Abstract
As the number of mammalian genomes to be completely sequenced continues to grow, researchers attempting to identify mutations responsible for inherited disease increasingly take advantage of studies undertaken in alternative species, usually humans, to identify and investigate previously identified “candidate genes” in their own species. This chapter describes the identification of mic-rosatellites closely associated with candidate genes and their subsequent analysis in cohorts of samples segregating a disease or trait of interest for an association between the candidate genes and the condition under investigation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
1. Kijas JM, Bauer TR, Jr., Gafvert S, Marklund S, Trowald-Wigh G, Johannisson A, Hedhammar A, Binns M, Juneja RK, Hickstein DD, Andersson L (1999) A missense mutation in the beta-2 integrin gene (ITGB2) causes canine leukocyte adhesion deficiency. Genomics 61:101–107
2. Henthorn PS, Liu J, Gidalevich T, Fang J, Casal ML, Patterson DF, Giger U (2000) Canine cystinuria: Polymorphism in the canine SLC3A1 gene and identification of a nonsense mutation in cystinuric Newfoundland dogs. Hum Genet 107:295–303
3. Occhiodoro T, Anson DS (1996) Isolation of the canine alpha-L-fucosidase cDNA and definition of the fucosidosis mutation in English Springer Spaniels. Mamm Genome 7:271–274
4. Skelly BJ, Sargan DR., Herrtage ME, Winchester BG (1996) The molecular defect underlying canine fucosidosis. J Med Genet 33:284–288
5. Starkey MP, Scase TJ, Mellersh CS, Murphy S (2005) Dogs really are man's best friend— Canine genomics has applications in veterinary and human medicine! Brief Funct Genomic Proteomic 4:112–28
6. Giger U, Sargan DR, McNiel EA (2006) Breed-specific heriditary diseases and genetic screening. In: Ostrander EA, Giger U, Lindblad-Toh K (eds)The dog and its genome. Cold Spring Harbor Laboratory Press, New York, pp. 249–289
7. Akhmedov NB, Baldwin VJ, Zangerl B, Kijas JW, Hunter L, Minoofar,KD, Mellersh C, Ostrander EA, Acland GM, Farber DB, Aguirre GD (2002) Cloning and characterization of the canine photoreceptor specific cone-rod homeobox (CRX) gene and evaluation as a candidate for early onset photoreceptor diseases in the dog. Mol Vis 8:79–84
8. Safra N, Ling GV, Schaible RH, Bannasch DL (2005) Exclusion of urate oxidase as a candidate gene for hyperuricosuria in the Dalmatian dog using an interbreed backcross. J Hered 96:750–754
9. Brenig B, Pfeiffer I, Jaggy A, Kathmann I, Balzari M, Gaillard C, Dolf G (2003) Analysis of the 5′ region of the canine PAX3 gene and exclusion as a candidate for Dalmatian deafness. Anim Genet 34:47–50
10. Aguirre-Hernandez J, Sargan DR (2005) Evaluation of candidate genes in the absence of positional information: A poor bet on a blind dog! J Hered 96:475–484
11. Mellersh CS, Pettitt L, Forman OP, Vaudin M, Barnett KC (2006) Identification of mutations in HSF4 in dogs of three different breeds with hereditary cataracts. Vet Ophthalmol 9:369–378
12. Lathrop GM, Lalouel JM, Julier C, Ott J (1984) Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 81:3443–3446
13. Cottingham RW Jr, Idury RM, Schaffer AA (1993) Faster sequential genetic linkage computations. Am J Hum Genet 53:252–263
14. O'Connell JR, Weeks DE (1995) The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet 11:402–408
15. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander E S (1996) Parametric and nonparametric linkage analysis: A unified multipoint approach. Am J Hum Genet 58:1347–1363
16. Gudbjartsson DF, Thorvaldsson T, Kong A, Gunnarsson G, Ingolfsdottir A (2005) Allegro version 2. Nat Genet 37:1015–1016
17. Gudbjartsson DF, Jonasson K, Frigge ML, Kong A (2000) Allegro, a new computer program for multipoint linkage analysis. Nat Genet 25:12–13
18. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265
19. Almasy L, Warren DM (2005) Software for quantitative trait analysis. Hum Genomics 2:191–195
20. Francisco LV, Langston AA, Mellersh CS, Neal CL, Ostrander EA (1996) A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mamm Genome 7:359–362
21. Sutter NB, Eberle MA, Parker HG, Pullar BJ, Kirkness EF, Kruglyak L, Ostrander EA (2004) Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res 14:2388–2396
22. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: Methods in molecular biology. Humana Press, Totowa, NJ, pp. 365–386
23. Oetting WS, Lee HK, Flanders DJ, Wiesner GL, Sellers TA, King RA (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458
24. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC (2003) The dog genome: Survey sequencing and comparative analysis. Science 301:1898–1903
25. Strachan T, Read A (2003) Human molecular genetics. Garland Publishing, New York
26. Barnes M R, Gray IC (2003) Bioinformatics for geneticists. John Wiley and Sons, New York
27. Koenig IR, König IR, Ziegler A (2006) A statistical approach to genetic epidemiology. Wiley-VCH, Hoboken, NJ
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Mellersh, C. (2008). Microsatellite-Based Candidate Gene Linkage Analysis Studies. In: Starkey, M., Elaswarapu, R. (eds) Genomics Protocols. Methods in Molecular Biology™, vol 439. Humana Press. https://doi.org/10.1007/978-1-59745-188-8_5
Download citation
DOI: https://doi.org/10.1007/978-1-59745-188-8_5
Publisher Name: Humana Press
Print ISBN: 978-1-58829-871-3
Online ISBN: 978-1-59745-188-8
eBook Packages: Springer Protocols