HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups

By A. Kloss-Brandstätter, D. Pacher, S. Schönherr, H. Weissensteiner, Robert Binna, Günther Specht, F. Kronenberg. Human Mutation, 2011

514 citations recorded by the source corpus.

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. Hum Mutat 31:–8, 2010. © 2010 Wiley‐Liss, Inc.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2d8d4c855173a5d7913506caaf8cccb8b9e95c0d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Mannis van Oven
2. Lukas Forer

In Molecular Biology

1. Mannis van Oven
2. Janet Kelso
3. Gabriel Renaud
4. Lukas Forer
5. Vincent Procaccio
6. Dimitra Chalkia

Citations in the corpus

• mtDNA Variation and Analysis Using MITOMAP and MITOMASTER (2013, methodology): “Haplotyping is based on Phylotree (van Oven and Kayser, 2009) and is generated by Mitomaster using the Haplogrep engine (Kloss-Brandstatter et al., 2011).”
• Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA (2015, methodology): “Using HaploGrep [26, 27], we determined that our inferred mitochondrial genome pertained to the T2b3 haplogroup with a confidence of 93.1 %.”
• PhyloTree Build 17: Growing the human mitochondrial DNA tree (2015, methodology): “PhyloTree has been widely adopted as the reference phylogeny for human mtDNA and serves as the underlying haplogroup classification system for EMPOP [2], HaploGrep [3] and Phy-Mer [4], among others [5].”
• HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing (2016, methodology): “In addition to the already implemented Kulczynski distance (1), the Jaccard index, the Hamming distance and the Kimura 2parameter distance were included (24) (see Supplementary Table S2 and 3 for performance comparison).”