Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Quinn, Emma M ^a   Cormican, Paul ^a   Kenny, Elaine M ^a   Hill, Matthew ^a   Anney, Richard ^a   Gill, Michael ^a   Corvin, Aiden P ^a   Morris, Derek W ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; EXON; GENE EXPRESSION; GENETIC VARIABILITY; GENOME ANALYSIS; LYMPHOBLASTOID CELL LINE; RNA ANALYSIS; RNA SEQUENCE; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

CELL LINE; COMPUTATIONAL BIOLOGY; EXONS; GENE EXPRESSION; GENOMICS; GENOTYPE; HUMANS; LYMPHOCYTES; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA;

EID: 84875451981     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058815     Document Type: Article

References (44)

1. Hoheisel JD, (2006) Microarray technology: beyond transcript profiling and genotype analysis. Nat Rev Genet 7: 200-210.
2. Gresham D, Dunham MJ, Botstein D, (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet 9: 291-302.
3. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
4. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
5. Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, et al. (2008) Genomic Convergence Analysis of Schizophrenia: mRNA Sequencing Reveals Altered Synaptic Vesicular Transport in Post-Mortem Cerebellum. PLoS ONE 3: e3625.
6. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
7. Heap GA, Yang JHM, Downes K, Healy BC, Hunt KA, et al. (2010) Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Human Molecular Genetics 19: 122-134.
8. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
9. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, et al. (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45: 81-94.
10. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu X-D, et al. (2009) An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16: 130-137.
11. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, et al. (2008) A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science 321: 956-960.
12. Sie L, Loong S, Tan EK, (2009) Utility of lymphoblastoid cell lines. J Neurosci Res 87: 1953-1959.
13. Herbeck JT, Gottlieb GS, Wong K, Detels R, Phair JP, et al. (2009) Fidelity of SNP Array Genotyping Using Epstein Barr Virus-Transformed B-Lymphocyte Cell Lines: Implications for Genome-Wide Association Studies. PLoS ONE 4: e6915.
14. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, et al. (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207.
15. WTCCC (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
16. Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, et al. (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464: 713-720.
17. Tejero ME, Voruganti VS, Proffitt JM, Curran JE, Goring HHH, et al. (2008) Cross-species replication of a resistin mRNA QTL, but not QTLs for circulating levels of resistin, in human and baboon. Heredity 101: 60-66.
18. Ding J, Gudjonsson JE, Liang L, Stuart PE, Li Y, 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.
19. Rollins B, Martin MV, Morgan L, Vawter MP, (2010) Analysis of whole genome biomarker expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet 153B: 919-936.
20. Bullaughey K, Chavarria CI, Coop G, Gilad Y, (2009) Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet 18: 4296-4303.
21. -Genomes-Project-Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
22. Ku CS, Loy EY, Salim A, Pawitan Y, Chia KS, (2010) The discovery of human genetic variations and their use as disease markers: past, present and future. J Hum Genet 55: 403-415.
23. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276.
24. Botstein D, Risch N, (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33Suppl: 228-237.
25. Chepelev I, Wei G, Tang Q, Zhao K, (2009) Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq. Nucleic Acids Res 37: e106.
26. Cirulli ET, Singh A, Shianna KV, Ge D, Smith JP, et al. (2010) Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol 11: R57.
27. Canovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF, (2010) SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 21: 592-598.
28. Peng Z, Cheng Y, Tan BC-M, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotech 30: 253-260.
29. Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, et al. (2011) Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12: 199.
30. Vidal RO, do Nascimento LC, Mondego JM, Pereira GA, Carazzolle MF, (2012) Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 35: 331-334.
31. Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, et al. (2012) RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout. PLoS ONE 7: e36264.
32. Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W, (2010) Calling SNPs without a reference sequence. BMC Bioinformatics 11: 130.
33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
34. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
35. Huang R, Jaritz M, Guenzl P, Vlatkovic I, Sommer A, et al. (2011) An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One. 6: e27288.
36. Koehler R, Issac H, Cloonan N, Grimmond SM, (2011) The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics 27: 272-274.
37. Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, et al. (2012) Fast Computation and Applications of Genome Mappability. PLoS ONE 7: e30377.
38. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A, (2007) Widespread Monoallelic Expression on Human Autosomes. Science 318: 1136-1140.
39. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, et al. (2009) Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner. Science 325: 1246-1250.
40. Tuch BB, Laborde RR, Xu X, Gu J, Chung CB, et al. (2010) Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations. PLoS ONE 5: e9317.
41. Turro E, Su SY, Goncalves A, Coin LJ, Richardson S, et al. (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol 12: R13.
42. Keegan LP, Gallo A, O'Connell MA, (2001) The many roles of an RNA editor. Nat Rev Genet 2: 869-878.
43. Wulff B-E, Sakurai M, Nishikura K, (2011) Elucidating the inosinome: global approaches to adenosine-to-inosine RNA editing. Nat Rev Genet 12: 81-85.
44. Kiran A, Baranov PV, (2010) DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 26: 1772-1776.