Mining for single nucleotide polymorphisms in pig genome sequence data

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Kerstens, Hindrik H D ^a   Kollers, Sonja ^b   Kommadath, Arun ^a   del Rosario, Marisol ^a   Dibbits, Bert ^a   Kinders, Sylvia M ^a   Crooijmans, Richard P ^a   Groenen, Martien A M ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b IPG   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTROLLED STUDY; GENE CLUSTER; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME ANALYSIS; MINING; NONHUMAN; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE; WILD TYPE; ANIMAL; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC MARKER; GENETICS; GENOME; METHODOLOGY;

ANIMALIA; SUIDAE; SUS; SUS SCROFA;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLUSTER ANALYSIS; GENETIC MARKERS; GENOME; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 60549096098     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-4     Document Type: Article

References (37)

1. Fahrenkrug SC Freking BA Smith TPL Rohrer GA Keele JW Single nucleotide polymorphism (SNP) discovery in porcine expressed genes Anim Genet 2002, 33:186-195 10.1046/j.1365-2052.2002.00846.x 12030921
2. Uenishi H Eguchi-Ogawa T Shinkai H Okumura N Suzuki K Toki D Hamasima N Awata T PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences Nucleic Acids Res 2007, 35:D650-D653 1751553 17145712 10.1093/ nar/gkl954
3. Panitz F Stengaard H Hornshøj H Gorodkin J Hedegaard J Cirera S Thomsen B Madsen LB Høj A Vingborg RK Zahn B Wang X Wang X Wernersson R Jørgensen CB Scheibye-Knudsen K Arvin T Lumholdt S Sawera M Green T Nielsen BJ Havgaard JH Brunak S Fredholm M Bendixen C SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation Bioinformatics 2007, 13:i387-i391 10.1093/bioinformatics/ btm192
4. Sherry ST Ward M Sirotkin K dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation Genome Res 1999, 9:677-679 10447503
5. Frazer IHCA Ballinger DG R Cox D Hinds DA Stuve LL Gibbs RA Belmont JW Boudreau A Hardenbol P Leal SM Pasternak S Wheeler DA Willis TD Yu F Yang H Zeng C Gao Y Hu H Hu W Li C Lin W Liu S Pan H Tang X Wang J Wang W Yu J Zhang B Zhang Q Zhao H Zhao H Zhou J Gabriel SB Barry R Blumenstiel B Camargo A Defelice M Faggart M Goyette M Gupta S Moore J Nguyen H Onofrio RC Parkin M Roy J Stahl E Winchester E Ziaugra L Altshuler D Shen Y Yao Z Huang W Chu X He Y Jin L Liu Y Shen Y Sun W Wang H Wang Y Wang Y Xiong X Xu L Waye MMY Tsui SKW Xue H Wong JT Galver LM Fan J Gunderson K Murray SS Oliphant AR Chee MS Montpetit A Chagnon F Ferretti V Leboeuf M Olivier J Phillips MS Roumy S Sallée C Verner A Hudson TJ Kwok P Cai D Koboldt DC Miller RD Pawlikowska L Taillon-Miller P Xiao M Tsui L Mak W Song YQ Tam PKH Nakamura Y Kawaguchi T Kitamoto T Morizono T Nagashima A Ohnishi Y Sekine A Tanaka T Tsunoda T Deloukas P Bird CP Delgado M Dermitzakis ET Gwilliam R Hunt S Morrison J Powell D Stranger BE Whittaker P Bentley DR Daly MJ Bakker PIWd Barrett J Chretien YR Maller J McCarroll S Patterson N Pe'er I Price A Purcell S Richter DJ Sabeti P Saxena R Schaffner SF Sham PC Varilly P Altshuler D Stein LD Krishnan L Smith AV Tello-Ruiz MK Thorisson GA Chakravarti A Chen PE Cutler DJ Kashuk CS Lin S Abecasis GR Guan W Li Y Munro HM Qin ZS Thomas DJ McVean G Auton A Bottolo L Cardin N Eyheramendy S Freeman C Marchini J Myers S Spencer C Stephens M Donnelly P Cardon LR Clarke G Evans DM Morris AP Weir BS Tsunoda T Mullikin JC Sherry ST Feolo M Skol A Zhang H Zeng C Zhao H Matsuda I Fukushima Y Macer DR Suda E Rotimi CN Adebamowo CA Ajayi I Aniagwu T Marshall PA Nkwodimmah C Royal CDM Leppert MF Dixon M Peiffer A Qiu R Kent A Kato K Niikawa N Adewole IF Knoppers BM Foster MW Clayton EW Watkin J Gibbs RA Belmont JW Muzny D Nazareth L Sodergren E Weinstock GM Wheeler DA Yakub I Gabriel SB Onofrio RC Richter DJ Ziaugra L Birren BW Daly MJ Altshuler D Wilson RK Fulton LL Rogers J Burton J Carter NP Clee CM Griffiths M Jones MC McLay K Plumb RW Ross MT Sims SK Willey DL Chen Z Han H Kang L Godbout M Wallenburg JC L'Archevêque P Bellemare G Saeki K Wang H An D Fu H Li Q Wang Z Wang R Holden AL Brooks LD McEwen JE Guyer MS Wang VO Peterson JL Shi M Spiegel J Sung LM Zacharia LF Collins FS Kennedy K Jamieson R Stewart J A second generation human haplotype map of over 3.1 million SNPs Nature 2007, 449:851-861 10.1038/ nature06258 17943122
