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https://www.readbyqxmd.com/read/29739989/haplotypic-polymorphisms-and-mutation-rate-estimates-of-22-y-chromosome-strs-in-the-northern-chinese-han-father-son-pairs
#1
Yaran Yang, Weini Wang, Feng Cheng, Man Chen, Tong Chen, Jing Zhao, Chong Chen, Yan Shi, Chen Li, Chuguang Chen, Yacheng Liu, Jiangwei Yan
Y chromosome Short tandem repeats (Y-STRs) analysis has been widely used in forensic identification, kinship testing, and population evolution. An accurate understanding of haplotype and mutation rate will benefit these applications. In this work, we analyzed 1123 male samples from Northern Chinese Han population which including 578 DNA-confirmed father-son pairs at 22 Y-STRs loci. A total of 537 haplotypes were observed and the overall haplotype diversity was calculated as 1.0000 ± 0.0001. Except that only two haplotypes were observed twice, all the rest of the 535 were unique...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29737420/genetic-polymorphisms-of-32-y-str-loci-in-meizhou-hakka-population
#2
Weian Du, Weibin Wu, Zihao Wu, Longjun Guo, Bangchao Wang, Ling Chen
Using AGCU Y24 Plus PCR Amplification Kit, 32 Y short tandem repeat (STR) loci were analyzed in 355 unrelated male participants of Meizhou city in Guangdong Province of China. By analyzing 341 different haplotypes, it was found that haplotype diversity (HD) and discrimination capacity (DC) were 0.9995 and 0.9605, respectively. Population relationships were analyzed by comparing Hakka population with ten other populations. The results indicate that Meizhou Hakka population was closely related to Guangdong Han population...
May 8, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29679929/a-phylogenetic-framework-facilitates-y-str-variant-discovery-and-classification-via-massively-parallel-sequencing
#3
Tunde I Huszar, Mark A Jobling, Jon H Wetton
Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega's prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing...
April 12, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29679928/likelihood-ratio-development-for-mixed-y-str-profiles
#4
Duncan Taylor, James Curran, John Buckleton
In this paper we introduce a new likelihood ratio method for evaluating mixed Y-STR profiles that is based on the premise that, given a haplotype has been seen in the person of interest, the most likely source of a second haplotype, matching at all or most loci, is in an individual with a recent common ancestor. We have called the new method the "Haplotype centred" (HC) method for likelihood ratio derivation. For single source, unambiguous haplotypes the HC method performs identically with the Kappa method proposed by Brenner...
April 7, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29666998/male-dna-under-female-fingernails-after-scratching-transfer-and-persistence-evaluation-by-rt-pcr-analysis-and-y-str-typing
#5
Alessandra Iuvaro, Carla Bini, Silvia Dilloo, Stefania Sarno, Susi Pelotti
The collection of biological debris beneath fingernails can be useful in forensic casework when a struggle between the victim and the offender is suspected. In the present study, we set up a controlled scratching experiment in which female volunteers scratched the male volunteers' forearms, simulating a defensive action during an assault. A total of 160 fingernail samples were collected: 80 "control samples" before the scratching, 40 samples immediately after the scratching (t = 0 h), and 40 samples 5 h after the scratching (t = 5 h)...
April 17, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29627344/corrigendum-to-development-of-an-italian-rm-y-str-haplotype-database-results-of-the-2013-gefi-collaborative-exercise-forensic-sci-int-genet-15-2015-56-63
#6
C Robino, A Ralf, S Pasino, M R De Marchi, K N Ballantyne, A Barbaro, C Bini, E Carnevali, L Casarino, C Di Gaetano, M Fabbri, G Ferri, E Giardina, A Gonzalez, G Matullo, A L Nutini, V Onofri, A Piccinini, M Piglionica, E Ponzano, C Previderè, N Resta, F Scarnicci, G Seidita, S Sorçaburu-Cigliero, S Turrina, A Verzeletti, M Kayser
No abstract text is available yet for this article.
April 4, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29588179/assessment-of-a-subset-of-slowly-mutating-y-strs-for-forensic-and-evolutionary-studies
#7
Miriam Baeta, Carolina Núñez, Patricia Villaescusa, Urko Ortueta, Nerea Ibarbia, Rene J Herrera, José Luis Blazquez-Caeiro, Juan José Builes, Susana Jiménez-Moreno, Begoña Martínez-Jarreta, Marian M de Pancorbo
Y-specific short tandem repeat (Y-STR) loci display different mutation rates and consequently are suitable for forensic, genealogical, and evolutionary studies that require different levels of timelines and resolution. Recent efforts have focused on implementing Rapidly Mutating (RM) Y-STRs to assess male specific profiles. However, due to their high mutation rate their use in kinship testing or in phylogenetic studies may be less reliable. In the present study, a novel Slowly Mutating Y-STR (SM) panel, including DYS388, DYS426, DYS461 (Y-GATA-A7...
