ArticleForensic science international. Genetics2013
Concept for estimating mitochondrial DNA haplogroups using a maximum likelihood approach (EMMA).
Article in Forensic science international. Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- Article
- Quantitation of human mitochondrial DNA and whole mtGenomes sequencing of fingernail/hair shaft samples.Forensic sciences research · 2025Article
- Analysis of maternal genetic structure of mitochondrial DNA control region from Tai-Kadai-speaking Buyei population in southwestern China.BMC genomics · 2024Article
- Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus).Genome biology and evolution · 2023Article
- High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia.Genes · 2023Article
- HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.PLoS computational biology · 2023Article
- Article
- Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography.BMC genomics · 2022Article
- Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.BioMed research international · 2022Article
- Post hoc deconvolution of human mitochondrial DNA mixtures by EMMA 2 using fine-tuned Phylotree nomenclature.Computational and structural biotechnology journal · 2022Article
- Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system.Forensic sciences research · 2022Article
- A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data.Scientific reports · 2021Article
- Sweet tooth: DNA profiling of a cranium from an isolated retained root fragment.Journal of forensic sciences · 2021Article
- Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences.International journal of molecular sciences · 2021Article
- Mitochondrial DNA control region diversity in a population from Parana state-increasing the Brazilian forensic database.International journal of legal medicine · 2019Article
- Article
- Big data analysis of human mitochondrial DNA substitution models: a regression approach.BMC genomics · 2018Article
- Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations.Scientific reports · 2018Article
- Article
- Analysis of human mitochondrial DNA sequences from fecally polluted environmental waters as a tool to study population diversity.AIMS environmental science · 2017Article
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4 authors.
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Abstract
The assignment of haplogroups to mitochondrial DNA haplotypes contributes substantial value for quality control, not only in forensic genetics but also in population and medical genetics. The availability of Phylotree, a widely accepted phylogenetic tree of human mitochondrial DNA lineages, led to the development of several (semi-)automated software solutions for haplogrouping. However, currently existing haplogrouping tools only make use of haplogroup-defining mutations, whereas private mutations (beyond the haplogroup level) can be additionally informative allowing for enhanced haplogroup assignment. This is especially relevant in the case of (partial) control region sequences, which are mainly used in forensics. The present study makes three major contributions toward a more reliable, semi-automated estimation of mitochondrial haplogroups. First, a quality-controlled database consisting of 14,990 full mtGenomes downloaded from GenBank was compiled. Together with Phylotree, these mtGenomes serve as a reference database for haplogroup estimates. Second, the concept of fluctuation rates, i.e. a maximum likelihood estimation of the stability of mutations based on 19,171 full control region haplotypes for which raw lane data is available, is presented. Finally, an algorithm for estimating the haplogroup of an mtDNA sequence based on the combined database of full mtGenomes and Phylotree, which also incorporates the empirically determined fluctuation rates, is brought forward. On the basis of examples from the literature and EMPOP, the algorithm is not only validated, but both the strength of this approach and its utility for quality control of mitochondrial haplotypes is also demonstrated.
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