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Thread: New DNA Papers

  1. #1491
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    Haplogroup prediction using Y-chromosomal STRs in the general population of Bosnia and Herzegovina

    Abstract
    Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-SNP markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-STR markers using different software packages, and this method gained much attention recently due to its labor-, time- and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey's Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a and E1b1b being the most prevalent with frequencies of 43.13%, 14.79% and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.

    https://www.frontiersin.org/articles...71467/abstract

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  3. #1492
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    Russian Federation
    Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India

    Abstract
    India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no study has attempted to model and evaluate how these factors have interacted to shape the patterns of genetic diversity within India. We merged all publicly available data from the Indian subcontinent into a data set of 891 individuals from 90 well-defined groups. Bringing together geography, genetics, and demographic factors, we developed Correlation Optimization of Genetics and Geodemographics to build a model that explains the observed population genetic substructure. We show that shared language along with social structure have been the most powerful forces in creating paths of gene flow in the subcontinent. Furthermore, we discover the ethnic groups that best capture the diverse genetic substructure using a ridge leverage score statistic. Integrating data from India with a data set of additional 1,323 individuals from 50 Eurasian populations, we find that Indo-European and Dravidian speakers of India show shared genetic drift with Europeans, whereas the Tibeto-Burman speaking tribal groups have maximum shared genetic drift with East Asians.

    https://academic.oup.com/mbe/article/38/5/1809/6108106

    8FE728D5-97FA-4881-AB39-7CC90D474357.jpeg

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  5. #1493
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    Poland England Ireland Munster

    Resource Profile and User Guide of the Polygenic Index Repository (23andMe)

    Resource Profile and User Guide of the Polygenic Index Repository
    Joel Becker, Casper A.P. Burik, Grant Goldman, Nancy Wang, Hariharan Jayashankar, Michael Bennett, Daniel W. Belsky, Richard Karlsson Linnér, Rafael Ahlskog, Aaron Kleinman, David A. Hinds, 23andMe Research Group, Avshalom Caspi, David L Corcoran, Terrie E. Moffitt, Richie Poulton, Karen Sugden, Benjamin S. Williams, Kathleen Mullan Harris, Andrew Steptoe, Olesya Ajnakina, Lili Milani, Tõnu Esko, William G. Iacono, Matt McGue, Patrick K.E. Magnusson, Travis T. Mallard, K. Paige Harden, Elliot M Tucker-Drob, Pamela Herd, Jeremy Freese, Alexander Young, Jonathan P. Beauchamp, Phillip Koellinger, Sven Oskarsson, Magnus Johannesson, Peter M. Visscher, Michelle N. Meyer, David Laibson, David Cesarini, Daniel J. Benjamin, Patrick Turley, Aysu Okbay

    This article is a preprint and has not been certified by peer review [what does this mean?].

    Abstract
    Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is rapidly growing. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs' prediction accuracies, we constructed them using genome-wide association studies - some of which are novel - from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the "additive SNP factor." Regressions in which the true regressor is the additive SNP factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.

    Competing Interest Statement
    D.A.H., A.K., and members of the 23andMe Research Team are current or former employees of 23andMe, Inc. and hold stock or stock options in 23andMe.
    YFull: YF14620 (Dante Labs 2018)

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  7. #1494
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    Quantitative monitoring of nucleotide sequence data ...

    Quantitative monitoring of nucleotide sequence data from genetic resources in context of their citation in the scientific literature
    Matthias Lange, Blaise Alako, Guy Cochrane, Mehmood Ghaffar, Martin Mascher, Pia-Katharina Habekost, Upneet Hillebrand, Uwe Scholz, Florian Zunder, Jens Freitag, Amber Hartman Scholz
    dbstract
    Background: Linking nucleotide sequence data (NSD) to scientific publication citations can enhance understanding of NSDs provenance, scientific use, and re-use in the community. By connecting publications with NSD records, NSD geographical provenance information, and author geographical information, it becomes possible to assess the contribution of NSD to infer trends in scientific knowledge gain at the global level. Findings: For this data note, we extracted and linked records from the European Nucleotide Archive to citations in open-access publications aggregated at Europe PubMed Central. A total of 8,464,292 ENA accessions with geographical provenance information were associated with publications. We conducted a data quality review to uncover potential issues in publication citation information extraction and author affiliation tagging and developed and implemented best-practice recommendations for citation extraction. Flat data tables and an data warehouse with an interactive web application were constructed to enable ad hoc exploration of NSD use and summary statistics. Conclusions: The extraction and linking of NSD with associated publication citations enables transparency. The quality review contributes to enhanced text mining methods for identifier extraction and use. Furthermore, the global provision and use of NSD enables scientists around the world to join literature and sequence databases in a multidimensional fashion. As a concrete use case, statistics of country clusters were visualized with respect to NSD access in the context of discussions around digital sequence information under the United Nations Convention on Biological Diversity
    YFull: YF14620 (Dante Labs 2018)

