Heterozygosity increases microsatellite mutation rate, linking it to demographic history

BMC Genetics

Volumn 9, Issue , 2008, Pages

  Amos, William ^a   Flint, Jonathan ^b   Xu, Xin ^c  

^a Department of Zoology ^*  (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ARTICLE; DEMOGRAPHY; GENE MUTATION; GENETIC DISTANCE; GENETIC VARIABILITY; GENOME SIZE; GENOMIC INSTABILITY; GEOGRAPHY; HETEROZYGOSITY; HUMAN; MICROSATELLITE MARKER; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; PEDIGREE; PLESIOMORPHY; POPULATION GENETICS; POPULATION SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; GENETICS; GENOTYPE; HETEROZYGOTE; MUTATION;

MICROSATELLITE DNA;

DEMOGRAPHY; GENETICS, POPULATION; GENOTYPE; HETEROZYGOTE; HUMANS; MICROSATELLITE REPEATS; MUTATION; PEDIGREE;

EID: 58149523728     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-9-72     Document Type: Article

References (35)

1. Amos W Sawcer SJ Feakes R Rubinsztein DC Microsatellites show mutational bias and heterozygote instability Nature Genet 1996, 13:390-391. 10.1038/ ng0896-390 8696328
2. van Treuren R Kuittinen H Kärkkäinen K Baena-Gonzalez E Savolainen O Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana Mol Biol Evol 1997, 14:220-229. 9066790
3. Ellegren H Primmer CR Sheldon BC Microsatellite evolution: directionality or bias in locus selection Nature Genet 1995, 11:360-362. 10.1038/ng1295-360 7493011
4. Zhu Y Queller DC Strassman JE et al A phylogenetic perspective on sequence evolution at microsatellite loci J Mol Evol 2000, 50:324-338. 10795824
5. Ellegren H Microsatellite mutations in the germline: Implications for evolutionary inference Trends Genet 2000, 16:551-558. 10.1016/ S0168-9525(00)02139-9 11102705
6. Mahtani MM Willard HF A polymorphic X-linked tetranucleotide repeat locus displaying a high rate of new mutation: Implications for mechanisms of mutation at short tandem repeat loci Hum Mol Genet 1993, 2:431-437. 10.1093/hmg/2.4.431 8504304
7. Zhivotovsky LA Feldman MW Grishechkin SA Biased mutation and microsatellite variation Mol Biol Evol 1997, 14:926-933. 9287425
8. Weber JL Informativeness of human (dC-dA)n. (dG-dT)n polymorphisms Genomics 1990, 7:524-530. 10.1016/0888-7543(90)90195-Z 1974878
9. Garza JC Slatkin M Freimer NB Microsatellite allele frequencies in humans and chimpanzees with implications for constraints on allele size Mol Biol Evol 1995, 12:594-604. 7659015
10. Amos W Clarke A Body temperature predicts maximum microsatellite length in mammals Biol Lett 2008. 18522923
11. Jin L Macaubas C Hallmayer J Kimura A Mignot E Mutation rate varies among alleles at a microsatellite locus: Phylogenetic evidence Proc Natl Acad Sci USA 1996, 93:15285-15288. 10.1073/pnas.93.26.15285 8986803 26396
12. Di Rienzo A Peterson AC Garza JC Valdes AM Slatkin M Mutational processes of simple sequence repeat loci in human populations Proc Natl Acad Sci USA 1994, 91:3166-3170. 10.1073/pnas.91.8.3166 8159720 43536
13. Goldstein DB Ruiz Linares A Cavalli-Sforza LL Feldman MW Genetic absolute dating based on microsatellites and the origin of modern humans Proc Natl Acad Sci USA 1995, 92:6723-6727. 10.1073/pnas.92.15.6723 7624310 41401
14. Vigouroux Y Matsuoka Y Doebley J Directional evolution for microsatellite size in maize Mol Biol Evol 2003, 20:1480-1483. 10.1093/ molbev/msg156 12832640
15. Hanford MG Rushton BC Gowen LC Farber RA Microsatellite mutation rates in cancer cell lines deficient or proficient in mismatch repair Oncogene 1998, 16:2389-2393. 10.1038/sj.onc.1201751 9620556
