DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

Gusmão, Leonor; Butler, John M.; Carracedo, Ángel; Gill, Peter; Kayser, Manfred; Mayr, Wolfgang R.; Morling, Niels; Prinz, Mechthild; Roewer, Lutz; Tyler‐Smith, Chris; Schneider, P. M.

doi:10.1007/s00414-005-0026-1

Cited by 205 publications

(90 citation statements)

References 52 publications

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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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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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“…The Y-STR alleles were designated according to the ISFG recommendations. 15 Several additional Y-STRs had already been studied in a subset of these samples using the PowerPlex Y System (Promega Corporation, Madison, WI, USA), following the protocol described by Arroyo-Pardo and collaborators. 16 …”

Section: Y-str Typingmentioning

confidence: 99%

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

et al. 2012

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Human Y chromosomes belonging to the haplogroup R1b1-P25, although very common in Europe, are usually rare in Africa. However, recently published studies have reported high frequencies of this haplogroup in the central-western region of the African continent and proposed that this represents a 'back-to-Africa' migration during prehistoric times. To obtain a deeper insight into the history of these lineages, we characterised the paternal genetic background of a population in Equatorial Guinea, a Central-West African country located near the region in which the highest frequencies of the R1b1 haplogroup in Africa have been found to date. In our sample, the large majority (78.6%) of the sequences belong to subclades in haplogroup E, which are the most frequent in Bantu groups. However, the frequency of the R1b1 haplogroup in our sample (17.0%) was higher than that previously observed for the majority of the African continent. Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa. The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene.

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“…Allele nomenclature was according to Butler where it was necessary to change nomenclature for compatibility with ISFG recommendations [11]. Compared to Butler et al [5], seven repeats were subtracted from DYS439, three subtracted from DYS448, and eight added to Y-GATA-H4.1.…”

Section: Y-str Nomenclaturementioning

confidence: 99%

“…Compared to Butler et al [5], seven repeats were subtracted from DYS439, three subtracted from DYS448, and eight added to Y-GATA-H4.1. Note that Y-GATA-H4.1 was previously referred to as Y-GATA-H4 [5], a name now used to refer to a larger amplicon including additional repeats [11]; in addition, the repeat motif is now (AGAT), rather than (TAGA). For DYS425, the repeat motif was taken to be (TGT) [12], and alleles in three reference chromosomes [6] defined by sequencing: YCC15 (allele 13), YCC24 (allele 12) and YCC43 (allele 12).…”

Section: Y-str Nomenclaturementioning

confidence: 99%

26-Locus Y-STR typing in a Bhutanese population sample

Parkin

Kraayenbrink

Driem

et al. 2006

Forensic Science International

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Abstract26 Y-chromosome short tandem repeat (STR) loci were amplified in a sample of 856 unrelated males from Bhutan, using two multiplex polymerase chain reaction (PCR) assays. The first multiplex is the Y-STR 20plex described by Butler et al. (2002), and the second is a novel (but overlapping) 14plex that targets six additional Y-STRs (DYS425, DYS434, DYS435, DYS436, DYS461, DYS462) and also amplifies the amelogenin locus. The 26 loci give a discriminating power of 0.9957, though even at this resolution one haplotype occurs 24 times. We identify novel alleles at five loci, and microvariants at a further three, which were characterised by sequencing. haplotypes for these samples have been submitted to the Y-STR Haplotype Reference Database.3

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DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

Cited by 205 publications

References 52 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

The genetic landscape of Equatorial Guinea and the origin and migration routes of the Y chromosome haplogroup R-V88

26-Locus Y-STR typing in a Bhutanese population sample

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