Brief communication: Multiplex X/Y‐PCR improves sex identification in aDNA analysis

Hummel, Susanne; Herrmann, Bernd

doi:10.1002/ajpa.10172

Cited by 16 publications

(11 citation statements)

References 27 publications

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“…Previously, it was hypothesized that a strong selection advantage may have been conferred to carriers of the nonfunctional CCR5 allele, which drove its frequency rapidly upward in ancestral Caucasian populations. Resistance to an Methods: The skeletons of the burial sites of Goslar, Alia and the Lichtenstein cave had previously been genetically analyzed in studies that aimed at the reconstruction of kinship on an individual and population level 13,[19][20][21] or that focused on the DF508 mutation at the cystic fibrosis locus. 22 In all cases, the DNA was preserved in excellent condition.…”

Section: Ccr5-d32mentioning

confidence: 99%

Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons

et al. 2005

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A mutant allele of the chemokine receptor CCR5 gene (CCR5-D32), which confers resistance to HIV-1 infection, is believed to have originated from a single mutation event in historic times, and rapidly expanded in Caucasian populations, owing to an unknown selective advantage. Among other candidates, the plague bacillus Yersinia pestis was implicated as a potential source of strong selective pressure on European populations during medieval times. Here, we report amplifications of the CCR5-D32 DNA sequence from up to 2900-year-old skeletal remains from different burial sites in central Germany and southern Italy. Furthermore, the allele frequency of CCR5-D32 in victims of the 14th century plague pandemic in Lü beck/ northern Germany was not different from a historic control group. Our findings indicate that this mutation was prevalent already among prehistoric Europeans. The results also argue against the possibility of plague representing a major selective force that caused rapid increase in CCR5-D32 gene frequencies within these populations. Genes and Immunity (2005) The human chemokine receptor CCR5 serves, together with CD4, as the principal coreceptor for macrophagetropic (R5) human immunodeficiency virus type 1 (HIV-1) strains. 1 A large number of genetic variants in the coding or the promotor region of the CCR5 gene have been identified in different ethnic groups. 2,3 Several of these naturally occurring mutations result in alterations of the receptor's amino-acid sequence and affect the ability of CCR5 to act as a chemokine receptor or HIV coreceptor. 4,5 The finding that nonfunctional receptor alleles are relatively frequent among different human populations has led to the hypothesis that a selective advantage might be associated with the loss of CCR5 function.The CCR5-D32 mutant, which is characterized by a 32-bp deletion in the gene segment encoding the second extracellular loop of the receptor, provides an instructive example of how host genetic variation may contribute to HIV-related pathology. Individuals homozygous for CCR5-D32 are almost completely protected against HIV-1 infection due to the absence of functional receptors from the cell surface. 6-8 Population surveys revealed a north to south gradient of CCR5-D32 allele frequencies of 16 to 3% across Europe and its absence in individuals of nonCaucasian descent. 9-11 Determination of the intrahaplotypic variation of flanking microsatellite loci in strong linkage disequilibrium with CCR5-D32 allowed calculation of the approximate age of the CCR5-D32 containing ancestral haplotype. Two different studies that analyzed separate microsatellite markers concluded that the CCR5-D32 allele originated from a single mutation event that took place in historic times approximately 700 years (95% confidence interval (CI): 275-1800) 11 to 3500 years (CI 400-13 000) 10 ago in northeastern Europe. Both studies assumed a heterozygote advantage of the CCR5-D32 mutant. The European locale and timing of the bubonic plague of the 14th century coincide with the calculat...

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Section: Ccr5-d32mentioning

confidence: 99%

Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons

et al. 2005

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“…Some proposed methods have been based on the analyses of genetic markers lying in the Y chromosome [59]–[61], or in the use of both X-chromosomal and Y-chromosomal STRs [47]. Furthermore, a new method to sex determination using shotgun sequencing has been reported [62], although it might be too expensive for routine application in a large number of samples.…”

Section: Introductionmentioning

confidence: 99%

Sex Determination in Highly Fragmented Human DNA by High-Resolution Melting (HRM) Analysis

2014

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Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.

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“…Previous ancient molecular approaches for sex identification have targeted amelogenin genes (Haak et al, 2008;Lassen et al, 2000;Shaw et al, 2015;Svensson et al, 2012), zinc finger protein genes (ZFX/Y) (Svensson et al, 2008) sex-linked Y-or W-chromosome sequences (Allentoft et al, 2010;Bunce et al, 2003;Cappellini et al, 2004) or a combination of markers (Arslan et al, 2011;Pag•s et al, 2009;Schmidt et al, 2003). In many cases, molecular sex identification techniques suffer from a high failure rate, due to the low quantity of single-copy sex markers in archaeological samples (Alonso et al, 2004;PŠŠbo et al, 2004).…”

Section: Challenges With Existing Dna-based Sex Identification Technimentioning

confidence: 99%

Identifying the sex of archaeological turkey remains using ancient DNA techniques

Speller

Yang

2016

Journal of Archaeological Science: Reports

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ABSTRACT'!Accurate sex identification of archaeological turkey remains is important for deciphering hunting and husbandry practices in pre-contact North America, particularly in the Southwest United States and Mesoamerica where domestic turkeys were raised. Although the sexual dimorphism of turkeys means that relatively complete elements can be distinguished using osteometric approaches, sexing fragmentary or juvenile remains is challenging. Here, we propose a simple and highly-sensitive coamplification approach which targets highly-repetitive DNA (hrDNA) sequences on the turkey Wchromosome. This technique simultaneously co-amplifies both hrDNA and mitochondrial DNA (mtDNA) fragments: the amplification of the W chromosome identifies the heterogametic sex (females), while the mtDNA fragment acts as an internal positive control to monitor for false negative results. To demonstrate the sensitivity and accuracy of this technique, we applied it to 20 modern turkeys and 117 archaeological turkey bones from 25 sites (ca. AD700-1700), including 32 samples from Sand Canyon Pueblo (AD1250-1300). We amplified ancient DNA from 86% of the ancient remains, demonstrating the sensitivity of the technique for targeting nuclear DNA. The correspondence between morphological size and the genetic sex identification for 100% of the complete skeletal elements demonstrates the accuracy and robusticity of this approach. Although within the larger regional assemblage, more males than females were identified (61% vs 39%), the site-specific analysis at Sand Canyon Pueblo suggests that adult male and female turkeys were present in a relatively even ratio. !

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Brief communication: Multiplex X/Y‐PCR improves sex identification in aDNA analysis

Cited by 16 publications

References 27 publications

Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons

Detection of the CCR5-Δ32 HIV resistance gene in Bronze Age skeletons

Sex Determination in Highly Fragmented Human DNA by High-Resolution Melting (HRM) Analysis

Identifying the sex of archaeological turkey remains using ancient DNA techniques

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