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HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing

Hansi Weissensteiner, Dominic Pacher, Anita Kloss-Brandstätter, Lukas Forer, Günther Specht, Hans-Jürgen Bandelt, Florian Kronenberg, Antonio Salas, Sebastian Schönherr
2016 Nucleic Acids Research  
Furthermore, the handling of high-throughput data in form of VCF files is now directly supported.  ...  In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence.  ...  FUNDING The project was supported by the Austrian Cancer Society/Tirol and by the Tyrolean Science Fund (Tiroler Wissenschaftsfonds). Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkw233 pmid:27084951 pmcid:PMC4987869 fatcat:x6lgpctt4ndhza5gekfxpszcly

Scalable Data Analysis of Mitochondrial DNA in the Era of High-Throughput Data Generation

Hansi Weissensteiner
2019 Figshare  
This work presents new algorithms and workflows to manage and analyze mtDNA data derived from high-throughput devices, like massive parallel sequencing data.  ...  One central aspect of this thesis is the classification of mtDNA data to phylogenetic clusters, used for mtDNA quality control and for detection of contamination patterns.  ...  Acknowledgements This present work would not have been possible without the support of Dr. Sebastian Schönherr and Lukas Forer PhD, thanks guys!  ... 
doi:10.6084/m9.figshare.8937899 fatcat:7g5oihrq2vekhb2d3apehiv4sm

Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods

Alexandros Heraclides, Eva Fernández-Domínguez
2022 International Journal of Molecular Sciences  
All these factors complicate a reliable reconstruction of consensus aDNA sequences in reads from high-throughput sequencing platforms.  ...  Raw genomic data (BAM/FASTQ) from a total of 17 previously published whole ancient human genomes ranging from the 14th to the 7th millennium BCE were retrieved and mitochondrial consensus sequences were  ...  of the current study.  ... 
doi:10.3390/ijms23094651 pmid:35563041 pmcid:PMC9104972 fatcat:kjepfeanhfcvthtqm7rtoons2y

Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus

Ashot Margaryan, Miroslava Derenko, Hrant Hovhannisyan, Boris Malyarchuk, Rasmus Heller, Zaruhi Khachatryan, Pavel Avetisyan, Ruben Badalyan, Arsen Bobokhyan, Varduhi Melikyan, Gagik Sargsyan, Ashot Piliposyan (+6 others)
2017 Current Biology  
Highlights d We analyzed 52 full mitochondrial genomes from ancient humans in the South Caucasus d The results show a high level of maternal genetic continuity in this region d Cultural shifts across eight  ...  millennia have not changed the maternal gene pool .dk (A.M.), meallentoft@snm.ku.dk (M.E.A.) http://dx.  ...  HaploGrep 2: mitochondrial haplogroup classification in the era of highthroughput sequencing. Nucleic Acids Res. 44 (W1), W58-W63. 47. Excoffier, L., and Lischer, H.E.L. (2010).  ... 
doi:10.1016/j.cub.2017.05.087 pmid:28669760 fatcat:jz24mo2lmzha3gr6wpkasoib4e

New Evidence of Ancient Mitochondrial DNA of the Southern Andes (Calchaquí Valleys, Northwest Argentina, 3,600–1,900 Years before Present)

Parolin, Cortés, Basso, Scattolin
2019 Human Biology: The Official Publication of the American Association of Anthropological Genetics  
Our results show that the Cajón Valley sample, with predominance of D1 and C1, differs from that commonly observed in ancient and modern Andean populations, which usually show a high prevalence of haplogroup  ...  Mitochondrial HVR-1 haplotypes were assigned to three of the four founding haplogroups, D1 (57.1%), C1 (28.5%), and B2 (14.2%), with absence of A2.  ...  for the Promotion of Science and Technology, Argentina (ANPCyT).  ... 
doi:10.13110/humanbiology.91.4.02 pmid:32767894 fatcat:iqyjh4bfwbce3dgujw4ezpwx3y

Using MutPred derived mtDNA load scores to evaluate mtDNA variation in hypertension and diabetes in a two-population cohort: The SABPA study

Marianne Venter, Leone Malan, Etresia van Dyk, Joanna L. Elson, Francois H. van der Westhuizen
2017 Journal of Genetics and Genomics  
Using MutPred derived mtDNA load scores to evaluate mtDNA variation in hypertension and diabetes in a two-population cohort: The SABPA study.  ...  HaploGrep 2: mitochondrial haplogroup 601 classification in the era of high-throughput sequencing.  ...  presence of African sequences in the GenBank 359 database.  ... 
doi:10.1016/j.jgg.2016.12.003 pmid:28298255 fatcat:ip4bylhz4rb7rcuasphclucn4a

Germline selection shapes human mitochondrial DNA diversity

Wei Wei, Salih Tuna, Michael J. Keogh, Katherine R. Smith, Timothy J. Aitman, Phil L. Beales, David L. Bennett, Daniel P. Gale, Maria A. K. Bitner-Glindzicz, Graeme C. Black, Paul Brennan, Perry Elliott (+27 others)
2019 Science  
However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325  ...  Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation.  ...  ., HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res 44, W58-63 (2016). 58. L. B.  ... 
doi:10.1126/science.aau6520 pmid:31123110 fatcat:se46qs7ntvhlliv3mf3qqiv3ui

Ancient DNA Analysis of the Thulamela Remains: Deciphering the Migratory Patterns of a Southern African Population

