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https://www.readbyqxmd.com/read/29275088/genetic-analysis-of-southern-brazil-subjects-using-the-powerseq%C3%A2-auto-y-system-for-short-tandem-repeat-sequencing
#1
Deborah S B S Silva, Fernanda R Sawitzki, Melissa K R Scheible, Sarah F Bailey, Clarice S Alho, Seth A Faith
With the advent of Next-Generation Sequencing technology, sequencing of short tandem repeats (STRs) allows for a more detailed analysis when compared to size-based fragment methods (capillary electrophoresis-CE). The implementation of high-throughput sequencing can help uncover deeper genetic diversities of different populations. Subjects from the South region of Brazil present a particular and more homogeneous ancestry background when compared to other regions of the country. Both autosomal and Y- STRs have been analyzed in these individuals; however, all analyses published to date encompass data from CE-based fragment analysis...
December 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29245063/background-levels-of-male-dna-in-the-vaginal-cavity
#2
Patricia P Albani, Jayshree Patel, Rachel I Fleming
In alleged sexual assault investigations, the detection of male DNA on female intimate swabs can be established through Y-STR profiling. However, in cases where the defendant lives in the same dwelling as the complainant, the defendant may argue that his DNA was transferred through normal social contact, and dispute that intimate contact occurred. This study aimed to determine whether or not male DNA could be detected in samples collected from the vaginal cavity after everyday activities. A total of 300 samples from eight individuals were subjected to DNA quantification and Y-STR amplification...
December 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29220824/extensive-geographical-and-social-structure-in-the-paternal-lineages-of-saudi-arabia-revealed-by-analysis-of-27-y-strs
#3
Yahya M Khubrani, Jon H Wetton, Mark A Jobling
Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74...
December 2, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29219270/-genetic-polymorphisms-of-17-y-str-loci-in-nantong-han-population
#4
M Yang, S X Xu, H Y Qin, H Zhang, H Yi, H J Han, D T Dong, Y H Zhang, S L Li
OBJECTIVES: To analyze the genetic phenotypes of Nantong Han population and evaluate the application value of 17 Y-STR loci in Nantong population. METHODS: The peripheral blood samples were collected from 343 unrelated Nantong Han males and the genomic DNA were extracted by Chelex-100 method. Genotyping was performed using the AmpFℓSTR Yfiler™ Kit. The results were compared with other 12 Han populations, including Anhui, Jiangsu, Jiangxi, Shandong, Shanghai, Zhejiang (1), Lanzhou, Nanyang, Luzhou, Mudanjiang, Shanxi and Zhejiang (2), and 9 minority populations (Mongol, Xibe, Tibetan in Lhasa, Tibetan in Qinghai, Kazak, Uighur, Manchu, Paiwan in Taiwan and Tujia)...
August 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29219264/-identification-of-y-chromosomal-genetic-types-for-the-soldier-s-remains-from-huaihai-campaign
#5
C Z Wang, S Q Wen, M S Shi, X E Yu, X J Wang, Y L Pan, Y F Zhang, H Li, J Z Tan
OBJECTIVES: To identify the Y-chromosomal genetic types for the soldier's remains from Huaihai Campaign, and to offer a clue for search of their paternal relatives. METHODS: DNA of the remains were extracted by the ancient DNA extraction method. Yfiler kit was used for the multiplex amplification of 17 Y-STR loci. The haplogroups of the samples were speculated. Detailed genotyping of the selected Y-SNP was performed based on the latest Y-chromosome phylogenetic tree...
August 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29197717/inferring-chinese-surnames-with-y-str-profiles
#6
Cheng-Min Shi, Changzhen Li, Liang Ma, Lianjiang Chi, Jing Zhao, Wuzhou Yuan, Zhendiao Zhou, Jiang-Wei Yan, Hua Chen
Co-ancestry of human surnames and Y-chromosomes in most human populations and social groups suggests the possibility of inferring one from the other. However, such an intuitive perspective remains to be formally explored. In the present study, we develop two computational methods, based on cosine distance (dcos) and coalescence distance (dcoal) respectively, to infer surnames from Y-STR profiles. We also survey Y-STR variations at 15 loci for 19,009 individuals of Shandong Province in China. For a total of 266 surnames included in the data set, our methods can pinpoint to a single surname with an average accuracy of 65%, and with an average accuracy higher than 80% when providing >4 candidate surnames...
November 24, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29193490/the-eastern-side-of-the-westernmost-europeans-insights-from-subclades-within-y-chromosome-haplogroup-j-m304
#7
Licínio Manco, Joana Albuquerque, Maria Francisca Sousa, Rui Martiniano, Ricardo Costa de Oliveira, Sofia Marques, Verónica Gomes, António Amorim, Luís Alvarez, Maria João Prata
OBJECTIVES: We examined internal lineages and haplotype diversity in Portuguese samples belonging to J-M304 to improve the spatial and temporal understanding of the introduction of this haplogroup in Iberia, using the available knowledge about the phylogeography of its main branches, J1-M267 and J2-M172. METHODS: A total of 110 males of Portuguese descent were analyzed for 17 Y-chromosome bi-allelic markers and seven Y-chromosome short tandem repeats (Y-STR) loci...
