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.
Repeat Expansion Pathologies
- Huntington Disease (HD): HTT exon 1 CAG triplet repeats. Normal: ≤26 repeats; Full penetrance: ≥40 repeats.
- Fragile X Syndrome (FXS): FMR1 5' UTR CGG repeats. Premutation: 55–200; Full mutation: >200 repeats leading to hypermethylation and gene shutdown.
- Amyotrophic Lateral Sclerosis / FTD: C9orf72 intronic GGGGCC hexanucleotide expansion (hundreds to thousands of repeats).
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 alleles2. 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