Chapter 11: Repeat Expansion Disorders & Mitochondrial Genome Pathogenicity

Chapter 11: Repeat Expansion Disorders & Mitochondrial Genome Pathogenicity

Standard short-read variant callers (e.g. GATK) assume simple SNPs and small indels (<50 bp). They fail completely on two critical classes of clinical disease: Short Tandem Repeat (STR) Expansions and Mitochondrial (mtDNA) Pathogenic Heteroplasmies.

1. Calling Expanded Repeats with ExpansionHunter

# Detect repeat expansion from BAM alignment using locus catalog
ExpansionHunter \\
    --reads patient_wgs.bam \\
    --reference ref_grch38.fa \\
    --variant-catalog /opt/variant_catalog_hg38.json \\
    --output-prefix ./expansion_results/patient_str

# Outputs:
#   ├── patient_str.vcf   -> Standard VCF with REPID and repeat allele counts
#   └── patient_str.json  -> Detailed confidence intervals for both alleles

2. Mitochondrial Heteroplasmy and Clinical Thresholds

Human cells contain hundreds to thousands of circular mitochondrial genomes (mtDNA, 16,569 bp). In mitochondrial disorders (e.g. MELAS, MERFF, Leigh syndrome), mutant and wild-type mtDNA molecules coexist in a state called heteroplasmy. Clinical symptoms typically manifest only when the mutant heteroplasmy percentage exceeds a biochemical threshold (typically 60–80%).

# Call low-frequency heteroplasmies with Mutect2 in mitochondria mode
gatk Mutect2 \\
    -R ref_grch38.fa \\
    -L chrM \\
    -I patient_wgs.bam \\
    --mitochondria-mode \\
    -O mtdna_variants.vcf.gz