November 29, 2017: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/29177704/inconsistent-genotyping-call-at-dys389-locus-and-implications-for-interpretation
#8
Zhiyong Liu, Dongtao Jia, Jingjing Zhang, Chen Li, Xi Zhang, Yaran Yang, Meng Yang, Man Chen, Zailiang Yu, Yan Wang, Jiangwei Yan
The male-specific Y chromosome short tandem repeat (STR) locus is used widely in forensic case, which are useful molecular tool to providing the biological evidence for male/female mixture and paternal lineage cases. The Y-STR analysis has been greatly facilitated by advent of commercial multiplex kit. However, even with well-designed robust multiplex kit, abnormal genotyping profile may be observed when encountering with mutations, such as deletion/duplication within the target region or mutation at the primer binding site...
November 24, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29175725/estimation-of-the-number-of-contributors-of-theoretical-mixture-profiles-based-on-allele-counting-does-increasing-the-number-of-loci-increase-success-rate-of-estimates
#9
Gina M Dembinski, Carl Sobieralski, Christine J Picard
DNA mixtures are more frequently encountered in casework due to increased kit sensitivity, protocols with increased cycle number, and requests for low copy number DNA samples to be tested. Generally, the first step in mixture interpretation is determining the number of contributors, with the most common approach of maximum allele count. Although there are previous studies regarding the accuracy of this approach, none have evaluated the accuracy with the newly expanded U.S. core STR loci. In this work, 4,976,355 theoretical mixture combinations were generated with the PowerPlex® Fusion 6C system which includes 23 autosomal STR loci and three Y-STR loci...
November 20, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29162904/whole-y-chromosome-sequences-reveal-an-extremely-recent-origin-of-the-most-common-north-african-paternal-lineage-e-m183-m81
#10
Neus Solé-Morata, Carla García-Fernández, Vadim Urasin, Asmahan Bekada, Karima Fadhlaoui-Zid, Pierre Zalloua, David Comas, Francesc Calafell
E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150717/genetic-diversity-and-phylogenetic-study-of-the-chinese-gelao-ethnic-minority-via-23-y-str-loci
#11
Pengyu Chen, Yanyan Han, Guanglin He, Haibo Luo, Tianzhen Gao, Feng Song, Dengfu Wan, Jian Yu, Yiping Hou
Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex(®) Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0...
November 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29150183/genetic-analysis-of-29-y-str-loci-in-the-chinese-han-population-from-shanghai
#12
Yuxiang Zhou, Chengchen Shao, Liming Li, Yaqi Zhang, Baonian Liu, Qinrui Yang, Qiqun Tang, Shilin Li, Jianhui Xie
The analysis of Y chromosomal short tandem repeats (Y-STRs) provides important information that can be used to forensic investigation and population studies. In this study, typing of 29 Y-STRs included in the PowerPlex(®) Y23 system (PPY23) and Yfiler™ Plus system (Yfiler plus) was performed on 843 unrelated male samples from Han population in Shanghai. Besides null, duplicate, and intermediate alleles reported in previous studies, an allele of 10 at DYS643 with a 2-base deletion in the flanking region was initially observed...
November 11, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29125104/polymorphisms-of-23-y-chromosome-str-loci-in-a-han-population-in-jiangsu-province
#13
Jun Ma, Ai-Hua Zhu, Jin-Wei Shi, Ming Jin, Hua-Jie Ba, Zhi-Guang Ping
Objective To investigate the polymorphisms of 23 Y-STR loci in a Han population in Jiangsu province. Methods Blood samples were collected from 4821 unrelated healthy Han males in Jiangsu province. DNA templates were amplified by PowerPlex Y23 kit,and the amplification products were detected by 3500xL genetic analyzer. Then,we calculated the allele frequencies and gene diversities respectively,as well as the haplotype frequencies and haplotype diversities. Results The gene diversity of these 23 Y-STR loci ranged 0...
October 30, 2017: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
https://www.readbyqxmd.com/read/29111271/forensic-characteristics-and-phylogenetic-analysis-of-two-han-populations-from-the-southern-coastal-regions-of-china-using-27-y-str-loci
#14
Mengge Wang, Zheng Wang, Yaqing Zhang, Guanglin He, Jing Liu, Yiping Hou
Currently, the largest national database within the Y-STR Haplotype Reference Database (YHRD, https://yhrd.org, release 55) is China, which has a very large Y-STR haplotype profiles. However, no haplotype data was available for Hainan province, the smallest and southernmost province of China. Herein, 280 unrelated male Chinese Han individuals residing in Hainan province were recruited and genotyped with 27 Y-STR loci. Moreover, 136 Han individuals from Shenzhen, the largest migrant city in China, also investigated...