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  9. #1495
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    Canada China
    "The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations"
    Kai Tätte, Ene Metspalu, Helen Post, Leire Palencia-Madrid, Javier Rodríguez Luis, Maere Reidla, Anneliis Rea, Erika Tamm, Everett J. Moding, Marian M. de Pancorbo, Ralph Garcia-Bertrand, Mait Metspalu & Rene J. Herreram European Journal of Human Genetics (2021) Published:23th March 2021
    https://www.nature.com/articles/s414...-00837-6#Sec12

    Abstract
    This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.
    Last edited by Shuzam87; 05-16-2021 at 05:27 AM.

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  11. #1496
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    Canada China
    "Development and validation of a custom panel including 183 Y‐SNPs for Chinese Y‐chromosomal haplogroups dissection using a MALDI‐TOF MS system"
    Min Li, Yilun Zhang, Li Luo, Yingnan Bian, Chengtao Li First published:27 August 2020
    https://doi.org/10.1002/elps.202000145
    https://analyticalsciencejournals.on...elps.202000145

    Abstract
    Y‐chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y‐chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high‐resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y‐SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case‐type samples using a MALDI‐TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI‐TOF MS platform were fully consistent with those obtained from the next‐generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, bloodstain on FTA card samples could be dissected by direct PCR amplification on the MALDI‐TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost‐effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.
    Last edited by Shuzam87; 05-16-2021 at 05:28 AM.

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  13. #1497
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    "Exploitation of a novel slowly mutating Y‐STRs set and evaluation of slowly mutating Y‐STRs plus Y‐SNPs typing strategy in forensic genetics and evolutionary research"
    Jing Liu, Tianyue Ming, Min Lang, Hai Liu, Minkun Xie, Jienan Li, Mengge Wang, Feng Song, Guanglin He, Shouyu Wang, Zheng Wang, Yiping Hou First published:12 January 2021
    https://doi.org/10.1002/elps.202000302
    https://analyticalsciencejournals.on...elps.202000302

    Abstract
    The Y‐chromosome short tandem repeats (Y‐STRs) loci with different mutation rates existing in the Y chromosome non‐recombination region (NRY) allow to be applied in human forensics, genealogical researches, historical investigations and evolutionary studies. Currently, there is a high demand for pedigree search to narrow the scope of crime investigations. However, the commonly used Y‐STRs kits generally contain Y‐STRs with high mutation rates that could cause individuals from the same pedigree to display different haplotypes. Herein, we put forward a new strategy of Slowly Mutating (SM) Y‐STRs plus Y‐SNPs typing, which could not only improve the resolution and accuracy of pedigree search, but also be applicable to evolutionary research. First, we developed a nine SM Y‐STRs assay by evaluating their mutation rates in 210 pedigrees. Then the gene diversity and efficiency of the SM Y‐STRs and 172 Y‐SNPs sets were investigated by 2304 unrelated males from 24 populations. Furthermore, network and time estimation analyses were performed to evaluate the new strategy's capability to reconstruct phylogenetic tree and reliability to infer the time to the most recent common ancestor (TMRCA). The nine SM Y‐STRs assay even had a higher resolution and a comparable capacity of revealing population genetic differentiation compared to 172 Y‐SNPs system. This new strategy could optimize the phylogenetic tree generated by commonly used Y‐STR panels and obtain a quite consistent time estimations with the published dating.
    Last edited by Shuzam87; 05-16-2021 at 05:28 AM.

