Haplotracker

Haplotracker predicts mitochondrial DNA (mtDNA) haplogroups from control-region and short fragmented sequences to enable haplogroup assignment and sub-haplogroup tracking for degraded samples.

Key Features:

• Novel algorithm: Employs an algorithm based on Phylotree Build 17 and a haplotype database of over 118,869 entries for haplogroup estimation from mtDNA control-region fragments.
• High accuracy in haplogroup prediction: Demonstrates higher concordance for top-ranking haplogroups (56.6%) in blind simulations compared with MitoTool (29.4%) and HaploGrep 2 (33.9%).
• Sub-haplogroup tracking: Narrows candidate haplogroups and identifies differential coding-region variants to refine and confirm sub-haplogroup assignments.
• Variant information: Reports sample variants with frequencies from a large mtGenome database to aid identification of common, rare, and potentially pathogenic mutations.
• Conserved-region mapping for primer design: Provides conserved-region mapping to support PCR primer design targeting diagnostic variants.
• Laboratory validation: Demonstrated utility through application to an ancient DNA extract.

Scientific Applications:

• Population genetics: Assigns mtDNA haplogroups for population-structure and evolutionary analyses.
• Forensic analysis: Enables haplogrouping of degraded or fragmented forensic and ancient DNA samples.
• Medical genetics: Supports investigation of mtDNA-associated mutations by providing variant frequency context from an mtGenome database.

Methodology:

Predicts haplogroups from control-region sequences using an algorithm based on Phylotree Build 17 and a haplotype database of >118,869 entries; validated on 8,216 control-region sequences and evaluated on 46,322 control-region sequences, including repeated blind simulations.