October 27, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29099847/a-glimpse-at-the-intricate-mosaic-of-ethnicities-from-mesopotamia-paternal-lineages-of-the-northern-iraqi-arabs-kurds-syriacs-turkmens-and-yazidis
#15
Serkan Dogan, Cemal Gurkan, Mustafa Dogan, Hasan Emin Balkaya, Ramazan Tunc, Damla Kanliada Demirdov, Nihad Ahmed Ameen, Damir Marjanovic
Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others...
2017: PloS One
https://www.readbyqxmd.com/read/29054426/origin-of-the-myotonic-dystrophy-type-1-mutation-in-mexican-population-and-influence-of-amerindian-ancestry-on-ctg-repeat-allelic-distribution
#16
N M Murillo-Melo, L C Márquez-Quiróz, R Gómez, L Orozco, E Mendoza-Caamal, Y S Tapia-Guerrero, R Camacho-Mejorado, H Cortés, A López-Reyes, C Santana, G Noris, O Hernández-Hernández, B Cisneros, J J Magaña
Myotonic dystrophy type 1 is caused by expansion of a CTG trinucleotide repeat situated in the DMPK gene. Worldwide genetic studies suggest a single or limited number of mutational events cause the disease. However, distribution of CTG alleles and disease incidence varies among ethnicities. Due to the great ethnic diversity of the Mexican population, the present study was aimed at analyzing the impact of different lineages in shaping the CTG-repeat allelic distribution in the contemporary Mexican-Mestizo population as well as to shed light on the DM1 ancestral origin...
September 21, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/29052042/paternal-lineage-affinity-of-the-malay-subethnic-and-orang-asli-populations-in-peninsular-malaysia
#17
SyedHassan SharifahNany RahayuKarmilla, Alwi R Aedrianee, Sundararajulu Panneerchelvam, Mohd Nor Norazmi, Abdullah Nur Azeelah, Zainuddin Zafarina
Peninsular Malaysia is populated by the Malays, Chinese, Indians, and Orang Asli. We have analyzed 17 Y-STRs loci for 243 randomly unrelated individuals, which include 153 Malays (7 Acheh, 13 Champa, 11 Rawa, 9 Kedah, 23 Minang, 15 Bugis, 43 Kelantan, 14 Jawa, and 18 Bugis) and 90 Orang Asli [54 Semang (16 Kensiu, 13 Lanoh, 25 Bateq); 30 Senoi (21 Semai, 9 Che Wong); and 6 Proto-Malay (6 Orang Kanaq)] from selected settlements in Peninsular Malaysia using the AmpFlSTR Yfiler™ kit (Applied Biosystems™). The overall haplotype diversity is 0...
October 19, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29046953/snp-typing-using-the-hid-ion-ampliseq%C3%A2-identity-panel-in-a-southern-chinese-population
#18
Ran Li, Chuchu Zhang, Haiyan Li, Riga Wu, Haixia Li, Zhenya Tang, Chenhao Zhen, Jianye Ge, Dan Peng, Ying Wang, Hongying Chen, Hongyu Sun
In the present study, 90 autosomal single nucleotide polymorphisms (SNPs) and 34 Y chromosomal SNPs were sequenced simultaneously using HID-Ion AmpliSeq™ Identity Panel on the Ion PGM™ platform for 125 samples in a southern Chinese population. Raw data were analyzed and forensic parameters were calculated. Haplogrouping concordance was also assessed using alternative methods based on Y-SNP haplotypes and Y-STR haplotypes. The results showed that allelic imbalance occurred more frequently with low coverage while several SNPs with high coverage were also observed with poor allelic balance, including rs214955, rs430046, rs7520386, rs876724, rs9171188, rs16981290, and rs2032631...
October 18, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28979290/y-str-haplogroup-diversity-in-the-jat-population-reveals-several-different-ancient-origins
#19
David G Mahal, Ianis G Matsoukas
The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28948851/y-chromosome-haplotypes-reveal-relationships-between-populations-of-the-arabian-peninsula-north-africa-and-south-asia
#20
Rebecca J Jones, Guan K Tay, Aurélie Mawart, Habiba Alsafar
BACKGROUND: The United Arab Emirates (UAE) is positioned at the crossroads of human migration out of Africa and through to Asia and Europe. AIM: To compare the degree of genetic diversity of the Arabian UAE population with populations in other countries from the Middle East, South Asia and North Africa. SUBJECTS AND METHODS: Twenty-seven Y-STR were analysed in 217 individuals. Y-STR haplotypes from this study were compared to population data stored in YHRD, using MDS and AMOVA...
October 16, 2017: Annals of Human Biology
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