene expression. Nature 430, 743–747 (2004)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848–853 (2007)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Wilhelm, B. T. et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453, 1239–1243 (2008)
  Article CAS ADS PubMed Google Scholar
• Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet. 10, 57–63 (2009)
  Article CAS PubMed Google Scholar
• Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628 (2008)
  CAS PubMed Google Scholar
• Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956–960 (2008)
  Article CAS ADS PubMed Google Scholar
• ’t Hoen, P. A. C. et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 36, e141 (2008)
  Article PubMed PubMed Central Google Scholar
• Maher, C. A. et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 458, 97–101 (2009)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genet. 40, 1413–1415 (2008)
  Article CAS PubMed Google Scholar
• Cloonan, N. et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 5, 613–619 (2008)
  Article CAS PubMed Google Scholar
• Frazer, K. A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–861 (2007)
  Article CAS ADS PubMed Google Scholar
• Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Hubbard, T. J. et al. Ensembl 2009. Nucleic Acids Res. 37, D690–D697 (2009)
  Article CAS PubMed Google Scholar
• Zheng, S. & Chen, L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res. 37, e75 (2009)
  Article PubMed PubMed Central Google Scholar
• Hiller, D., Jiang, H., Xu, W. & Wong, W. H. Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009)
• Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509–1517 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nature Genet. 39, 906–913 (2007)
  Article CAS PubMed Google Scholar
• Stranger, B. E. et al. Population genomics of human gene expression. Nature Genet. 39, 1217–1224 (2007)
  Article CAS PubMed Google Scholar
• Stranger, B. E. et al. Genome-wide associations of gene expression variation in humans. PLoS Genet. 1, e78 (2005)
  Article PubMed PubMed Central Google Scholar
• Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature XXX, XXX–XXX (2010)
  Google Scholar
• Veyrieras, J. B. et al. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet. 4, e1000214 (2008)
  Article PubMed PubMed Central Google Scholar
• Pastinen, T. & Hudson, T. J. Cis-acting regulatory variation in the human genome. Science 306, 647–650 (2004)
  Article CAS ADS PubMed Google Scholar
• Verlaan, D. J. et al. Targeted screening of _cis_-regulatory variation in human haplotypes. Genome Res. 19, 118–127 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, K. et al. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nature Methods 6, 613–618 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009)
  Article PubMed PubMed Central Google Scholar
• Sabatti, C. & Risch, N. Homozygosity and linkage disequilibrium. Genetics 160, 1707–1719 (2002)
  PubMed PubMed Central Google Scholar
• Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509–1517 (2008)
  Article CAS PubMed PubMed Central Google Scholar
• Sammeth, M. Alternative splicing events are bubbles in splicing graphs. J. Comput. Biol. 16, 1117–1140 (2009)
  Article CAS MathSciNet PubMed Google Scholar
• Oshlack, A. & Wakefield, M. J. Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 4, 14 (2009)
  Article PubMed PubMed Central Google Scholar
• Ahuja, R. K., Magnanti, T. L. & Orlin, J. B. Network Flows: Theory, Algorithms and Applications (Prentice Hall, 1993)
  MATH Google Scholar
• Cormen, T. H., Leiserson, C. E., Rivest R. L & Stein, C. in Introduction to Algorithms, 2nd ed., Ch. 29 770–821 (MIT Press and McGraw-Hill, 2001)
  MATH Google Scholar