Forensic & Medical Mitochondrial DNA Analysis

Developed in collaboration with leading forensic and medical laboratories, GeneMarkerHTS software provides rapid analysis of multiple samples using consensus and motif alignments:

  • Unique motif alignment technology
    • Automates the requirements set by The DNA Commission of the International Society for Forensic Genetics
    • Fulfills the forensic alignment recommendations.
    • Provides recognition and proper assignment of motifs and indels consistent with phylogenetic and forensic considerations
  • Consensus alignment
    • To the preloaded Revised Cambridge Reference Sequence or to other references

Motif alignment reduces manual edits for forensic alignment

Figure 1: GeneMarkerHTS software has an extensive, preloaded forensic motif file as well as a motif editor to assist labs in adding new motifs.

Automatic Features Include:

  • Three alignment algorithms that best suit the analysis needs:
    • Initial Alignment to a reference genome (Revised Cambridge Reference Sequence is preloaded into GeneMarkerHTS)
    • Adjust alignment with motifs to ensure the alignment is consistent with forensic variant reporting
    • Adjust alignment using the consensus; improving alignment around indels
  • Analysis across the origin
  • Forensic or standard nomenclature
  • Maintain health privacy with an administrative option that blocks display of disease associated positions

Analysis Results Include:

  • Consensus sequence, Variants, SNPs, Indels
  • Depth of coverage graphics
  • Consensus sequence aligned to reference (IUPAC nomenclature)
    • Whole mtDNA genome, spanning the origin
    • Specified areas of interest, such as control region, HV1, HV2
  • Read pile-up (with depth and direction indicators)
  • Compare multiple samples in single view
    • Synchronized view - scroll and zoom multiple samples
  • Comparison viewer - table with sample-to-sample and variant composition

GeneMarkerHTS Software Viewing Options:

  • Users can customize color-coding for nucleotides and highlight edits
  • ‘Global’ and ‘Zoom’ views for the whole mtDNA genome alignment
    • The Global View shows the depth of coverage with forward read coverage in blue and reverse read coverage in red
    • The Zoom View allows users to zoom-in on the range displayed in the pile-up

Figure 2: Global view (left) and Zoom view (right).

View up to 4 samples simultaneously

Figure 3: Synchronized viewing of multiple samples

Compare analysis results of multiple samples

Figure 4: Sample-to-sample comparison (top) and variant comparison of all samples in the project (bottom)

GMHTS Software can Export a Variety of Reports:

  • Consensus sequence
  • Variant reports – SNPs, heteroplasmy, and insertions and deletions
  • Variant reports are EMPOP (EDNAP mtDNA Population Database) compatible

Minimum Recommended processing hardware:

  • 64-bit Windows OS 12 GB RAM 2.4GHzDual Quad Core Processor.

Reference Material: