HaploGrep
A fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups
Bibliographic Data
| ID | 23385667 |
|---|---|
| Authors | Anita Kloss-Brandstätter, Anita Kloss‐Brandstätter (0000-0002-0873-6704, Innsbruck Medical University, corresponding author), Dominic Pacher (Universität Innsbruck), Sebastian Schönherr (Innsbruck Medical University), Hansi Weissensteiner (0000-0002-2871-8669, Innsbruck Medical University), Robert Binna (0000-0003-1062-8419, Universität Innsbruck), Günther Specht (0000-0003-0978-7201, Universität Innsbruck), Fredi Kronenberg (0000-0003-2229-1120, Innsbruck Medical University), Florian Kronenberg |
| Year | 2011 |
| Volume | 32 |
| Issue | 1 |
| Pages | 25-32 |
| Publication date | 2011-01-01 |
| Peer Reviewed | Yes |
| Open Access | Yes |
| Type | ARTICLE |
| Venue | Human Mutation (JOURNAL) |
| Journal identifiers | ISSN: 1059-7794 • E-ISSN: 1098-1004 |
| Publisher | Hindawi Limited (PUBLISHER) |
| DOI | 10.1002/humu.21382 |
| PMID | 20960467 |
| OpenAlex | W2037764582 |
| Language | EN |
| Citations received | 86 |
| References cited | 49 |
An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at.
Allele · Biology · Computational biology · Evolutionary biology · Gene · Haplogroup · Haplotype · Human mitochondrial DNA haplogroup · Mitochondrial DNA · Phylogenetic tree · Population · Forensic and Genetic Research · Genetics · Genomics and Phylogenetic Studies · Metabolomics and Mass Spectrometry Studies
Mitochondrial DNA diversity of the Roma from northeastern Bosnia, Bosnia and Herzegovina
Linajes Maternos en Muestras Antiguas De La Puna Jujeña. Comparacion Con Estudios De La Region Centro-Sur Andina
Patrones de migración y niveles de diversidad genética de linajes maternos en la población de La Esperanza, provincia de Jujuy
Diversidad Genética en Restos Humanos Arqueológicos Del Sitio El Diquecito (Costa Sur, Laguna Mar Chiquita, Provincia De Córdoba)
Linajes Mitocondriales en Muestras De Esquina De Huajra (Jujuy, Argentina). Aportes Al Estudio De La Ocupación Incaica en La Región Y La Procedencia De Sus Habitantes
Diversidad genética en restos humanos de contextos arqueológicos tardíos de la provincia de Santiago del Estero a partir del estudio de ADN mitocondrial
Ancient DNA Analysis of the Thulamela Remains
Explorando dinámicas poblacionales ancestrales en el noreste peruano
La Menorca talayótica desde el punto de vista genético
Population genomics of Bronze Age Eurasia
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia
Analysis of Uniparental Lineages in Two Villages of Santiago del Estero, Argentina, Seat of Pueblos de Indios in Colonial Times
Uniparental Genetic Analyses Reveal the Major Origin of Fujian Tanka from Ancient Indigenous Daic Populations
Mitochondrial DNA Analysis of Mazahua and Otomi Indigenous Populations from Estado de México Suggests a Distant Common Ancestry
U5a1 Mitochondrial DNA Haplotype Identified in Eneolithic Skeleton from Shatar Chuluu, Mongolia
Mitochondrial DNA Analysis of Mazahua and Otomi Indigenous Populations from Estado de México Suggests a Distant Common Ancestry
Genetic Relationships between Mesoamerican Ancient Populations and with American Greater Southwest and Caribbean Populations Close to Mesoamerican Borders
Between Valleys and Mountains. The Dzedzvebi Plateau as an Intermediate Settlement Site of Late Chalcolithic and Early Bronze Age Communities in the Lesser Caucasus
Genome flux and stasis in a five millennium transect of European prehistory
Schmutzi
Genomic evidence for the Pleistocene and recent population history of Native Americans
HaploGrep 2
Years of Parallel Societies in Stone Age Central Europe
Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity
Archaeogenomic evidence reveals prehistoric matrilineal dynasty
Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria
The makers of the Protoaurignacian and implications for Neandertal extinction
Archival, paleopathological and aDNA-based techniques in leprosy research and the case of Father Petrus Donders at the Leprosarium ‘Batavia’, Suriname
Identification of the geographic origins of people buried in the cemetery of the Salesian Mission of Tierra del Fuego through the analyses of mtDNA and stable isotopes
Ancient DNA and paleoproteomic analysis on Roman Imperial-era individuals from Histria, Romania
Spirit Eye Cave
First analysis of ancient mtDNA genetic diversity in Northern coast of Argentinean Patagonia
Recovered identities
The kinship of two 12th Dynasty mummies revealed by ancient DNA sequencing
Archaeological questions and genetic answers
