Properties of novel and widely studied Y-STR loci in three South African populations

Leat, Neil; Ehrenreich, Liezle; Benjeddou, Mongi; Cloete, Kevin Wesley; Davison, Sean

doi:10.1016/j.forsciint.2006.07.009

Cited by 26 publications

(11 citation statements)

References 26 publications

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“…Three of those markers had only population data and no mutation data previously reported: DYS711 (Leat et al, 2007;Maybruck et al, 2009;Zhang, Yang, Niu, & Guo, 2012); DYS712; DYS713 (Leat et al, 2007;Liu et al, 2019;Maybruck et al, 2009;Zhang et al, 2012). For one of the previously discovered Y-STR markers, DYS724, mutation data were previously inferred from population data (Chandler, 2006) and later from deep-rooted pedigrees (Boattini et al, 2019;Claerhout et al, 2018), while mutation data from comprehensive father-son pair analysis as in the present study were not previously reported.…”

Section: Mutation Analysismentioning

confidence: 54%

“…novel Y-STRs not previously described at all, and four Y-STRs previously described in population studies. The previously discovered Y-STRs were: DYS713 (Leat, Ehrenreich, Benjeddou, Cloete, & Davison, 2007), later also described as DYS685 (Maybruck, Hanson, Ballantyne, Budowle, & Fuerst, 2009); DYS711 (Leat et al, 2007), later also described as DYS688 (Maybruck et al, 2009); DYS712 (Leat et al, 2007); and CDY (included in commercial products of Family-TreeDNA), later also described as DYS724 (Jacobs et al, 2009).…”

Section: Mutation Analysismentioning

confidence: 99%

“…One Y-STR markers was previously discovered (Leat et al, 2007), and population data were published: DYS714 (Leat et al, 2007;Liu et al, 2019;Zhang et al, 2012). One of the nine novel FM Y-STRs is also used by FamilyTreeDNA under the name: DYR33, but no marker information was found in scientific publications.…”

Section: Mutation Analysismentioning

confidence: 99%

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Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

et al. 2020

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Short tandem repeat polymorphisms on the male‐specific part of the human Y‐chromosome (Y‐STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10−3 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y‐STR markers with untypically high mutation rates (>10−2), termed rapidly mutating (RM) Y‐STRs, and showed that they improved male relative differentiation over standard Y‐STRs. By applying a newly developed in silico search approach to the Y‐chromosome reference sequence, we identified 27 novel RM Y‐STR candidates. Genotyping them in 1,616 DNA‐confirmed father–son pairs for mutation rate estimation empirically highlighted 12 novel RM Y‐STRs. Their capacity to differentiate males related by 1, 2, and 3 meioses was 27%, 47%, and 61%, respectively, while for all 25 currently known RM Y‐STRs, it was 44%, 69%, and 83%. Of the 647 Y‐STR mutations observed in total, almost all were single repeat changes, repeat gains, and losses were well balanced; allele length and fathers' age were positively correlated with mutation rate. We expect these new RM Y‐STRs, together with the previously known ones, to significantly improving male relative differentiation in future human genetic applications.

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Section: Mutation Analysismentioning

confidence: 54%

Section: Mutation Analysismentioning

confidence: 99%

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Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

et al. 2020

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“…19 Thus, in addition to R V and R H , mean allele repeat count (A: estimated from the population data), CG content in motif (P CG : proportion of CG base pairs in the motif), and the categorical variables motif size (M: tri-, tetra-, penta-or hexanucleotide motif) and repeat structure (S: simple versus complex) were considered explanatory variables. Information about Y-STR motifs was obtained from Kayser et al, Järve et al, Gusmão et al and Leat et al [21][22][23][24] Problems of multicollinearity were evaluated on the full model (containing all explanatory variables), as collinear variables represent partial redundant information and correlations between variables generate unreliable individual estimates of regression coefficients. Alternative models obtained after removing different combinations of collinear variables were considered and reduced by stepwise removal of variables to minimize Akaike information criterion (AIC, ie, a standard procedure to find the explanatory variable combination, which accounts for the maximum of the variability with the minimum number of variables).…”

Section: Discussionmentioning

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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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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“…No polymorphisms were observed for the Xhosa population for 16 out of the 20 SNPs investigated in this study. In a previous study aimed at the development of male specific genotyping systems for use in sexual assault cases in South Africa, low levels of polymorphism were also observed for the Xhosa population (Leat et al , 2004a,b, 2007). …”

Section: Discussionmentioning

confidence: 98%

Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1) in the Xhosa population of South Africa

et al. 2014

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Human organic cation transporter 1 is primarily expressed in hepatocytes and mediates the electrogenic transport of various endogenous and exogenous compounds, including clinically important drugs. Genetic polymorphisms in the gene coding for human organic cation transporter 1, SLC22A1, are increasingly being recognized as a possible mechanism explaining the variable response to clinical drugs, which are substrates for this transporter. The genotypic and allelic distributions of 19 nonsynonymous and one intronic SLC22A1 single nucleotide polymorphisms were determined in 148 healthy Xhosa participants from South Africa, using a SNAPshot® multiplex assay. In addition, haplotype structure for SLC22A1 was inferred from the genotypic data. The minor allele frequencies for S14F (rs34447885), P341L (rs2282143), V519F (rs78899680), and the intronic variant rs622342 were 1.7%, 8.4%, 3.0%, and 21.6%, respectively. None of the participants carried the variant allele for R61C (rs12208357), C88R (rs55918055), S189L (rs34104736), G220V (rs36103319), P283L (rs4646277), R287G (rs4646278), G401S (rs34130495), M440I (rs35956182), or G465R (rs34059508). In addition, no variant alleles were observed for A306T (COSM164365), A413V (rs144322387), M420V (rs142448543), I421F (rs139512541), C436F (rs139512541), V501E (rs143175763), or I542V (rs137928512) in the population. Eight haplotypes were inferred from the genotypic data. This study reports important genetic data that could be useful for future pharmacogenetic studies of drug transporters in the indigenous Sub-Saharan African populations.

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Properties of novel and widely studied Y-STR loci in three South African populations

Cited by 26 publications

References 26 publications

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

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

Genetic polymorphisms and haplotypes of the organic cation transporter 1 gene (SLC22A1) in the Xhosa population of South Africa

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