MitoFREQ: A novel approach for mitogenome frequency estimation from top-level haplogroups and single nucleotide...

Area of Science:

• Forensic Genetics
• Population Genetics
• Bioinformatics

Background:

• Quantifying the evidential value of forensic lineage markers is challenging.
• Population frequencies of mitochondrial DNA (mtDNA) markers are crucial but often limited.
• Existing databases like HelixMTdb and gnomAD lack direct querying for individual mitogenome frequencies.

Purpose of the Study:

• To introduce MitoFREQ, a novel method for estimating population frequencies of whole mitochondrial DNA genome sequences (mitogenomes).
• To leverage large-scale mitogenome datasets (HelixMTdb, gnomAD) for improved forensic statistical analysis.
• To develop a robust and accessible tool for forensic geneticists.

Main Methods:

• Utilized HelixMTdb and gnomAD resources containing 195,983 and 56,406 mitogenomes, respectively.
• Developed a method classifying mitogenomes into top-level haplogroups (TLHGs) using single nucleotide variant (SNV) allele frequencies.
• Employed a weighted frequency estimation based on the rarest SNV within a TLHG and the TLHG frequency itself.

Main Results:

• The MitoFREQ method provides higher population frequency estimates compared to using refined haplogroups.
• Top-level haplogrouping is achievable with as few as 227 specific positions, enabling use with low-quality samples.
• The method demonstrated robustness on both forensic reference datasets and diverse GenBank mitogenomes, yielding likelihood ratios from 100-100,000.

Conclusions:

• MitoFREQ offers a robust approach to estimate mitogenome population frequencies, enhancing the statistical power of forensic mtDNA evidence.
• The method's ability to work with limited data positions makes it suitable for degraded or low-quality forensic samples.
• An open-source R package, mitofreq, has been developed for practical implementation, including a user-friendly Shiny app.