Haplotracker
Human mtDNA Haplogroup classification

Track by Sequence

fragments/ full mtGenome

Track by Variant profiles

fragments/ full mtGenome

Conserved Region Map

for primer/ probe design


High-resolution haplogrouping with control/coding regions

High-resolution mtDNA haplogroup prediction using the Sanger sequencing of small fragmented control region sequences, tracking with coding region sequences for confirmation or sub-haplogrouping by narrowing and differentiating highly ranked haplogroups. BioMed Research Internaltional/2022/5344418


High accuracy using control region sequences

Highly accurate prediction of haplogroup (HG) using control region (CR) or hypervariable region sequence fragments.

  • Using a novel algorithm based on PhyloTree definitions and our scoring system built with big data of haplotypes (n=118,869)
  • Extensively evaluated with 54,538 CR sequence samples comparing with HaploGrep 2.

Haplotracker characterization of Phylotree CR sequences

Characterization of Phylotree-provided control region sequences tested for haplogroup classification by Haplotracker. Of Phylotree-provided control region (CR) sequences (n=8216), 56.6% sequences (in blues) were classified in agreement with Phylotree-defined haplogroups (HGs). The sequences were predominantly scored (39%). The scores of 22% sequences contributed to HG classification by Haplotracker algorithm. A small number of scored sequences (7%) were found in the remaining CR sequences (in oranges) that were not haplogrouped according to Phylotree HGs


Minimum number of amplicons for Haplotracker using CR/CdR sequences

Minimum number of amplicons required by Haplotracker in discriminating between haplogroups using mtDNA control and coding region sequences. All dstinct haplogroup reference sequences available in Phylotree Build 17 (n=4680) were tested in silico using Haplotracker to estimate the minimum number of amplicons for haplogrouping of various haplogroup samples. Haplotracker determined that the haplogroups of 13 samples (amplicons '0' in this plot) were not identical to the Phylotree-defined haplogroups even using full-length sequences. Except for these samples the summarized results were as follows. Haplotracker classified 95% of the haplogroups as identical to the Phylotree definition using up to 12 amplicons. With up to 25 amplicons, all haplogroups (98.4%) with the exception of some belonging to the two super-haplogroups (M and H) were determined in agreement with the Phylotree definition


A novel tracking solution

It was established through repeated blind simulation tests

  • Inputs sequence fragments via a unique user-friendly interface.
  • Minimizes the number of tests for HG tracking by narrowing down the predicted HGs by the integration of HGs to their MRCAs (most recent common ancestors).
  • Proposes differential variants between HGs.
  • Re-tracks with the fragments of proposed variants to confirm the HGs or to track sub-HGs.

Additional tools

  • 'HG tracking by fragment variant profiles' for variant profile input instead of sequences once the sample fragments are sequenced and their variants are extracted using the main tool.
  • 'Conserved region mapping tool for primer design' to secure successful PCR that is necessary to obtain additional sequences for further tracking.
  • 'HG database' to explore Phylotree HGs and their sub-haplogroups with their defining variant profiles.
  • 'Differntiation between HGs' to find differential variant information among user-inputted HGs.
  • QC tools: analysis of potential artificial recombination (included in main tools) and potential phantom mutants in a dataset
  • Variant format conversion tool for Phlyotreee, MitoTool, HaploGrep 2, and EMPOP
  • Major HG-specific variants

Super-HG prediction rates with CR sequences

Super-HG prediction rates



References

References