Dante

Dante implements an alignment-free algorithm for genotyping and characterizing short tandem repeat (STR) and tandem repeat (TR) alleles at user-specified known loci from second-generation and third-generation sequencing data.

Key Features:

• Multi-platform sequencing support: Dante analyzes both short-read massively parallel sequencing (sr-MPS) and long-read massively parallel sequencing (lr-MPS) data for repeat characterization across a wide range of loci.
• Nucleotide-resolution genotyping: The tool determines genotypes at nucleotide resolution, including characterization and phasing of complex repeat motifs containing several different motifs.
• Short-read allele analysis: For sr-MPS data, Dante determines allele size and sequence composition of alleles with spanning reads, identifies alleles exceeding read length by estimating presence from partial read evidence, and supports visualization of sequence composition of partial reads.
• Long-read allele analysis: For lr-MPS data, Dante determines allele size and sequence composition of identified alleles where complete repeat regions are typically sequenced.
• Stutter correction: Dante implements correction for copy number defects caused by polymerase-induced stutter effect.
• Expansion prediction: The tool predicts STR expansions that cannot be fully captured by inherently short MPS reads.
• Natural variation handling: The method accounts for variation in repeat count, sequencing errors, ambiguous bases, and complex loci.

Scientific Applications:

• Clinical genotyping: Dante outperformed HipSTR and GATK genotyping tools on simulated datasets and targeted sequencing datasets of protein coding parts of thousands of selected clinically relevant genes.
• Expansion disorder diagnostics: Dante predicted allele expansions in all tested clinical cases, including myotonic dystrophy type 2 (DM2) where a modified version achieved 97% genotyping concordance with conventional PCR and repeat-primed PCR methods.
• Complex motif phasing: The tool enables phasing of entire complex motifs such as the CNBP-complex motif in DM2 diagnostics.
• Normal-range allele characterization: Whole genome sequencing with Dante enables detailed sequence structure characterization of normal-range alleles.

Methodology:

Dante uses an alignment-free algorithm that analyzes sequence reads originating from STR loci of interest without requiring read alignment to a reference genome.