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HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing
2016
Nucleic Acids Research
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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
2019
Figshare
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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
2022
International Journal of Molecular Sciences
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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
2017
Current Biology
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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)
2019
Human Biology: The Official Publication of the American Association of Anthropological Genetics
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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
2017
Journal of Genetics and Genomics
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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
2019
Science
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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
2019
Journal of African Archaeology
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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]
2019
bioRxiv
pre-print
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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
2017
PLoS ONE
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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
2017
Current Biology
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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
2020
Social Science Research Network
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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
2020
Zenodo
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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
2018
Science
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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]
2018
bioRxiv
pre-print
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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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