Twelve short tandem repeat loci Y chromosome haplotypes: Genetic analysis on populations residing in North America

Budowle, Bruce; Adamowicz, Mike; Aranda, Xavier G.; Barna, Charles; Chakraborty, Ranajit; Cheswick, Dan; Dafoe, Bradley; Eisenberg, Arthur J.; Frappier, Roger; Gross, Ann Marie; Ladd, Carll; Lee, Hee Suk; Milne, Scott C.; Meyers, Carole; Prinz, Mechthild; Richard, Melanie L.; Saldanha, Gabriela; Tierney, Amy A.; Viculis, Lori; Krenke, Benjamin E.

doi:10.1016/j.forsciint.2005.01.010

Cited by 66 publications

(58 citation statements)

References 31 publications

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“…However, these various populations are all much the same in the average mutation rate for minimal haplotype STRs, most near ranging around 1.5-3.0×10 −3 [8,10,12,13,15,16,19,20,25]. The present study and those by Budowle et al [18] and Gusmão et al [20] do not show a statistically significant difference for the average mutation rate across minimal haplotype STRs (P> 0.05). This demonstrates that differences in haplogroupspecific mutation rates are not significant [15].…”

Section: Resultssupporting

confidence: 50%

“…Among these, 278 haplotypes (78.3%) were observed once, 22 were observed twice (12.4%), two were observed three times (1.7%), one was observed four times (1.1%), two were observed five times (2.8%), and the other two were The average overall mutation rates estimated for 9-17 STRs in various populations [8,10,12,13,[15][16][17][18][19][20]29] ranged from 1.6×10 −3 [18] to 4.3×10 −3 [17]. Including our data, these values are not significantly different from each other (P>0.05), except for that obtained from the present study and those by Budowle et al [18] and Gusmão et al [20] (P<0.05). However, these various populations are all much the same in the average mutation rate for minimal haplotype STRs, most near ranging around 1.5-3.0×10 −3 [8,10,12,13,15,16,19,20,25].…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, knowledge of mutation rates is also essential for consistently dating the origin of Y-chromosomal lineages defined by single-nucleotide polymorphisms (SNP) in molecular-anthropology studies [9][10][11]. Until now, more than 200 Y-STR polymorphisms have been described, but studies on Y-STR mutation rates are still insufficient and have considered only a restricted number of markers [8,10,[12][13][14][15][16][17][18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

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Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

et al. 2006

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We analyzed 369 Korean father/son haplotype transfers in 355 families at 22 Y-STRs (DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS388, DYS437, DYS438, DYS439, DYS446, DYS447, DYS448, DYS449, DYS456, DYS458, DYS464, DYS635, and GATA H4.1). A total of 350 haplotypes were observed with an overall haplotype diversity of 0.9999. Among these, 345 were unique and five were found twice. Furthermore, 36 mutations were identified, giving locus-specific mutation rate estimates between 0.0 and 19.0 x 10(-3) per generation and an average mutation rate estimate of 3.9 x 10(-3) (95% CI 2.7-5.4 x 10(-3)). The compilation of Y-STR mutation events for the present study and previous studies demonstrates that DYS449, DYS458, DYS635, DYS456 and DYS439 are the most prone to mutations and that their overall average mutation rate estimate is 2.36 x 10(-3) (95% CI 2.03-2.73 x 10(-33)).

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Section: Resultssupporting

confidence: 50%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

et al. 2006

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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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“…Since we are comparing all 102 possible pairs of men, the observations in the contingency table are not independent (a match between 103 man 1 and 2 and a match between man 1 and 3 means there will be a match between man 1 and 3). 104 Therefore, similar to [7,12,13], the distribution of the chi-square test statistic, assuming independence, 105 was determined by a permutation test. We constructed new databases containing 2085 men by making 106 permutations of the auto and Y-chromosomal DNA profiles in our database.…”

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confidence: 99%

The combined evidential value of autosomal and Y-chromosomal DNA profiles obtained from the same sample

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Sjerps

Meester³

et al. 2014

Int J Legal Med

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When a Y-chromosomal and a (partial) autosomal DNA profile are obtained from one crime 7 sample, and both profiles match the suspect's profiles, we would like to know the combined evidential 8 value. To calculate the likelihood ratio of observing the autosomal and Y-chromosomal DNA profiles com-9 bined, we need to know the conditional random match probability of the observed autosomal DNA profile, 10 given the Y-chromosomal match. We examine this conditional probability in two ways: (1) with a database 11 containing 2085 men, and (2) using a simulation model. We conclude that if the Y-chromosomal DNA 12 profiles match, we can still regard the autosomal DNA profile as independent from the Y-chromosomal 13 DNA profile if the matching person is not a descendant of the father of the donor of the (crime) sample. 14 The evidential value can in that case be computed by multiplying the random match probabilities of the 15 individual profiles.

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Twelve short tandem repeat loci Y chromosome haplotypes: Genetic analysis on populations residing in North America

Cited by 66 publications

References 31 publications

Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs

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

The combined evidential value of autosomal and Y-chromosomal DNA profiles obtained from the same sample

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