An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay

BMC Genetics

Volumn 8, Issue , 2007, Pages

  Seo, Bo Young ^a   Park, Eung Woo ^b   Ahn, Sung Jin ^a   Lee, Sang Ho ^a   Kim, Jae Hwan ^a   Im, Hyun Tae ^a   Lee, Jun Heon ^c   Cho, In Cheol ^b   Kong, Il Keun ^a   Jeon, Jin Tae ^a  

^a Gyeongsang National University   (South Korea)

^b National Institute of Animal Science   (South Korea)

^c Chungnam National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CHROMOSOME NUMBER; DIAGNOSTIC ACCURACY; GENE ASSIGNMENT; GENE CLUSTER; GENETIC ANALYSIS; GENETIC DISORDER; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; NONHUMAN; NUCLEIC ACID ANALYSIS; NUMERICAL CHROMOSOME ABERRATION; OLIGONUCLEOTIDE LIGATION ASSAY; QUANTITATIVE ASSAY; SENSITIVITY AND SPECIFICITY; SWINE; ANIMAL; DNA MICROARRAY; DNA SEQUENCE; FEMALE; GENE DOSAGE; GENE DUPLICATION; GENETICS; GENOTYPE; HAIR COLOR; MALE; POLYMERASE CHAIN REACTION;

ANIMALIA; PIERIS BRASSICAE; SUIDAE; SUS;

ANIMALS; FEMALE; GENE DOSAGE; GENE DUPLICATION; GENOTYPE; HAIR COLOR; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SUS SCROFA;

EID: 38949180308     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-8-81     Document Type: Article

References (23)

1. Redon R Ishikawa S Fitch KR Feuk L Perry GH Andrews TD Fiegler H Shapero MH Carson AR Chen W Cho EK Dallaire S Freeman JL Gonzalez JR Gratacos M Huang J Kalaitzopoulos D Komura D MacDonald JR Marshall CR Mei R Montgomery L Nishimura K Okamura K Shen F Somerville MJ Tchinda J Valsesia A Woodwark C Yang F Zhang J Zerjal T Zhang J Armengol L Conrad DF Estivill X Tyler-Smith C Carter NP Aburatani H Lee C Jones KW Scherer SW Hurles ME Global variation in copy number in the human genome Nature 2006, 444:444-454 10.1038/nature05329 17122850
2. Stranger BE Forrest MS Dunning M Ingle CE Beazley C Thorne N Redon R Bird commercial pigs de Grassi A Lee C Tyler-Smith C Carter N Scherer SW Tavare S Deloukas P Hurles ME Dermitzakis ET Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 2007, 315:848-853 10.1126/science.1136678 17289997
3. Kehrer-Sawatzki H What a difference copy number variation makes Bioessays 2007, 29:311-313 10.1002/bies.20554 17373652
4. Pielberg G Day AE Plastow GS Andersson L A sensitive method for detecting variation in copy numbers of duplicated genes Genome Res 2003, 13:2171-2177 403722 12952884 10.1101/gr.1188203
5. Nevilie M Selzer R Aizenstein B Maguire M Hogan K Walton R Welsh K Neri B de Arruda M Characterization of cytochrome P450 2D6 alleles using the Invader system Biotechniques 2002 Suppl 34 Suppl 43
6. Aldred PM Hollox EJ Armour JA Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3 Hum Mol Genet 2005, 14:2045-2052 10.1093/hmg/ddi209 15944200
7. Johansson Moller M Chaudhary R Hellmen E Hoyheim B Chowdhary B Andersson L Pigs with the dominant white coat color phenotype carry a duplication of the KIT gene encoding the mast/stem cell growth factor receptor Mamm Genome 1996, 7: 822-830 10.1007/s003359900244 8875890
8. Hirooka H de Koning DJ van Arendonk JA Harlizius B de Groot PN Bovenhuis H Genome scan reveals new coat color loci in exotic pig cross J Hered 2002, 93:1-8 10.1093/jhered/93.1.1 12011168
9. Marklund S Kijas J Rodriguez-Martinez H Ronnstrand L Funa K Moller M Lange D Edfors-Lilja I Andersson L Molecular basis for the dominant white phenotype in the domestic pig Genome Res 1998, 8:826-833 310759 9724328
10. Johansson M Ellegren H Marklund L Gustavsson U Ringmar-Cederberg E Andersson K Edfors-Lilja I Andersson L The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8 Genomics 1992, 14:965-969 10.1016/S0888-7543(05)80118-1 1362182
11. Giuffra E Evans G Tornsten A Wales R Day A Looft H Plastow G Andersson L The Belt mutation in pigs is an allele at the Dominant White (I/KIT) locus Mamm Genome 1999, 10:1132-1136 10.1007/s003359901178 10594235
12. Pielberg G Olsson C Syvanen AC Andersson L Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig Genetics 2002, 160:305-311 1461930 11805065
13. Everitt B Cluster Analysis London: Heinemann Educational Books 1974
14. SAS Institute Inc SAS/STAT 9.1 user's guide Cary, N.C.: SAS Institute 2004, 6:1377-1427
15. Kar P Polipalli SK Chattopadhyay S Hussain Z Malik A Husain SA Medhi S Begum N Prevalence of hepatitis B virus genotype D in precore mutants among chronic liver disease patients from New Delhi, India Dig Dis Sci 2007, 52:565-569 10.1007/s10620-006-9625-z 17211692
16. Kasehagen LJ Mueller I McNamara DT Bockarie MJ Kiniboro B Rare L Lorry K Kastens W Reeder JC Kazura JW Zimmerman PA Changing patterns of Plasmodium blood-stage infections in the Wosera region of Papua New Guinea monitored by light microscopy and high throughput PCR diagnosis Am J Trop Med Hyg 2006, 75:588-596 17038678
17. Michel CE Sonnex C Carne CA White JA Magbanua JP Nadala EC Jr Lee HH Chlamydia trachomatis Load at Matched Anatomic Sites: Implications for Screening Strategies J Clin Microbiol 2007, 45:1395-1402 1865904 17376879 10.1128/JCM.00100-07
18. Milan D Jeon JT Looft C Amarger V Robic A Thelander M Rogel-Gaillard C Paul S Iannuccelli N Rask L Ronne H Lundstrom K Reinsch N Gellin J Kalm E Roy PL Chardon P Andersson L A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle Science 2000, 288:1248-1251 10.1126/science.288.5469.1248 10818001
19. Di Fiore F Blanchard F Charbonnier F Le Pessot F Lamy A Galais MP Bastit L Killian A Sesboue R Tuech JJ Queuniet AM Paillot B Sabourin JC Michot F Michel P Frebourg T Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by Cetuximab plus chemotherapy Br J Cancer 2007, 96:1166-1169 10.1038/sj.bjc.6603685 17375050
20. Miller SA Dykes DD Polesky HF A simple salting out procedure for extracting DNA from human nucleated cells Nucleic Acids Res 1988, 16:1215 334765 3344216 10.1093/nar/16.3.1215
21. Walsh PS Metzger DA Higuchi R Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material Biotechniques 1991, 10:506-513 1867860
22. Yerle M Echard G Robic A Mairal A Dubut-Fontana C Riquet J Pinton P Milan D Lahbib-Mansais Y Gellin J A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics Cytogenet Cell Genet 1996, 73:194-202 8697807
23. Website title http://www.toulouse.inra.fr/lgc/pig/pcr/pcr.htm