Literature DB >> 34072215

Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences.

Arne Dür1, Nicole Huber2, Walther Parson2,3.   

Abstract

In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.

Entities:  

Keywords:  alignment; haplogroup; mitochondrial DNA; phylogeny

Year:  2021        PMID： 34072215     DOI： 10.3390/ijms22115747

Source DB:  PubMed          Journal:  Int J Mol Sci        ISSN： 1422-0067            Impact factor:   5.923


  18 in total

1.  Consistent treatment of length variants in the human mtDNA control region: a reappraisal.

Authors:  H-J Bandelt; W Parson
Journal:  Int J Legal Med       Date:  2007-03-09       Impact factor: 2.686

2.  EMPOP--a forensic mtDNA database.

Authors:  Walther Parson; Arne Dür
Journal:  Forensic Sci Int Genet       Date:  2007-03-07       Impact factor: 4.882

3.  HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment.

Authors:  Dario Vianello; Federica Sevini; Gastone Castellani; Laura Lomartire; Miriam Capri; Claudio Franceschi
Journal:  Hum Mutat       Date:  2013-06-12       Impact factor: 4.878

4.  An update to MitoTool: using a new scoring system for faster mtDNA haplogroup determination.

Authors:  Long Fan; Yong-Gang Yao
Journal:  Mitochondrion       Date:  2013-04-28       Impact factor: 4.160

5.  DNA Commission of the International Society for Forensic Genetics: revised and extended guidelines for mitochondrial DNA typing.

Authors:  W Parson; L Gusmão; D R Hares; J A Irwin; W R Mayr; N Morling; E Pokorak; M Prinz; A Salas; P M Schneider; T J Parsons
Journal:  Forensic Sci Int Genet       Date:  2014-07-29       Impact factor: 4.882

6.  Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.

Authors:  Mannis van Oven; Manfred Kayser
Journal:  Hum Mutat       Date:  2009-02       Impact factor: 4.878

7.  Next generation database search algorithm for forensic mitogenome analyses.

Authors:  Nicole Huber; Walther Parson; Arne Dür
Journal:  Forensic Sci Int Genet       Date:  2018-09-09       Impact factor: 4.882

8.  SAM: String-based sequence search algorithm for mitochondrial DNA database queries.

Authors:  Alexander Röck; Jodi Irwin; Arne Dür; Thomas Parsons; Walther Parson
Journal:  Forensic Sci Int Genet       Date:  2010-11-05       Impact factor: 4.882

9.  Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes.

Authors:  Martin Bodner; Ugo A Perego; Gabriela Huber; Liane Fendt; Alexander W Röck; Bettina Zimmermann; Anna Olivieri; Alberto Gómez-Carballa; Hovirag Lancioni; Norman Angerhofer; Maria Cecilia Bobillo; Daniel Corach; Scott R Woodward; Antonio Salas; Alessandro Achilli; Antonio Torroni; Hans-Jürgen Bandelt; Walther Parson
Journal:  Genome Res       Date:  2012-02-14       Impact factor: 9.043

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

Authors:  Hansi Weissensteiner; Dominic Pacher; Anita Kloss-Brandstätter; Lukas Forer; Günther Specht; Hans-Jürgen Bandelt; Florian Kronenberg; Antonio Salas; Sebastian Schönherr
Journal:  Nucleic Acids Res       Date:  2016-04-15       Impact factor: 16.971
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  8 in total

1.  A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data.

Authors:  Stephanie L Battle; Daniela Puiu; Joost Verlouw; Linda Broer; Eric Boerwinkle; Kent D Taylor; Jerome I Rotter; Stephan S Rich; Megan L Grove; Nathan Pankratz; Jessica L Fetterman; Chunyu Liu; Dan E Arking
Journal:  NAR Genom Bioinform       Date:  2022-05-17

2.  Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set.

Authors:  Qiong Lan; Congying Zhao; Chong Chen; Hui Xu; Yating Fang; Hongbing Yao; Bofeng Zhu
Journal:  Front Genet       Date:  2022-04-27       Impact factor: 4.772

3.  Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample.

Authors:  Martin Bodner; Christina Amory; Anna Olivieri; Francesca Gandini; Irene Cardinali; Hovirag Lancioni; Gabriela Huber; Catarina Xavier; Maria Pala; Alessandro Fichera; Lisa Schnaller; Mario Gysi; Stefania Sarno; Davide Pettener; Donata Luiselli; Martin B Richards; Ornella Semino; Alessandro Achilli; Antonio Torroni; Walther Parson
Journal:  Int J Mol Sci       Date:  2022-06-16       Impact factor: 6.208

4.  From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel.

Authors:  Filipe Cortes-Figueiredo; Filipa S Carvalho; Ana Catarina Fonseca; Friedemann Paul; José M Ferro; Sebastian Schönherr; Hansi Weissensteiner; Vanessa A Morais
Journal:  Int J Mol Sci       Date:  2021-11-06       Impact factor: 5.923

5.  Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics.

Authors:  Claire-Elise Fischer; Marie-Hélène Pemonge; Isaure Ducoussau; Ana Arzelier; Maïté Rivollat; Frederic Santos; Hélène Barrand Emam; Alexandre Bertaud; Alexandre Beylier; Elsa Ciesielski; Bernard Dedet; Sophie Desenne; Henri Duday; Fanny Chenal; Eric Gailledrat; Sébastien Goepfert; Olivier Gorgé; Alexis Gorgues; Gertrud Kuhnle; François Lambach; Anthony Lefort; Amandine Mauduit; Florent Maziere; Sophie Oudry; Cécile Paresys; Estelle Pinard; Suzanne Plouin; Isabelle Richard; Muriel Roth-Zehner; Réjane Roure; Corinne Thevenet; Yohann Thomas; Stéphane Rottier; Marie-France Deguilloux; Mélanie Pruvost
Journal:  iScience       Date:  2022-03-16

6.  Post hoc deconvolution of human mitochondrial DNA mixtures by EMMA 2 using fine-tuned Phylotree nomenclature.

Authors:  Arne Dür; Nicole Huber; Alexander Röck; Cordula Berger; Christina Amory; Walther Parson
Journal:  Comput Struct Biotechnol J       Date:  2022-07-02       Impact factor: 6.155

Review 7.  Mitochondria in Mycobacterium Infection: From the Immune System to Mitochondrial Haplogroups.

Authors:  Felipe Gouvea de Souza; Giovanna C Cavalcante
Journal:  Int J Mol Sci       Date:  2022-08-23       Impact factor: 6.208

8.  Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia.

Authors:  Irene Cardinali; Martin Bodner; Marco Rosario Capodiferro; Christina Amory; Nicola Rambaldi Migliore; Edgar J Gomez; Erdene Myagmar; Tumen Dashzeveg; Francesco Carano; Scott R Woodward; Walther Parson; Ugo A Perego; Hovirag Lancioni; Alessandro Achilli
Journal:  Front Genet       Date:  2022-01-06       Impact factor: 4.599
  8 in total

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