Table 2.
Significant outliers called by STRling in 260 individuals from the 1000 Genomes Project. We performed joint-calling and outlier testing, then filtered the results to 32 well-characterized known pathogenic STR loci (see the “Methods” section). There were 204 significant STRling calls across ten loci (the others had no significant calls), resulting in an estimated FDR of 0.078. Of these, most also had evidence of a short, likely non-pathogenic allele (reads and read pairs spanning the locus), suggesting heterozygosity
| Disease | Significant outlier | Evidence of a short allele | Proportion significant outlier | STRling est. > pathogenic threshold | Inheritance | Notes |
|---|---|---|---|---|---|---|
| CANVAS | 12 | 12 | 0.0462 | 0 | AR | 0.7% carrier frequency [10] |
| DBQD2 | 5 | 5a | 0.0192 | 0 | AR | |
| DM2 | 7 | 7 | 0.0269 | 0 | AD | Age onset: ~30–40 |
| FRA12A | 57 | 57 | 0.219 | 0 | AD | |
| FRAXE | 7 | 7 | 0.0269 | 0 | XR | |
| FRDA | 61 | 61 | 0.235 | 1 | AR | Age onset: 5–25 |
| FTDALS1 | 33 | 32 (1a) | 0.127 | 0 | AD | Age onset: 27–85 |
| FXS | 0 | N/A | 0 | 0 | XD | Multiple syndromes with varying pathogenic size thresholds and age of onset: FXS 2, FXTAS 60–65, POI? |
| SCA10 | 8 | 8 | 0.0308 | 0 | AD | Age onset: 12–48 |
| SCA8 | 14 | 14 | 0.0538 | 1 | AD | Age onset: 1–73 |
Novel STR disease loci (not in the reference genome) are indicated in bold/underline
AD Autosomal dominant, AR Autosomal recessive, XD X-linked dominant, XR X-linked recessive
aNo spanning reads, spanning pairs only