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• W2149015441 abstract "The above paper, which is published in this issue of the Journal, requires the following Corrigendum to be made. Following the availability of this paper on the Journal's Articles in Press website, we (the authors) were contacted by a number of experts in the field of population genetics directly and via the editors of the Journal to point out an error in the original analysis of independence between D12S391 and vWA using father/son paternity samples. This correspondence has led to the reanalysis of the father/son paternity data and the writing of this Corrigendum. In the original paper, father/son pairs were used to determine the gametic phase of alleles at D12S391 and vWA by determining which alleles were transmitted from father to son as a haplotype, assuming no recombination during meiosis. After phasing there were four D12S391/vWA haplotypes for each father/son pair—two haplotypes for the father and two haplotypes for the son. A father and son share one of their two D12S391/vWA haplotypes that was transmitted from the father to the son during meiosis. The phased father/son dataset was used for linkage disequilibrium analysis in the original paper. Also, the frequencies of the D12S391/vWA haplotypes were calculated using the four phased genotypes of the father/son pairs and were provided in the original Supplementary Data. We became aware that the phased father/son dataset mistakenly included both pairs of haplotypes so that the paternally transmitted haplotype was counted twice (i.e., once for the father and once for the son). A transmitted haplotype is not independent between a father/son pair and should not have been counted separately for linkage disequilibrium analysis and haplotype frequency calculations. Also, it was determined that the phase of some father/son genotypes could not be definitively determined without the genotype of the mother, which was unavailable in this dataset. Two parallel methods were used to revise the D12S391/vWA haplotype data used for linkage disequilibrium analysis: Dataset 1: The father/son dataset was reduced by removing one count of the paternally transmitted haplotype in addition to removing sample pairs if the gametic phase was ambiguous. The revised dataset included three haplotypes per father/son pair (one haplotype for the father and two haplotypes for the son) for all unambiguously phased father/son pairs. Linkage disequilibrium analysis was performed as described in “Materials and Methods” section of the original paper. Dataset 2: The expectation-maximization (EM) algorithm was used to estimate the four parental haplotypes (two paternal and two maternal) for each son, assuming a recombination fraction of 0.108 [[1]Budowle B. Ge J. Chakraborty R. Eisenberg A.J. Green R. Mulero J. Lagace R. Hennessy L. Population genetic analyses of the NGM STR loci.Int. J. Legal Med. 2011; 125: 101-109Crossref PubMed Scopus (60) Google Scholar]. From these estimated haplotypes, a maximum likelihood approach estimated the parental haplotype frequencies [[2]Ceppellini R. Siniscalco M. Smith C.A. The estimation of gene frequencies in a random-mating population.Ann. Hum. Genet. 1955; 20: 97-115Crossref PubMed Scopus (194) Google Scholar]. Note that the non-transmitted maternal haplotype provided little information for calculating haplotype frequency estimates. The haplotype frequency estimates were used as the revised dataset for linkage disequilibrium analysis. For linkage disequilibrium analysis, a likelihood ratio test was performed that compared the likelihood of the data based on the estimated haplotype frequencies (i.e., assuming linkage disequilibrium) to the likelihood of the data assuming no association (i.e., linkage equilibrium) [[3]Lange K. Boehnke M. Extensions to pedigree analysis. V. Optimal calculation of Mendelian likelihoods.Hum. Hered. 1983; 33: 291-301Crossref PubMed Scopus (61) Google Scholar]. Since the likelihood ratio test does not perform well if there are many haplotypes with low frequencies, alleles with frequencies below 5% were pooled for each locus prior to linkage disequilibrium analysis. Upon revised analysis of D12S391/vWA haplotypes, no significant evidence of linkage disequilibrium was observed between the D12S391 and vWA loci in the U.S. population groups (Table 1). These findings are consistent with the linkage disequilibrium analysis results using unrelated U.S. population samples as described in the original paper. Furthermore, the conclusion of independence between D12S391 and vWA is consistent with findings from two recent articles [1Budowle B. Ge J. Chakraborty R. Eisenberg A.J. Green R. Mulero J. Lagace R. Hennessy L. Population genetic analyses of the NGM STR loci.Int. J. Legal Med. 2011; 125: 101-109Crossref PubMed Scopus (60) Google Scholar, 4Phillips C. Fernandez-Formoso L. Garcia-Magariños M. Porras L. Tvedebrink T. Amigo J. Fondevila M. Gomez-Tato A. Alvarez-Dios J. Freire-Aradas A. Gomez-Carballa A. Mosquera-Miguel A. Carracedo Á. Lareu M.V. Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel.Forensic Sci. Int. Genet. 2011; 5: 155-169Abstract Full Text Full Text PDF PubMed Scopus (90) Google Scholar]. Thus, the single-locus genotype probabilities for the D12S391 and vWA loci may be multiplied to determine the profile match probability when unrelated individuals are involved.Table 1P-value results from analysis of linkage disequilibrium (LD) of the D12S391 and vWA loci using U.S. father/son paternity samples. The original data included four haplotypes for each father/son pair, including some pairs with ambiguous phase. Dataset 1 consisted of three definitively phased haplotypes for each father/son pair. Dataset 2 consisted of estimated parental haplotype frequencies. Significance level, p < 0.05 (in bold). N = number of haplotypes.PopulationOriginal dataDataset 1Dataset 2NLDNLDNLDAfrican American3560.02752140.48883560.8756Caucasian3960.00012500.21953960.1685Hispanic3800.09152280.71053800.8857Asian3960.00312170.13173960.6541 Open table in a new tab After acceptance of the original paper, the authors became aware of a study by Budowle et al. that reported no significant linkage disequilibrium between D12S391 and vWA using a set of unrelated U.S. population samples [[1]Budowle B. Ge J. Chakraborty R. Eisenberg A.J. Green R. Mulero J. Lagace R. Hennessy L. Population genetic analyses of the NGM STR loci.Int. J. Legal Med. 2011; 125: 101-109Crossref PubMed Scopus (60) Google Scholar]. Using multi-generation family samples, this study estimated a recombination fraction of 0.108 between D12S391 and vWA, thus, indicating “close” linkage between the loci [[1]Budowle B. Ge J. Chakraborty R. Eisenberg A.J. Green R. Mulero J. Lagace R. Hennessy L. Population genetic analyses of the NGM STR loci.Int. J. Legal Med. 2011; 125: 101-109Crossref PubMed Scopus (60) Google Scholar]. The effect of linkage is an increased tendency for alleles at physically close loci to be transmitted together during meiosis. Since there is no evidence for linkage disequilibrium between the two loci, it does not seem necessary to use haplotype frequencies. Instead, an independent occurrence of alleles at both loci for the calculation of (two-locus) genotype frequencies can be assumed. Nevertheless, completely ignoring linkage between the two loci can lead to incorrect inference in certain kinship scenarios, at least if transmission over more than two meioses is observed [5Krawczak M. Kinship testing with X-chromosomal markers: mathematical and statistical issues.Forensic Sci. Int. Genet. 2007; 1: 111-114Abstract Full Text Full Text PDF PubMed Scopus (41) Google Scholar, 6Nothnagel M. Schmidtke J. Krawczak M. Potentials and limits of pairwise kinship analysis using autosomal short tandem repeat loci.Int. J. Legal Med. 2010; 124: 205-215Crossref PubMed Scopus (43) Google Scholar]. This erratum provides the maximum likelihood estimates of the D12S391/vWA haplotype frequencies (alleles have not been pooled) and should be used in lieu of the haplotype frequency table provided as Supplementary Data in the original paper. We thank Rolf Fimmers and Andreas Tillmar for their assistance with the different approaches for data reduction and phasing. Download .xls (.04 MB) Help with xls files Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samplesForensic Science International: GeneticsVol. 5Issue 5PreviewRecently, the European Network of Forensic Science Institutes voted to adopt five additional STR loci (D12S391, D1S1656, D2S441, D10S1248, and D22S1045) to their existing European Standard Set of seven STRs (TH01, vWA, FGA, D8S1179, D18S51, D21S11, and D3S1358). The D12S391 and vWA loci are located 6.3 megabases (Mb) apart on chromosome 12. Ideally for use in forensic analyses, genetic markers on the same chromosome should be more than 50 Mb in physical distance in order to ensure full recombination and thus independent inheritance. Full-Text PDF" @default.
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• W2149015441 title "Corrigendum to “Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samples” [Forensic Sci. Int.: Genet. (in press), doi:10.1016/j.fsigen.2010.09.003]" @default.
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