16. Yamada NA Castro A Farber RA Variation in the extent of microsatellite instability in human cell lines with defects in different mismatch repair genes Mutagenesis 2003, 18:277-282. 10.1093/mutage/18.3.277 12714694
17. Kolodner R Biochemistry and genetics of eukaryotic mismatch repair Genes Dev 1996, 10:1433-1442. 10.1101/gad.10.12.1433 8666228
18. Ellegren H Heterogeneous mutation processes in human microsatellites Nat Genet 2000, 24:400-402. 10.1038/74249 10742106
19. Xu X Peng M Fang Z Xu X The direction of microsatellite mutations is dependent upon allele length Nat Genet 2000, 24:396-399. 10.1038/74238 10742105
20. Xu X Rogus JJ Tewedow HA Yang J Wang Z Chen C Niu T Wang B Xu H Weiss S et al An extreme-sib-pair genome scan for genes regulating blood pressure Am J Hum Genet 1999, 64:1694-1701. 10.1086/302405 10330357 1377913
21. Liu H Prugnolle F Manica A Balloux F A geographically explicit genetic model of worldwide human-settlement history Am J Hum Genet 2006, 79:230-237. 10.1086/505436 16826514 1559480
22. Li JZ Absher DM Tang H Southwick AM Casto AM Ramachandran S Cann HL Barsh GS Feldman MW Cavalli-Sforza LL Myers RM Worldwide human relationships inferred from genomewide patterns of variation Science 2008, 319:1100-1104. 10.1126/science.1153717 18292342
23. Prugnolle F Manica A Balloux F Geography predicts neutral genetic diversity of human populations Curr Biol 2005, 15:R159-R160. 10.1016/ j.cub.2005.02.038 15753023 1800886
24. Manica A Amos W Balloux F et al The effect of ancient population bottlenecks on human phenotypes Nature 2007, 448:346-348. 10.1038/ nature05951 17637668 1978547
25. Linz B Balloux F Moodley Y Manica A Liu H Roumagnac P Falush D Stamer C Prugnolle F Merwe van der SW An African origin for the intimate association between humans and Helicobacter pylori Nature 2007, 445:915-918. 10.1038/nature05562 17287725 1847463
26. Huang Q-Y Xu F-H Shen H Deng H-Y Liu Y-J Liu Y-Z Li J-L Recker RR Deng H-W Mutations patterns at dinucleotide microsatellite loci in humans Am J Hum Genet 2002, 70:625-634. 10.1086/338997 11793300 384942
27. Yamada NA Smith GA Castro A Roques CN Boyer JC Farber RA Relative rates of insertion and deletion mutations in dinucleotide repeats of various lengths in mismatch repair proficient mouse and mismatch deficient human cells Mutat Res 2002, 499(2):213-225. 11827714
28. Rosenberg NA Li LM Ward R Pritchard JK Informativeness of genetic markers for inference of ancestry Am J Hum Genet 2003, 73:1402-1422. 10.1086/380416 14631557 1180403
29. Rosenberg NA Maghajan S Ramachandran S Zhao C Pritchard JK Feldman MW Clines, clusters, and the effect of study design on the inference of human population structure PLoS Genetics 2005, 1:660-671. 10.1371/ journal.pgen.0010070
30. Swinton J Amos W Measurement of distributional asymmetry in allele frequency distributions of microsatellites IMA J Math App Med Biol 2002, 19:257-273. 10.1093/imammb/19.4.257
31. Purvis A Rambaut A Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data CABIOS 1995, 11:247-251. 7583692
32. Kelkar YD YTyekucheva S Chlaromonte F Makova K The genome-wide determinants of human and chimpanzee microsatellite evolution Genome Res 2008, 18:30-38. 10.1101/gr.7113408 18032720 2134767
33. Rogers AR Jorde LB Ascertainment bias in estimates of average heterozygosity Am J Hum Genet 1996, 58:1033-1043. 1914628 8651264
34. Ramachandran S Deshpande O Roseman CC Rosenberg NA Feldman MW Cavalli-Sforza LL Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa Proc Natl Acad Sci USA 2005, 102:15942-15947. 10.1073/pnas.0507611102 16243969 1276087
35. Weber JL Wong C Mutation of human short tandem repeats Hum Mol Genet 1993, 2:1123-1128. 10.1093/hmg/2.8.1123 8401493