Mutation rates at Y chromosome short tandem repeats in Texas populations

Ge, Jianye; Budowle, Bruce; Aranda, Xavier G.; Planz, John V.; Eisenberg, Arthur J.; Chakraborty, Ranajit

doi:10.1016/j.fsigen.2009.01.007

Cited by 66 publications

(51 citation statements)

References 16 publications

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“…21 Lower mutability of shorter alleles compared with longer ones has been observed several times. 32,33,12,34 Accordingly, our results show that the variation in meiosis mutation rates could be significantly explained by mean repeat count (Supplementary Tables S5 and S6). Furthermore, when no diversity variable is included in the model, both repeat count and repeat motif contribute independently to explain the mutation rate variability (ie, model m3, Supplementary Table S5).…”

Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 57%

“…However, violations of this assumption have been reported both in phylogenetic and meiosis studies (eg, Dupuy et al, Ge et al, Forster et al and Nebel et al 33,34,38,39 ), suggesting that more complex models than SMM would better explain microsatellite variation. The ratio of variances in number of repeats between two loci can be still considered a good estimator of the ratio of mutation rates even in case of multistep mutations, provided that deviation from the SMM is similar for both loci (cf.…”

Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 99%

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Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Burgarella

Navascués

2010

Eur J Hum Genet

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Y-chromosome microsatellites (Y-STRs) are typically used for kinship analysis and forensic identification, as well as for inferences on population history and evolution. All applications would greatly benefit from reliable locus-specific mutation rates, to improve forensic probability calculations and interpretations of diversity data. However, estimates of mutation rate from father-son transmissions are available for few loci and have large confidence intervals, because of the small number of meiosis usually observed. By contrast, population data exist for many more Y-STRs, holding unused information about their mutation rates. To incorporate single locus diversity information into Y-STR mutation rate estimation, we performed a meta-analysis using pedigree data for 80 loci and individual haplotypes for 110 loci, from 29 and 93 published studies, respectively. By means of logistic regression we found that relative genetic diversity, motif size and repeat structure explain the variance of observed rates of mutations from meiosis. This model allowed us to predict locus-specific mutation rates (mean predicted mutation rate 2.12Â10 À3 , SD¼1.58Â10 À3 ), including estimates for 30 loci lacking meiosis observations and 41 with a previous estimate of zero. These estimates are more accurate than meiosis-based estimates when a small number of meiosis is available. We argue that our methodological approach, by taking into account locus diversity, could be also adapted to estimate population or lineage-specific mutation rates. Such adjusted estimates would represent valuable information for selecting the most reliable markers for a wide range of applications.

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Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 57%

Section: Mutation Rate Estimates For Y-strsmentioning

confidence: 99%

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Burgarella

Navascués

2010

Eur J Hum Genet

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“…The results were read from a 3730 sequencer (Supplementary Table S2), and ages of each clade was estimated from the median-joining networks within Network 4.6.1.1 (Fluxus) using the rho statistic. Both the evolutionary (6.9 × 10 − 4 per STR per generation) and the observed genealogical (2.1 × 10 − 3 per STR per generation) mutation rate were applied in this study, 24,25 assuming a generation time of 25 years. A Contour map was drawn based on the frequency distribution of Haplogroup O*-M134(xM117) generated in this study and previously published data (Supplementary Table S3) using the Kriging procedure with the aid of the Surfer 8.0 Software (Golden Software, Golden, CO, USA).…”

Section: Methodsmentioning

confidence: 99%

Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134

et al. 2015

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The human Y-chromosome haplogroup O-M134 is one of the most abundant paternal lineages in East Asian populations, comprising~13% of Han Chinese males, and also common in Kazakh, Korean, Japanese, Thai and so on. Despite its considerable prevalence, its current substructure is poorly resolved with only one downstream marker (M117) previously investigated. Here we address this deficiency by investigating some single-nucleotide polymorphisms (SNPs) previously reported being potentially associated with O-M134 based on high-throughput DNA-sequencing data. Using a panel of 1301 Chinese males we first identified 154 haplogroup O-M134 subjects. We then investigated the phylogenetic structure within this haplogroup using 10 SNPs (F444, F629, F3451, F46, F48, F209, F2887, F3386, F1739 and F152). Two major branches were identified, O-M117 and O-F444 and the latter was further divided into two main subclades, O-F629 and O-F3451, accounting for 10.84 and 0.92% of the Han Chinese, respectively. This update of O-M134 diversification permits better resolution of male lineages in population studies of East Asia.

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“…This information is required for fitting mutation models with alleledependent mutation rates. For studies that did not provide paternal allele frequencies, we tried to approximate these as follows: For four studies (Kayser et al 2000;Budowle et al 2005;Ge et al 2009;Goedbloed et al 2009), estimates were equated to the respective allele frequencies as reported for the relevant subpopulations in the Y Chromosome Haplotype Reference Database (Willuweit and Roewer 2007), Release 31. For the remaining studies, we adopted the allele frequencies reported in the studies themselves, although these estimates included not only fathers, but also unrelated individuals.…”

Section: Y-strsmentioning

confidence: 99%

Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites

et al. 2011

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The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.

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Mutation rates at Y chromosome short tandem repeats in Texas populations

Cited by 66 publications

References 16 publications

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Mutation rate estimates for 110 Y-chromosome STRs combining population and father–son pair data

Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134

Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites

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