Supplemented Data on Mutation Rates in 33 Autosomal Short Tandem Repeat Polymorphisms

Henke, Lotte; Henke, Jürgen

doi:10.1111/j.1556-4029.2006.00094.x

Cited by 13 publications

(7 citation statements)

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“…For the CODIS loci [18], FGA had the highest mutation rate, and TPOX and TH01 had the lowest mutation rates in each dataset. D18S51 had a moderate mutation rate in [17], [19], and this study, while the highest mutation rate was shown in AABB (Association of Blood Banks) data [18]. Furthermore, differences could be observed within the Chinese Han population [17] at the following loci: D3S1358, D5S818, D18S51, D21S11, and Penta E (Table S3).…”

Section: Resultsmentioning

confidence: 44%

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Mutation analysis of 24 short tandem repeats in Chinese Han population

Liu

et al. 2011

Int J Legal Med

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Germline mutations of 24 short tandem repeat (STR) loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, Penta E, D16S539, D18S51, Penta D, D21S11, D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05) were studied for 6,441 parent-child meioses taken from the paternity testing cases in Chinese Han population. In total, 195 mutations were identified at 22 of the 24 loci. Among them, 189 (96.92%) mutations were one step, five mutations (2.56%) were two step, and one mutation (0.51%) was three step. No mutation was found at the TH01 and TPOX loci. The overall mutation rate estimated was 0.0013 (95% CI 0.0011-0.0015), and the locus-specific mutation rate estimated ranged from 0 to 0.0034. There was a bias in the STR mutations that repeat gains were more common than losses (∼1.7:1). Mutation events in the male germline were more frequent than in the female germline (∼4.3:1). Furthermore, loci with a larger heterozygosity tended to have a higher mutation rate. Mutation in short alleles was biased towards expansion, whereas mutation in long alleles favored contraction. The long alleles have a higher allelic mutational probability than short alleles.

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Section: Resultsmentioning

confidence: 44%

“…In comparing locus-specific mutation rates with the data from other studies [17][18][19][20], we found that the mutation rate differences between datasets vary with the loci (Table S3). For the CODIS loci [18], FGA had the highest mutation rate, and TPOX and TH01 had the lowest mutation rates in each dataset.…”

Section: Resultsmentioning

confidence: 84%

Mutation analysis of 24 short tandem repeats in Chinese Han population

Liu

et al. 2011

Int J Legal Med

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“…On a per-generation basis, the mutation rates that we report for C. elegans and D. pulex are much lower than those previously estimated for humans (Heyer et al 1997;Brinkmann et al 1998;Sajantila et al 1999;Kayser et al 2000;Leopoldino and Pena 2003;Dupuy et al 2004;Ballard et al 2005;Gusmao et al 2005;Henke and Henke 2006;Yan et al 2006;Hohoff et al 2007;Lee et al 2007), but much higher than those for yeast (Henderson and Petes 1992;Strand et al 1993;Johnson et al 1996;Sia et al 1997Sia et al , 2001Wierdl et al 1997;Hawk et al 2005;Legendre et al 2007). In principle, such differences could simply arise as a consequence of the pronounced variation in the numbers of germline cell divisions per generation that exists among these species (1, 10, and $200, respectively, in Saccharomyces cerevisiae, C. elegans, and Homo sapiens; Kimble and Ward 1998;Crow 2000).…”

Section: Discussionmentioning

confidence: 43%

“…Such slippage adds or deletes repeat units from the newly synthesized strand at a frequency that depends on factors such as overall length, repeat type, flanking sequence, and recombination rate (Schlötterer 2000). Previous estimates of microsatellite mutation rates in animals ½direct estimates derived from individuals with known parentage (Brinkmann et al 1998;Sajantila et al 1999;Leopoldino and Pena 2003;Henke and Henke 2006;Hohoff et al 2007) and indirect estimates based on the application of models of microsatellite evolution to standing patterns of variation (Chakraborty et al 1997) are as high as 10 À3 and 10 À4 / locus/generation. Most studies show that the spectrum of microsatellite mutations is heavily dependent on allele size (Xu et al 2000;Lai and Sun 2003) and suggest that the mechanism may be more complex than the simple stepwise mutation model (Brohede et al 2002;Huang et al 2002;Calabrese and Durrett 2003).…”

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confidence: 99%

The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex

et al. 2008

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The effective use of microsatellite loci as tools for microevolutionary analysis requires knowledge of the factors influencing the rate and pattern of mutation, much of which is derived from indirect inference from population samples. Interspecific variation in microsatellite stability also provides a glimpse into aspects of phylogenetic constancy of mutational processes. Using long-term series of mutation-accumulation lines, we have obtained direct estimates of the spectrum of microsatellite mutations in two model systems: the nematode Caenorhabditis elegans and the microcrustacean Daphnia pulex. Although the scaling of the mutation rate with the number of tandem repeats is highly consistent across distantly related species, including yeast and human, the per-cell-division mutation rate appears to be elevated in multicellular species. Contrary to the expectations under the stepwise mutation model, most microsatellite mutations in C. elegans and D. pulex involve changes of multiple repeat units, with expansions being much more common than contractions.

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“…Those mutations can be explained by replication slippage, which is generally expected to be the major mechanism causing new STR mutations [22]. Mutations of autosomal STRs are reported to occur in approximately 0.2-0.4% of meiosis [23], and these observations are also similar to those of Y-STRs [24,25,26]. In contrast to the significant mutation rates of STR markers, a main advantage of SNPs is its negligible mutation rate.…”

Section: Resultsmentioning

confidence: 99%

Usefulness of SNPs as Supplementary Markers in a Paternity Case with 3 Genetic Incompatibilities at Autosomal and Y Chromosomal Loci

Lindner

Wurmb‐Schwark

Meier

et al. 2014

Transfus Med Hemother

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Background: In kinship testing, investigation of 15 short tandem repeats (STRs) usually provides decisive genetic information for resolving relationship cases. However, in complex deficiency cases, in cases with more than 2 mutations at different STR loci or when close (untested) relatives of the alleged father are suggested to be the biological father of the child, STR typing alone may not be sufficient. In these cases, the application of supplementary markers such as single nucleotide polymorphisms (SNPs) is recommended. Methods: We describe a paternity case with 3 genetic incompatibilities (Penta D, VWA, and DYS385) between the alleged father and the child after analyzing 23 autosomal and 16 Y chromosomal STR loci. The question arose as to whether the alleged father could be excluded and a related person could be the biological father of the child, or whether the observed genetic incompatibilities were mutations. Interestingly, the 2 excluded full brothers of the alleged father possessed identical genetic incompatibilities at locus VWA and DYS385 as the alleged father. Results and Conclusions: Additional performance of a 50-plex SNP assay demonstrated that the observed mismatches were indeed mutations and the alleged father was the biological father of the child. The results show the usefulness of SNPs as supplementary markers in relationship testing when STR analyses show ambiguous results.

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Supplemented Data on Mutation Rates in 33 Autosomal Short Tandem Repeat Polymorphisms

Abstract: POPULATION: 106–8598 meioses studied in German Caucasians.

Cited by 13 publications

References 5 publications

Mutation analysis of 24 short tandem repeats in Chinese Han population

Mutation analysis of 24 short tandem repeats in Chinese Han population

The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex

Usefulness of SNPs as Supplementary Markers in a Paternity Case with 3 Genetic Incompatibilities at Autosomal and Y Chromosomal Loci

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