Sampling distribution for microsatellites amplified by PCR: Mean field approximation and its applications to genotyping

Journal of Theoretical Biology

Volumn 228, Issue 2, 2004, Pages 185-194

  Lai, Yinglei ^a,b   Sun, Fengzhu ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Branching processes; Genotyping; Mean field approximation; Microsatellites; Polymerase chain reaction

Indexed keywords

MICROSATELLITE DNA;

GENOTYPE; MODEL; POLYMERASE CHAIN REACTION;

ARTICLE; BAYES THEOREM; GENE AMPLIFICATION; GENOTYPE; MATHEMATICAL MODEL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; THEORY;

GENE AMPLIFICATION; GENOTYPE; HUMANS; MICROSATELLITE REPEATS; MODELS, GENETIC; MUTATION; POLYMERASE CHAIN REACTION; SAMPLING STUDIES;

EID: 1942421307     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2003.12.014     Document Type: Article

References (26)

1. Ashley C.T., Warren S.T. Trinucleotide repeat expansion and human disease. Ann. Rev. Genet. 29:1995;703-728.
2. Athreya K.B., Ney P.E. Branching Processes. 1972;Springer, Berlin.
3. Barcellos L.F., Klitz W., Field L.L., Tobias R., Bowcock A.M., Wilson R., Nelson M.P., Nagatomi J., Thomson G. Association mapping of disease loci, by use of a pooled DNA genomic screen. Am. J. Hum. Genet. 61:1997;734-747.
4. Harris T.E. The Theory of Branching Processes. 1963;Springer, Berlin.
5. Kong A., Gudbjartsson D.F., Sainz J., Jonsdottir G.M., Gudjonsson S.A., Richardsson B., Sigurdardottir S., Barnard J., Hallbeck B., Masson G., Shlien A., Palsson S.T., Frigge M.L., Thorgeirsson T.E., Gulcher J.R., Stefansson K. A high-resolution recombination map of the human genome. Nat. Genet. 31:2002;241-247.
6. Lai Y., Sun F.Z. Microsatellite mutations during the polymerase chain reaction: mean field approximations and their applications. J. Theor. Biol. 224:2003;127-137.
7. Lai Y., Shinde D., Arnheim N., Sun F.Z. The mutation process of microsatellites during the polymerase chain reaction. J. Comp. Biol. 10:2003;143-155.
8. Miller M.J., Yuan B.Z. Semiautomatic resolution of overlapping stutter patterns in genotyping microsatellite analysis. Anal. Biochem. 251:1997;50-56.
9. Mullis K.B., Faloona F.A. Specific synthesis of DNA in vitro via a polymerase catalyzed chain reaction. Methods Enzymol. 155:1987;335-351.
10. Navidi W., Arnheim N. Analysis of genetic data from the polymerase chain reaction. Stat. Sci. 9:1994;320-333.
11. Olofsson P., Shaw C. Exact sampling formulas for multi-type Galton-Watson processes. J. Math. Biol. 45:2002;279-293.
12. Perlin M.W., Burks M.B., Hoop R.C., Hoffman E.P. Toward fully automated genotyping: allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy. Am. J. Hum. Genet. 55:1994;777-787.
13. Perlin M.W., Lancia G., Ng S.-K. Toward fully automated genotyping. genotyping microsatellite markers by deconvolution Am. J. Hum. Genet. 57:1995;1199-1210.
14. Piau D. Mutation-replication statistics of polymerase chain reactions. J. Comp. Biol. 9:2002;831-847.
15. Rosenberg N.A., Pritchard J.K., Weber J.L., Cann H.M., Kidd K.K., Zhivotovsky L.A., Feldman M.W. Genetic structure of human populations. Science. 298:2002;2381-2385.
16. Saiki R., Scharf S., Faloona F., Mullis K., Horn G.T., Erlich H.A., Arnheim N. Enzymatic amplification of. β -globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Science. 230:1985;1350-1354.
17. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K.B., Erlich H.A. Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:1988;487-491.
18. Scharf S.J., Horn G.T., Erlich H.A. Direct cloning and sequence analysis of enzymatically amplified genomic sequences. Science. 223:1986;1076-1078.
19. n microsatellites Nucl. Acid. Res. 31:2003;974-980.
20. Sun F.Z. The polymerase chain reaction and branching processes. J. Comp. Biol. 23:1995;3034-3040.
21. Wang D., Zhao C., Cheng R., Sun F.Z. Estimating the mutation rate during error-prone polymerase chain reaction. J. Comp. Biol. 7:2000;143-158.
22. Watson J.D., Gilman M., Witkowski J., Zoller M. Recombinant DNA. 1992;Scientific American Books, New York.
23. Weber J., May P. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44:1989;388-396.
24. Weber J.L., Wong C. Mutation of human short tandem repeats. Hum. Mol. Genet. 2:1993;1123-1128.
25. Weiss G., von Haeseler A. Modeling the polymerase chain reaction. J. Comp. Biol. 2:1995;49-61.
26. Weiss G., von Haeseler A. A coalescent approach to the polymerase chain reaction. Nucl. Acid. Res. 25:1997;3082-3087.