March 20, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29532149/17-y-str-haplotype-diversity-in-s%C3%A3-o-paulo-state-southeast-of-brazil
#8
Leandro Fonseca de Souza, Carlos Henrique Ares Silveira da Motta, Rodrigo Soares Moura-Neto
A sample of 158 Brazilian males from São Paulo (SP), Brazilian southeast, was typed for 17 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1, and DYS385ab). A total of 158 haplotypes were identified, of which all were unique. The haplotype diversity and discrimination capacity were calculated in 1.0 and the genetic diversity was 67.4%. Pairwise haplotype distances showed that the São Paulo population is not significantly different from Rio de Janeiro and Portugal, but is different from African and Native American...
March 12, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29511852/inference-of-maternal-uniparental-disomy-of-the-entire-chromosome-2-from-a-paternity-test
#9
Jesica Carina Guzmán-Alberto, Gabriela Martínez-Cortes, Héctor Rangel-Villalobos
Atypical situations arise during the constant resolution of paternity cases, which constitute challenges requiring additional genetic systems and non-standard methods. We report a paternity case presenting three alleged father (AF)-child incompatibilities for the markers TPOX, D2S441, and the indel locus B02 (11/11 vs 8/8; 14/14 vs 10/10; 2/2 vs1/1, respectively). Considering the presence of mutations/null alleles, the residual paternity indexes (PI) obtained with 23 autosomal short tandem repeats (STRs) and 38 indels suggest that the AF is the father (PI = 1...
March 6, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29506869/uk-and-irish-y-str-population-data-a-catalogue-of-variant-alleles
#10
Anastasia Aliferi, Jim Thomson, Andrew McDonald, Vanessa Molin Paynter, Steven Ferguson, Des Vanhinsbergh, Denise Syndercombe Court, David Ballard
A total of 3128 Y-STR profiles from three UK and one Irish population have been analysed with the PowerPlex Y23 system and are reported here. Instances of haplotype sharing between apparently unrelated individuals were identified and further investigated with the use of the 5 additional markers within the Yfiler Plus kit, resulting in a reduction by 76% in the number of shared haplotypes. Furthermore, Yfiler Plus was also employed to verify locus deletions and duplications observed in Y23 genotypes while inconsistencies between the two kits were sequenced, revealing underlying Y23 primer binding site mutations in loci DYS392 and DYS576...
May 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29502256/genetic-ancestry-of-families-of-putative-inka-descent
#11
José R Sandoval, Daniela R Lacerda, Marilza S Jota, Ronald Elward, Oscar Acosta, Donaldo Pinedo, Pierina Danos, Cinthia Cuellar, Susana Revollo, Fabricio R Santos, Ricardo Fujita
This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries...
March 3, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29476237/improved-y-str-typing-for-disaster-victim-identification-missing-persons-investigations-and-historical-human-skeletal-remains
#12
Angie Ambers, Jitka Votrubova, Daniel Vanek, Antti Sajantila, Bruce Budowle
Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies...
February 23, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29464703/a-comparison-among-three-multiplex-y-str-profiling-kits-for-sexual-assault-cases
#13
Benedita Ferreira-Silva, Margarida Fonseca-Cardoso, Maria João Porto, Teresa Magalhães, Laura Cainé
Biological evidence of sexual assault is one of the most difficult sample types to analyze in forensic laboratories. Y-STR markers are thus a valuable tool for analyzing these samples. The aim of this project was to compare three Y-STR commercial kits by analyzing their amplification performance on casework samples. Overall, 247 trace samples were analyzed with a Yfiler® Plus PCR Amplification Kit (Applied Biosystems), PowerPlex® Y23 (Promega® ) System and AmpFLSTR® Yfiler™ PCR Amplification Kit (Applied Biosystems)...