Molebogeng Bodiba, Maryna Steyn, Paulette Bloomer, Morongwa N. Mosothwane, Frank Rühli, Abigail Bouwman
2019 Journal of African Archaeology  
Poor quality and quantity of DNA meant that only haplogroups, not subhaplogroups, of the individuals could be traced.  ...  Although sequences were short, it seems that the Thulamela female aligns somewhat more with eastern populations as opposed to the male who aligns more with western groups.  ...  There are a myriad of phylogenetic tools that can aid one in assigning haplogroups to sample sequences, such as the online tool HaploGrep (153) (http://haplogrep.uibk.ac.at/).  ... 
doi:10.1163/21915784-20190017 fatcat:wzflxm346vfmdcqdzytpmpwcwm

Mitonuclear interactions influence Alzheimer's disease risk [article]

Shea J Andrews, Brian Fulton-Howard, Christopher Patterson, G Peggy McFall, Alden Gross, Elias K Michaelis, Alison M J Goate, Russell H Swerdlow, Judy Pa
2019 bioRxiv   pre-print
We examined the associations between mitochondrial DNA haplogroups (MT-hg) and their interactions with a polygenic risk score based on nuclear-encoded mitochondrial genes (nMT-PRS) with risk of dementia  ...  These results suggest that MT-hgs influence dementia risk, and that variants in the nuclear and mitochondrial genome interact to influence the age of onset of dementia.  ...  of Defense award number W81XWH-12-2-0012).  ... 
doi:10.1101/654400 fatcat:aesi2cfsf5coveookd54jt3k3a

The effect of foetal growth restriction on the development of migraine and tension-type headache in adulthood. The HUNT Study

Sigrid Børte, Bendik S. Winsvold, Synne Øien Stensland, Milada Cvancarova Småstuen, John-Anker Zwart, Olivier Baud
2017 PLoS ONE  
The genotyping was financed by the National Institute of health (NIH), University of Michigan, The Norwegian Research council, and Central Norway Regional Health Authority and the Faculty of Medicine and  ...  The genotype quality control and imputation of nuclear  ...  HaploGrep 2: mitochondrial haplogroup classification in the era of high- throughput sequencing. Nucleic Acids Res. 2016;44(W1):W58-63. 88. Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, et al.  ... 
doi:10.1371/journal.pone.0175908 pmid:28410431 pmcid:PMC5391957 fatcat:f2vq2jayhbdivifvyvnh3gevdy

Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada

Ana T. Duggan, Alison J.T. Harris, Stephanie Marciniak, Ingeborg Marshall, Melanie Kuch, Andrew Kitchen, Gabriel Renaud, John Southon, Ben Fuller, Janet Young, Stuart Fiedel, G. Brian Golding (+2 others)
2017 Current Biology  
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44 (W1), W58-W63. 49. van Oven, M. (2015).  ...  The haplogroup diversity in the MA and Beothuk is high, as hinted at in a previous study [10] .  ... 
doi:10.1016/j.cub.2017.08.053 pmid:29033326 fatcat:ngddkmqdwnhdvaufglvxg7slua

Archaeogenomic Distinctiveness of the Isthmo-Colombian Area

Marco Rosario Capodiferro, Alessandro Raveane, Nicola Rambaldi Migliore, Giulia Colombo, Linda Ongaro, Javier Rivera, Tomas Mendizábal, Iosvany Hernández-Mora, Maribel Tribaldos, Ugo Alessandro Perego, Christiana Lyn Scheib, Alessandra Modi (+23 others)
2020 Social Science Research Network  
in the Isthmo-Colombian area  ...  Article Archaeogenomic distinctiveness of the Isthmo-Colombian area Graphical abstract Highlights d Ancient Isthmian genomes address anthropological questions on pre-contact burials d The comparison with  ...  HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44 (W1), W58-W63.  ... 
doi:10.2139/ssrn.3661949 fatcat:xx3eapfmwbduhm5mzllgm6kovy

E-RIHS PP D8.2 Report on feasibility studies and integration of new services

Franco Niccolucci, Dimitris Kafetzopoulos, Nikos Psonis, Gloria López, Cecilia Calvo Simal, Sorin Hermon, Hans Huisman, Achille Felicetti, Rodorico Giorgi
2020 Zenodo  
This prepares E-RIHS for the delicate implementation of E-RIHS, tackling any potential flaws in its services.  ...  This is aims at preparing E-RIHS for the delicate implementation phase of E-RIHS, tackling any potential flaws in its services.  ...  of high-throughput sequencing (NGS).  ... 
doi:10.5281/zenodo.3946225 fatcat:jwczsxkye5gu3hbgxzftcbutee

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, Kate Domett, Giang Hai Nguyen (+22 others)
2018 Science  
Particularly profound changes in human culture were propelled by the spread of agriculture.  ...  In this scenario, the languages spoken by the majority of present-day people in Southeast Asia (e.g., Lao, Thai, Burmese, Malay) reflect later population movements.  ...  HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58-W63 (2016). 43. Poznik, G. D.  ... 
doi:10.1126/science.aat3188 pmid:29773666 fatcat:yrauwwivxjemxggdfizsb2jn5u

Ancient genomes document multiple waves of migration in Southeast Asian prehistory [article]

Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, Kate Domett, Giang Hai Nguyen (+22 others)
2018 bioRxiv   pre-print
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known.  ...  In a striking parallel with Europe, later sites from across the region show closer connections to present-day majority groups, reflecting a second major influx of migrants by the time of the Bronze Age  ...  HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58-W63 (2016). 43. Poznik, G. D.  ... 
doi:10.1101/279646 fatcat:andkgfljcjcbredic4hvn5jmwi
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