Genetic affiliations within a 19th century burial ground at Darwen, Lancashire, UK
Maternal Lineages during the Roman Empire, in the Ancient City of Gadir (Cádiz, Spain)
A population history of Tokelau – genetic variation and change in atoll populations
A multifaceted approach towards investigating childbirth deaths in double burials
An isotopic and genetic study of multi-cultural colonial New Zealand
Six complete mitochondrial genomes from Early Bronze Age humans in the North Caucasus
Maternal genetic link of a south Dravidian tribe with native Iranians indicating bidirectional migration
Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia)
Iron Age Italic population genetics
Linking between genetic structure and geographical distance
Mitochondrial super-haplogroup U diversity in Serbians
The genetic landscape of Mediterranean North African populations through complete mtDNA sequences
MtDNA and Y‐chromosomal diversity in the Chachapoya, a population from the northeast Peruvian Andes‐Amazon divide
The historical spread of A rabian P astoralists to the eastern A frican S ahel evidenced by the lactase persistence −13,915*G allele and mitochondrial DNA
Traces of forgotten historical events in mountain communities in C entral I taly
Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India
Over the sands and far away
Origins of marronage
Ancient mitochondrial DNA and ancestry of Paquimé inhabitants, Casas Grandes (A.D. 1200–1450)
Analysis of the mitochondrial Cytb gene sequence in human populations of northeastern Bosnia
Analysis of Uniparental Lineages in Two Villages of Santiago del Estero, Argentina, Seat of Pueblos de Indios in Colonial Times
Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel)
Hunter-gatherer genetic persistence at the onset of megalithism in western Iberia
Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians
Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel
Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus
Sex‐specific genetic diversity is shaped by cultural factors in Inner Asian human populations
Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia
High‐resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia
Genetic diversity in S vaneti and its implications for the human settlement of the H ighland C aucasus
The female ancestor's tale
Unraveling the complex maternal history of Southern African Khoisan populations
Nomadic pastoralists and sedentary farmers of the Sahel/Savannah Belt of Africa in the light of geometric morphometrics based on facial portraits
Internal diversification of non‐Sub‐Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara
Comprehensive view of the population history of A rabia as inferred by mt DNA variation
First analysis of mitochondrial lineages from the eastern Pampa–Patagonia transition during the final late Holocene
Pleistocene‐Holocene boundary in Southern Arabia from the perspective of human mtDNA variation
Matriclans shape populations
Combined methodologies for gaining much information from ancient dental calculus
Genetic and historical perspectives on the early medieval inhumations from the Menga dolmen, Antequera (Spain)
The Australian Barrineans and Their Relationship to Southeast Asian Negritos
A Genetic Analysis of Human Remains From Ak-Alakha-3 Burial Mound 1, Gorny Altai1
Mitochondrial DNA diversity in a Transbaikalian Xiongnu population
Mitogenomic diversity and stable isotopes provide insights into the maternal genetic history, mobility patterns, and diet of early medieval individuals from the Eastern Italian Alps
DNA profiling of Hungarian King Béla III and other skeletal remains originating from the Royal Basilica of Székesfehérvár
A multidisciplinary study of calcaneal trauma in Roman Italy
Anaemia (thalassaemia) in the Middle Euphrates Valley of Syria in the second-fourth centuries AD
Perinatal burials at pre-Hispanic noncemetery sites in Gran Canaria
A Probable Case of Thalassemia Intermedia from Tell Masaikh, Syria
Evaluation of Diammonium hydrogen phosphate and Ca(OH)2 nanoparticles for consolidation of ancient bones
Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes
The Phylogeny of the Four Pan-American MtDNA Haplogroups
Correcting for Purifying Selection
Median-joining networks for inferring intraspecific phylogenies
Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
| Unique citing works | 86 |
|---|---|
| Citations per year | 6,14 |
| Citation span | 2012 - 2026 (15) |
| Citation velocity | current |
| Highly cited | No |
| Citation types | Neutral: 68 |