Variation of 52 new Y-STR loci in the Y Chromosome Consortium worldwide panel of 76 diverse individuals

Lim, Sung-Soo; Xue, Yali; Parkin, Emma J.; Tyler‐Smith, Chris

doi:10.1007/s00414-006-0124-8

Cited by 37 publications

(22 citation statements)

References 11 publications

(17 reference statements)

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“…We investigated a Chinese family carrying the DFNY1 Y-linked hearing-impairment mutation [6] and genotyped two family members, DFNY1-66 (affected) and DFNY1-101 (unaffected), who were separated by 13 generations, with 67 Y-STRs [7]. We found that their Y haplotypes were indeed identical at all these loci (Table S1 in the Supplemental Data).…”

Section: Resultsmentioning

confidence: 98%

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

et al. 2009

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SummaryUnderstanding the key process of human mutation is important for many aspects of medical genetics and human evolution. In the past, estimates of mutation rates have generally been inferred from phenotypic observations or comparisons of homologous sequences among closely related species [1–3]. Here, we apply new sequencing technology to measure directly one mutation rate, that of base substitutions on the human Y chromosome. The Y chromosomes of two individuals separated by 13 generations were flow sorted and sequenced by Illumina (Solexa) paired-end sequencing to an average depth of 11× or 20×, respectively [4]. Candidate mutations were further examined by capillary sequencing in cell-line and blood DNA from the donors and additional family members. Twelve mutations were confirmed in ∼10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 × 10−8 mutations/nucleotide/generation (95% CI: 8.9 × 10−9–7.0 × 10−8), consistent with estimates of 2.3 × 10−8–6.3 × 10−8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed.

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Section: Resultsmentioning

confidence: 98%

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

et al. 2009

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“…However, reliable locus-specific mutation rates are needed to carefully choose loci to minimize the error rate in kinship analysis and sample identification 2 while obtaining the maximum discriminatory power (eg, Mulero et al, Lim et al and Vermeulen et al [3][4][5]. Also in population genetics and evolutionary studies, correct inferences on the timing of major demographic events, the age of the most common ancestor, as well as dating Y-lineages and tracing disease evolution are based on the knowledge of mutation rates (eg, Shi et al, Zerjal et al and Xue et al [6][7][8] ).…”

Section: Introductionmentioning

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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“…html). Up to now, reports on large volumes of population genetic data from a wide range of ethnic groups for the Y-STR loci have focused on the core loci [16][17][18][19], while several papers have reported polymorphic Y-STR loci other than the core loci [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of miniY-STR multiplex PCR systems for extended 16 Y-STR loci

et al. 2007

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We developed three short amplicon Y-chromosomal short tandem repeat (miniY-STR) polymerase chain reaction multiplex systems for 16 Y-STR loci (DYS441, DYS446, DYS462, DYS481, DYS485, DYS495, DYS505, DYS510, DYS511, DYS549, DYS 575, DYS578, DYS593, DYS618, DYS638, and DYS643), using newly designed primer sets. In an assay of 238 Japanese males using the three miniY-STR systems, amplification product lengths ranged from 91 to 151 bp for all 16 Y-STR loci. We identified 212 different haplotypes among the 238 individuals, finding haplotype diversity and discrimination capacity of 0.9974 and 0.8908, respectively. An assay of degraded DNA samples using the three miniY-STR multiplex systems, including artificially degraded samples and degraded forensic casework samples, proved remarkably effective. In conclusion, analyses of miniY-STR multiplex systems will play an important role in forensic applications involving degraded DNA samples for which genotyping using only commercial kits is ill-suited.

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Variation of 52 new Y-STR loci in the Y Chromosome Consortium worldwide panel of 76 diverse individuals

Cited by 37 publications

References 11 publications

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree

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

Evaluation of miniY-STR multiplex PCR systems for extended 16 Y-STR loci

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