SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Fujisawa, Hironori ^a,c   Horiuchi, Youko ^b,c   Harushima, Yoshiaki ^b,c   Takada, Toyoyuki ^b,c   Eguchi, Shinto ^a,c   Mochizuki, Takako ^b   Sakaguchi, Takayuki ^a,c   Shiroishi, Toshihiko ^b,c   Kurata, Nori ^b,c  

^a INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AFFYMETRIX GENECHIP; BETTER PERFORMANCE; FALSE POSITIVE RATES; HYBRIDIZATION SIGNAL; NUCLEOTIDE POLYMORPHISMS; OLIGONUCLEOTIDE MICROARRAY; SEQUENCE INFORMATIONS; SIMULTANEOUS DETECTION;

BIODIVERSITY; MAMMALS; OLIGONUCLEOTIDES;

TISSUE;

NUCLEOTIDE; MESSENGER RNA;

ANIMAL GENETICS; ARTICLE; BARLEY; GENE EXPRESSION; GENE SEQUENCE; GENETIC POLYMORPHISM; HYBRIDIZATION; NONHUMAN; PLANT GENETICS; RICE; STATISTICAL ANALYSIS; ALGORITHM; ANIMAL; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; MOUSE; ROC CURVE; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

HORDEUM; MUS;

ALGORITHMS; ANIMALS; GENE EXPRESSION PROFILING; GENOMICS; HORDEUM; MICE; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN; RNA, MESSENGER; ROC CURVE; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 67650550763     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-131     Document Type: Article

References (31)

1. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H et al Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14:1675-1680. 10.1038/nbt1296-1675 9634850
2. Kidgell C Volkman SK Daily J Borevitz JO Plouffe D Zhou Y Johnson JR Le Roch K Sarr O Ndir O et al A systematic map of genetic variation in Plasmodium falciparum PLoS Path 2006, 2:e57. 10.1371/journal.ppat.0020057
3. Winzeler EA Richards DR Conway AR Goldstein AL Kalman S McCullough MJ McCusker JH Stevens DA Wodicka L Lockhart DJ Davis RW Direct allelic variation scanning of the yeast genome Science 1998, 281:1194-1197. 10.1126/science.281.5380.1194 9712584
4. Turner TL Hahn MW Nuzhdin SV Genomic islands of speciation in Anopheles gambiae PLoS Biol 2005, 3:e285. 10.1371/journal.pbio.0030285 16076241 1182689
5. Borevitz JO Liang D Plouffe D Chang HS Zhu T Weigel D Berry CC Winzeler E Chory J Large-scale identification of single-feature polymorphisms in complex genomes Genome Res 2003, 13:513-523. 10.1101/gr.541303 12618383 430246
6. Borevitz JO Hazen SP Michael TP Morris GP Baxter IR Hu TT Chen H Werner JD Nordborg M Salt DE et al Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana Proc Natl Acad Sci USA 2007, 104:12057-12062. 10.1073/pnas.0705323104 17626786 1914337
7. Kumar R Qiu J Joshi T Valliyodan B Xu D Nguyen HT Single feature polymorphism discovery in rice PLoS ONE 2007, 2:e284. 10.1371/ journal.pone.0000284 17372626 1808426
8. Ronald J Akey JM Whittle J Smith EN Yvert G Kruglyak L Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays Genome Res 2005, 15:284-291. 10.1101/gr.2850605 15687292 546530
9. West MA van Leeuwen H Kozik A Kliebenstein DJ Doerge RW St Clair DA Michelmore RW High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis Genome Res 2006, 16:787-795. 10.1101/gr.5011206 16702412 1473188
10. Rostoks N Borevitz JO Hedley PE Russell J Mudie S Morris J Cardle L Marshall DF Waugh R Single-feature polymorphism discovery in the barley transcriptome Genome Biol 2005, 6:R54. 10.1186/gb-2005-6-6-r54 15960806 1175974
11. Cui X Xu J Asghar R Condamine P Svensson JT Wanamaker S Stein N Roose M Close TJ Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit Bioinformatics 2005, 21:3852-3858. 10.1093/bioinformatics/bti640 16118260
12. Luo ZW Potokina E Druka A Wise R Waugh R Kearsey MJ SFP Genotyping from Affymetrix arrays is robust but largely detects cis-acting expression regulators Genetics 2007, 176:789. 10.1534/genetics.106.067843 17409081 1894608
13. Kirst M Caldo R Casati P Tanimoto G Walbot V Wise RP Buckler ES Genetic diversity contribution to errors in short oligonucleotide microarray analysis Plant Biotechnol J 2006, 4:489-498. 17309725
14. Greenhall JA Zapala MA Caceres M Libiger O Barlow C Schork NJ Lockhart DJ Detecting genetic variation in microarray expression data Genome Res 2007, 17:1228-1235. 10.1101/gr.6307307 17609390 1933513
15. Hsieh WP Chu TM Wolfinger RD Gibson G Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles Genetics 2003, 165:747-757. 1462792 14573485
16. Alberts R Terpstra P Li Y Breitling R Nap JP Jansen RC Sequence polymorphisms cause many false cis eQTLs PLoS ONE 2007, 2:e622. 10.1371/ journal.pone.0000622 17637838 1906859
17. Gore M Bradbury P Hogers R Kirst M Verstege E van Oeveren J Peleman J Buckler E van Eijk M Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes Crop Science 2007, 47:S135-S148. 10.2135/cropsci2007.02.0085tpg
18. Bhat PR Lukaszewski A Cui X Xu J Svensson JT Wanamaker S Waines JG Close TJ Mapping translocation breakpoints using a wheat microarray Nucleic Acids Res 2007, 35:2936-2943. 10.1093/nar/gkm148 17439961 1888831
19. Tusher VG Tibshirani R Chu G Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci USA 2001, 98:5116-5121. 10.1073/pnas.091062498 11309499 33173
20. Windham MP Robustifying model fitting J Roy Statist Soc Ser B 1995, 57:599-609.
21. Basu A Harris IR Hjort NL Jones MC Robust and efficient estimation by minimising a density power divergence Biometrika 1998, 85:549-559. 10.1093/biomet/85.3.549
22. Jones MC Hjort NL Harris IR Basu A A comparison of related density-based minimum divergence estimators Biometrika 2001, 88:865-873. 10.1093/ biomet/88.3.865
23. Fujisawa H Eguchi S Robust parameter estimation with a small bias against heavy contamination J Multivariate Anal 2008, 99:2053-2081. 10.1016/j.jmva.2008.02.004
24. Scott DW Parametric statistical modeling by minimum integrated square error Technometrics 2001, 43:274-285. 10.1198/004017001316975880
25. International Rice Genome Sequencing Project The map-based sequence of the rice genome Nature 2005, 436: 793-800. 10.1038/nature03895 16100779
26. Yu J Wang J Lin W Li S Li H Zhou J Ni P Dong W Hu S Zeng C et al The genomes of Oryza sativa: A history of duplications PLoS Biol 2005, 3:e38. 10.1371/journal.pbio.0030038 15685292 546038
27. Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome Nature 2002, 420:520-562. 10.1038/ nature01262 12466850
28. Abe K Noguchi H Tagawa K Yuzuriha M Toyoda A Kojima T Ezawa K Saitou N Hattori M Sakaki Y et al Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis Genome Res 2004, 14:2439-2447. 10.1101/gr.2899304 15574823 534668
29. Hampel FR Ronchetti EM Rousseeuw PJ Stahel WA Robust statistics: The approach based on influence functions Wiley; 1986.
30. Marioni JC Mason CE Mane SM Stephens M Gilad Y RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays Genome Res 2008, 18:1509-1517. 10.1101/gr.079558.108 18550803 2527709
31. Cloonan N Forrest AR Kolle G Gardiner BB Faulkner GJ Brown MK Taylor DF Steptoe AL Wani S Bethel G et al Stem cell transcriptome profiling via massive-scale mRNA sequencing Nat Meth 2008, 5:613-619. 10.1038/ nmeth.1223