6. Wang DG Fan JB Siao CJ Berno A Young P Sapolsky R Ghandour G Perkins N Winchester E Spencer J Kruglyak L Stein L Hsie L Topaloglou T Hubbell E Robinson E Mittmann M Morris MS Shen N Kilburn D Rioux J Nusbaum C Rozen S Hudson TJ Lipshutz R Chee M Lander ES Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 1998, 280:1077-1082 10.1126/science.280.5366.1077 9582121
7. Trikka D Fang Z Renwick A Jones SH Chakraborty R Kimmel M Nelson DL Complex SNP-based haplotypes in three human helicases: Implications for cancer association studies Genome Res 2002, 12:627-639 187520 11932247 10.1101/gr.176702
8. Sawcer S Ban M Maranian M Yeo TW Compston A Kirby A Daly MJ Jager PLD Walsh E Lander ES Rioux JD Hafler DA Ivinson A Rimmler J Gregory SG Schmidt S Pericak-Vance MA Akesson E Hillert J Datta P Oturai A Ryder LP Harbo HF Spurkland A Myhr K Laaksonen M Booth D Heard R Stewart G Lincoln R Barcellos LF Hauser SL Oksenberg JR Kenealy SJ Haines JL Consortium IMSG A high-density screen for linkage in multiple sclerosis Am J Hum Genet 2005, 77:454-467 1226210 16080120 10.1086/444547
9. Schmidt S Pericak-Vance MA Sawcer S Barcellos LF Hart J Sims J Prokop AM Walt Jvd DeLoa C Lincoln RR Oksenberg JR Compston A Hauser SL Haines JL Gregory SG Group MSG Allelic association of sequence variants in the herpes virus entry mediator-B gene (PVRL2) with the severity of multiple sclerosis Genes Immun 2006, 7:384-392 10.1038/sj.gene.6364311 16738668
10. Consortium WTCC, (TASC) ASC Burton PR Clayton DG Cardon LR Craddock N Deloukas P Duncanson A Kwiatkowski DP McCarthy MI Ouwehand WH Samani NJ Todd JA Donnelly P Barrett JC Davison D Easton D Evans DM Leung H Marchini JL Morris AP Spencer CCA Tobin MD Attwood AP Boorman JP Cant B Everson U Hussey JM Jolley JD Knight AS Koch K Meech E Nutland S Prowse CV Stevens HE Taylor NC Walters GR Walker NM Watkins NA Winzer T Jones RW McArdle WL Ring SM Strachan DP Pembrey M Breen G Clair DS Caesar S Gordon-Smith K Jones L Fraser C Green EK Grozeva D Hamshere ML Holmans PA Jones IR Kirov G Moskivina V Nikolov I O'Donovan MC Owen MJ Collier DA Elkin A Farmer A Williamson R McGuffin P Young AH Ferrier IN Ball SG Balmforth AJ Barrett JH Bishop TD Iles MM Maqbool A Yuldasheva N Hall AS Braund PS Dixon RJ Mangino M Stevens S Thompson JR Bredin F Tremelling M Parkes M Drummond H Lees CW Nimmo ER Satsangi J Fisher SA Forbes A Lewis CM Onnie CM Prescott NJ Sanderson J Matthew CG Barbour J Mohiuddin MK Todhunter CE Mansfield JC Ahmad T Cummings FR et al. Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants Nat Genet 2007, 39(11):1329-1337 10.1038/ng.2007.17 17952073
11. Jungerius BJ Gu J Crooijmans RPMA Poel JJvd Groenen MAM Oost BAv Pas MFWt Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome Anim Biotechnol 2005, 16:41-54 10.1081/ ABIO-200053402 15926262
12. Humphray SJ Scott CE Clark R Marron B Bender C Camm N Davis J Jenks A Noon A Patel M Sehra H Yang F Rogatcheva MB Milan D Chardon P Rohrer G Nonneman D Jong Pd Meyers SN Archibald A Beever JE Schook LB Rogers J A high utility integrated map of the pig genome Genome Biol 2007, 8:R139 2323232 17625002 10.1186/gb-2007-8-7-r139
13. Schook LB Beever JE Rogers J Humphray S Archibald A Chardon P Milan D Rohrer G Eversole K Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome Comparative and Functional Genomics 2005, 6:251-255 10.1002/cfg.479
14. Myers EW Miller W Optimal alignments in linear space Comput Appl Biosci 1988, 4:11-17 3382986
15. Nickerson DA Tobe VO Taylor SL PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Res 1997, 25:2745-2751 146817 9207020 10.1093/ nar/25.14.2745
16. Nickerson DA Taylor SL Weiss KM Clark AG Hutchinson RG Stengård J Salomaa V Vartiainen E Boerwinkle E Sing CF DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene Nat Genet 1998, 19:233-240 10.1038/907 9662394
