My Forensic Loci queries

My Forensic Loci queries analyzes massive parallel sequencing (MPS) data to call alleles and assess forensic locus performance for short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling.

Key Features:

• Multiplexing Capability: Supports virtually unlimited multiplexing of loci and simultaneous analysis of STR and SNP loci, enabling analysis of many more loci than capillary electrophoresis (CE).
• Flexible Amplicon Analysis: Accommodates small amplicons without constraints on size separation, facilitating analysis of degraded or targeted PCR products.
• Robust Allele Calling: Uses a MySQL reference allele database and a generic maximal flanking algorithm to determine regions of interest (ROIs) and employs custom Python scripts to call alleles from raw MPS reads.
• Performance Assessment and Error Analysis: Implements methods to assess locus utility and performance in MPS and to distinguish unknown alleles not present in the database from sequencing errors.
• Application to Complex Samples: Has been applied to Illumina MiSeq data from a multilocus STR polymerase chain reaction (PCR) library, including single-contributor samples and multiple-person DNA mixtures, reporting high signal-to-noise ratios, accurate allele calls, and low detection limits for minor contributors.

Scientific Applications:

• Forensic Genomics: Provides allele calling and locus performance metrics for forensic DNA profiling using MPS.
• Molecular Autopsy: Can be applied to genetic analyses in legal medicine to support cause-of-death investigations.
• Mitochondrial DNA Research: Applicable to mitochondrial DNA studies and mixture analysis, including small amplicons and complex mixtures.

Methodology:

Uses a MySQL reference allele database, a generic maximal flanking algorithm to automatically determine ROIs, and custom Python scripts to call alleles from raw MPS data, with additional computational methods to assess locus performance and distinguish unknown alleles from sequencing errors.