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  15. #1498
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    "Autosomal genetics and Y-chromosome haplogroup L1b-M317 reveal Mount Lebanon Maronites as a persistently non-emigrating population"
    Daniel E. Platt, Hovig Artinian, Francis Mouzaya, Wissam Khalil, Francois G. Kamar, Elizabeth Matisoo-Smith, Francesc Calafell, Nassim Nicolas Taleb & Pierre Zalloua European Journal of Human Genetics volume 29, pages581–592 (2021)
    Published:04 December 2020

    https://www.nature.com/articles/s41431-020-00765-x

    Abstract
    Currently, there are 18 different religious communities living in Lebanon. While evolving primarily within Lebanon, these communities show a level of local isolation as demonstrated previously from their Y-haplogroup distributions. In order to trace the origins and migratory patterns that may have led to the genetic isolation and autosomal clustering in some of these communities we analyzed Y-chromosome STR and SNP sample data from 6327 individuals, in addition to whole genome autosomal sample data from 609 individuals, from Mount Lebanon and other surrounding communities. We observed Y chromosome L1b Levantine STR branching that occurred around 5000 years ago. Autosomal DNA analyses suggest that the North Lebanese Mountain Maronite community possesses an ancestral Fertile Crescent genetic component distinct from other populations in the region. We suggest that the Levantine L1b group split from the Caucasus ancestral group around 7300 years ago and migrated to the Levant. This event was distinct from the earlier expansions from the Caucasus region that contributed to the wider Levantine populations. Differential cultural adaption by populations from the North Lebanese Mountains are clearly aligned with the L1b haplotype STR haplogroup clusters, indicating pre-existing and persistent cultural barriers marked by the transmission of L1b lineages. Our findings highlight the value of uniparental haplogroups and STR haplotype data for elucidating biosocial events among these populations.
    Last edited by Shuzam87; 05-16-2021 at 05:29 AM.

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  17. #1499
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    Canada China
    “Genetic reconstruction and phylogenetic analysis by 193 Y‐SNPs and 27 Y‐STRs in a Chinese Yi ethnic group“
    Fei Wang, Feng Song, Mengyuan Song, Jienan Li, Mingkun Xie, Yiping Hou First published: 28 April 2021
    https://doi.org/10.1002/elps.202100003
    https://analyticalsciencejournals.on...elps.202100003

    Abstract
    Yi is the seventh‐largest ethnic group in China and features mountainous regional characteristics. The Liangshan Yi Autonomous Prefecture is the largest Yi agglomeration with isolated geographical conditions, profoundly impeding genetic communication. Here, we investigated 427 unrelated males of Liangshan from 193 Y‐chromosome single nucleotide polymorphisms (Y‐SNPs) and 27 Y‐chromosome short tandem repeats (Y‐STRs) to reveal the genetic structure and paternal phylogeny of the group. The haplogroup diversity reached 0.9169 with 46 different subhaplogroups by 193 Y‐SNPs, and the haplotype diversity reached 0.9999 by 27 Y‐STR loci. Multidimensional scaling (MDS), N‐J tree, and Network were constructed to decipher and visualize the genetic relations between Yi and worldwide groups. Our results revealed: (1) the Network by Y‐STRs and Y‐SNPs showed the haplogroup D1a1a‐M15 in the Liangshan Yi population was a ramification of Tibetan groups’ expansion from west to east on the plateau; (2) the haplogroup distribution and the mismatch mutation analysis indicated the haplogroup O2a2b1a1a1a4a2‐Z25929 of Liangshan Yi derived from manifold Southeast Asian immigrants; (3) a high‐resolution Y‐SNPs panel is vital to depict accurate paternal derivations and build an integrated and refining genetic structure of ethnic groups.
    Last edited by Shuzam87; 05-16-2021 at 05:29 AM.

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  19. #1500
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    Canada China
    “Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes”
    Anne-Mai Ilumäe, Helen Post, Rodrigo Flores, Monika Karmin, Hovhannes Sahakyan, Mayukh Mondal, Francesco Montinaro, Lauri Saag, Concetta Bormans, Luisa Fernanda Sanchez, Adam Ameur, Ulf Gyllensten, Mart Kals, Reedik Mägi, Luca Pagani, Doron M. Behar, Siiri Rootsi & Richard Villems European Journal of Human Genetics (2021) Published: 07 May 2021
    https://www.nature.com/articles/s414...al-information

    Abstract
    The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201, and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups, we disclose lineages that began to radiate ~1–3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of the influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.

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