February 21, 2018: Journal of Forensic Sciences
https://www.readbyqxmd.com/read/29452231/the-association-of-22-y-chromosome-short-tandem-repeat-loci-with-initiative-aggressive-behavior
#14
Chun Yang, Huajie Ba, Wei Zhang, Shuyou Zhang, Hanqing Zhao, Haiying Yu, Zhiqin Gao, Binbin Wang
Aggressive behavior represents an important public concern and a clinical challenge to behaviorists and psychiatrists. Aggression in humans is known to have an important genetic basis, so to investigate the association of Y chromosome short tandem repeat (Y-STR) loci with initiative-aggressive behavior, we compared allelic and haplotypic distributions of 22 Y-STRs in a group of Chinese males convicted of premeditated extremely violent crimes (n = 271) with a normal control group (n = 492). Allelic distributions of DYS533 and DYS437 loci differed significantly between the two groups (P < 0...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29433057/a-solution-for-the-rare-type-match-problem-when-using-the-dip-str-marker-system
#15
G Cereda, R D Gill, F Taroni
The rare type match problem is an evaluative challenging situation in which the analysis of a DNA profile reveals the presence of (at least) one allele which is not contained in the reference database. This situation is challenging because an estimate for the frequency of occurrence of the profile in a given population needs sophisticated evaluative procedures. The rare type match problem is very common when the DIP-STR marker system, which has proven itself very useful for dealing with unbalanced DNA mixtures, is used, essentially due to the limited size of the available database...
May 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29428588/corrigendum-to-development-of-an-italian-rm-y-str-haplotype-database-results-of-the-2013-gefi-collaborative-exercise-forensic-sci-int-genet-15-2015-56-63
#16
C Robino, A Ralf, S Pasino, M R De Marchi, K N Ballantyne, A Barbaro, C Bini, E Carnevali, L Casarino, C Di Gaetano, M Fabbri, G Ferri, E Giardina, A Gonzalez, G Matullo, A L Nutini, V Onofri, A Piccinini, M Piglionica, E Ponzano, C Previderè, N Resta, F Scarnicci, G Seidita, S Sorçaburu-Cigliero, S Turrina, A Verzeletti, M Kayser
No abstract text is available yet for this article.
May 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29387928/mutation-rates-at-42-y-chromosomal-short-tandem-repeats-in-chinese-han-population-in-eastern-china
#17
Weiwei Wu, Wenyan Ren, Honglei Hao, Hailun Nan, Xin He, Qiuling Liu, Dejian Lu
Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1...
January 31, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29360602/determining-y-str-mutation-rates-in-deep-routing-genealogies-identification-of-haplogroup-differences
#18
Sofie Claerhout, Michiel Vandenbosch, Kelly Nivelle, Leen Gruyters, Anke Peeters, Maarten H D Larmuseau, Ronny Decorte
Knowledge of Y-chromosomal short tandem repeat (Y-STR) mutation rates is essential to determine the most recent common ancestor (MRCA) in familial searching or genealogy research. Up to now, locus-specific mutation rates have been extensively examined especially for commercially available forensic Y-STRs, while haplogroup specific mutation rates have not yet been investigated in detail. Through 450 patrilineally related namesakes distributed over 212 deep-rooting genealogies, the individual mutation rates of 42 Y-STR loci were determined, including 27 forensic Y-STR loci from the Yfiler® Plus kit and 15 additional Y-STR loci (DYS388, DYS426, DYS442, DYS447, DYS454, DYS455, DYS459a/b, DYS549, DYS607, DYS643, DYS724a/b and YCAIIa/b)...
May 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29356946/genetic-characterization-of-rio-de-janeiro-for-different-y-str-sets
#19
Juliana Jannuzzi, Patrícia Domingues, Filipa Simão, Anna Carolina da Silva Chaves, Elizeu Fagundes de Carvalho, Leonor Gusmão
In this work, the YfilerPlus kit was used to investigate a sample of 258 males from Rio de Janeiro. In addition, the previous database of 760 Yfiler profiles deposited in the YHRD was updated to 1610. YfilerPlus markers showed a high haplotype diversity (0.99997), with only one haplotype shared by two individuals. When only considering the Yfiler markers, the haplotype diversity was slightly lower (0.99976), with 5 haplotypes shared by two individuals and 1 haplotype shared by three individuals. Low genetic distances were found between the Rio de Janeiro and European populations as well as the European/Hispanic American samples...
January 22, 2018: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29353342/genetic-analysis-of-17-y-str-loci-from-1026-individuals-of-han-populations-in-jilin-province-northeast-china
#20
Wen-Qing Chen, Zhen Feng, Wei Jin, Yi-Jun Zhang, Qiang Wang, Pei Li, Shi-Lin Li, Lan-Hai Wei, Gang Liu
In this study, 17 Y-chromosomal short tandem repeats (Y-STRs) were analyzed in 1026 male individuals of Han populations in Changchun City, Jilin Province, Northeast China. The haplotype diversity is 0.99892. The Changchun Han population is close to most Han populations and different from most other minority populations of China. Additionally, the Changchun Han show more affiliations with Han populations in North and Northeast China. These data provide a reference for the Y-STR database in Jilin Province, and they may be valuable for population genetic analysis...
January 20, 2018: International Journal of Legal Medicine
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