17. Rieder MJ Taylor SL Tobe VO Nickerson DA Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome Nucleic Acids Res 1998, 26:967-973 147367 9461455 10.1093/nar/26.4.967
18. Stephens M Sloan JS Robertson PD Scheet P Nickerson DA Automating sequence-based detection and genotyping of SNPs from diploid samples Nat Genet 2006, 38:375-381 10.1038/ng1746 16493422
19. Rasmus W Mikkel S Frank J Jan G Frank P Hans-Henrik S Ole C Thomas M Henrik H Ami K Jun W Bin L Songnian H Wei D Wei L Gane W Jun Y Jian W Christian B Merete F Soren B Huanming Y Lars B Pigs in sequence space: A 0.66× coverage pig genome survey based on shotgun sequencing BMC Genomics 2005, 6:70 1142312 15885146 10.1186/1471-2164-6-70
20. Flicek P Aken BL Beal K Ballester B Caccamo M Chen Y Clarke L Coates G Cunningham F Cutts T Down T Dyer SC Eyre T Fitzgerald S Fernandez-Banet J Gräf S Haider S Hammond M Holland R Howe KL Howe K Johnson N Jenkinson A Kähäri A Keefe D Kokocinski F Kulesha E Lawson D Longden I Megy K Meidl P Overduin B Parker A Pritchard B Prlic A Rice S Rios D Schuster M Sealy I Slater G Smedley D Spudich G Trevanion S Vilella AJ Vogel J White S Wood M Birney E Cox T Curwen V Durbin R Fernandez-Suarez XM Herrero J Hubbard TJP Kasprzyk A Proctor G Smith J Ureta-Vidal A Searle S Ensembl 2008 Nucleic Acids Res 2008, 36:D707-D714 2238821 18000006 10.1093/nar/gkm988
21. Ewing B Green P Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res 1998, 8:186-194 9521922
22. Ewing B Hillier L Wendl MC Green P Base-calling of automated sequencer traces using phred. I. Accuracy assessment Genome Res 1998, 8:175-185 9521921
23. Green P Phrap http://www.phrap.org
24. Ollivier L Alderson L Gandini GC Foulley JL Haley CS Joosten R Rattink AP Harlizius B Groenen MAM Amigues Y Boscher MY Russell G Law A Davoli R Russo V Matassino D Désautés C Fimland E Bagga M Delgado JV Vega-Pla JL Martinez AM Ramos AM Glodek P Meyer JN Plastow GS Siggens KW Archibald AL Milan D San Cristobal M Laval G Hammond K Cardellino R Chevalet C An assessment of European pig diversity using molecular markers: Partitioning of diversity among breeds Conserv Genet 2005, 6:729-741 10.1007/s10592-005-9032-6
25. Rohrer GA Freking BA Nonneman D Single nucleotide polymorphisms for pig identification and parentage exclusion Anim Genet 2007, 38:253-258 10.1111/j.1365-2052.2007.01593.x 17433014
26. Gu Z Hillier L Kwok PY Single nucleotide polymorphism hunting in cyberspace Hum Mutat 1998, 12:221-225 10.1002/ (SICI)1098-1004(1998)12:4<221::AID-HUMU1>3.0.CO;2-I 9744471
27. Taillon-Miller P Gu Z Li Q Hillier L Kwok PY Overlapping genomic sequences: A treasure trove of single-nucleotide polymorphisms Genome Res 1998, 8:748-754 310751 9685323
28. Picoult-Newberg L Ideker TE Pohl MG Taylor SL Donaldson MA Nickerson DA Boyce-Jacino M Mining SNPs from EST databases Genome Res 1999, 9:167-174 310719 10022981
29. Kwok PY Deng Q Zakeri H Taylor SL Nickerson DA Increasing the information content of STS-based genome maps: Identifying polymorphisms in mapped STSs Genomics 1996, 31:123-126 10.1006/geno.1996.0019 8808290
30. Garg K Green P Nickerson DA Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags Genome Res 1999, 9:1087-1092 310835 10568748 10.1101/gr.9.11.1087
31. Marth GT Korf I Yandell MD Yeh RT Gu Z Zakeri H Stitziel NO Hillier L Kwok PY Gish WR A general approach to single-nucleotide polymorphism discovery Nat Genet 1999, 23:452-456 10.1038/70570 10581034
32. Madsen BE Villesen P Wiuf C A periodic pattern of SNPs in the human genome Genome Res 2007, 17:1414-1419 1987342 17673700 10.1101/gr.6223207
33. Smith AFA Green P RepeatMasker http://www.repeatmasker.org
34. Zhang Z Schwartz S Wagner L Miller W A greedy algorithm for aligning DNA sequences J Comput Biol 2000, 7:203-214 10.1089/10665270050081478 10890397
35. Huang X Madan A CAP3: A DNA sequence assembly program Genome Res 1999, 9:868-877 310812 10508846 10.1101/gr.9.9.868
36. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215:403-410 2231712
37. Kent WJ BLAT - the BLAST-like alignment tool Genome Res 2002, 12:656-664 187518 11932250