Table 4.
Short tandem repeat candidates identified in our patient cohort
| Sample ID | Gene | Inheritance | Sequencing | Pathogenic SNV/indel/SV finding | Phenotype | STR finding | Molecular validation |
|---|---|---|---|---|---|---|---|
| 1901-P | AR | Inherited | WGS | No | Short stature, delayed gross motor, speech and language development, spasticity, cerebral palsy, and hypertonia | FM (full-penetrance) | FM (reduced/full-penetrance) |
| 1901-F | AR | . | WGS | . | . | FM (full-penetrance) | FM (reduced/full-penetrance) |
| 532-M | ATXN1 | . | WGS | . | . | FM (full-penetrance) | n.a. |
| 821-P | ATXN2 | Inherited | ES | No | Mild intellectual disabilities, systemic hypertension, cutis aplasia, congenital heart defect, and limb anomalies | Borderlinea | n.a. |
| 821-M | ATXN2 | . | ES | . | . | Borderlinea | n.a. |
| 1099-P | ATXN8 | Inherited | ES | No | Hearing loss, cataract, myopia, visceral (kidney and spleen) cysts, proteinuria, and dysmorphic facial features | FM (higher penetrance) | n.a. |
| 1099-M | ATXN8 | . | ES | . | . | FM (higher penetrance) | n.a. |
| 235-P | ATXN8 | Inherited | WGS | No | Mild to moderate intellectual disability, and psychosis | FM (higher penetrance) | n.a. |
| 235-M | ATXN8 | . | WGS | . | . | FM (higher penetrance) | n.a. |
| 2010-P | DMPK | Inherited | ES | Definite | Myotonic dystrophy type 1, inguinal hernias, joint hypermobility, strabismus, mild intellectual disability, and dysmorphic facial features | FM (full-penetrance) | FM (full-penetrance) |
| 2010-M | DMPK | . | ES | . | Myotonic dystrophy type 1 | FM (full-penetrance) | FM (full-penetrance) |
| 148-M | FMR1 | . | WGS | . | . | PM | n.a. (proband is negative for FMR1 FM) |
| 800-F | FMR1 | . | WGS | . | . | IM | n.a. |
| 480-P | FMR1 | Inherited | WGS | Probable | Moderate intellectual disability, language delay, autism, borderline macrocephaly, low set ears, down slanting palpebral fissures, high palate, and soft skin | PM | n.a. |
| 712-M | FMR1 | . | WGS | . | . | PM | n.a. (proband is negative for FMR1 FM) |
| 925-P | FMR1 | Inherited | WGS | No | Intellectual disability, developmental delay including speech delay, dysmorphic features, and behavioral challenges | PM | Negative for FM |
| 925-S | FMR1 | Inherited | WGS | No | Intellectual disability, autism, developmental delay, and dysmorphic features | IM | n.a. |
| 925-M | FMR1 | . | WGS | . | . | PM | n.a. |
| 1987-F | FXN | . | WGS | . | . | NL/FM | Heterozygous NL/FM carrier |
| 1530-P | HTT | Inherited | WGS | Uncertain | Global developmental delay, seizures, gliosis, developmental regression, encephalomalacia, hirsutism, nystagmus, optic atrophy, cyanosis, abnormal muscle tone, scoliosis, hearing impairment, and otitis media | FM (reduced penetrance) | FM (reduced penetrance) |
| 1530-F | HTT | . | WGS | . | . | FM (reduced penetrance) | FM (reduced penetrance) |
Probands with an identified STR candidate are given a “-P” suffix in the “Sample ID” column; sibling of the proband, “-S”; mother, “-M”; and father, “-F”. The genes harboring the STR candidate identified by our bioinformatics workflow and the inheritance pattern deciphered by comparing the proband’s STR call with that of the parents are reported. The “Sequencing” column shows the technology used: whole-genome sequencing (WGS) or exome sequencing (ES). The “Pathogenic SNV/indel/SV Finding” column indicates whether the proband has had a definite, probable, certain, or no diagnosis of a single-nucleotide variant (SNV), indel, or structural variant (SV). Phenotypic presentations reported in the probands, STR finding from our bioinformatics analysis, and the results from the molecular validation (if available) are also presented. NL normal, IM intermediate, PM premutation, FM full-mutation, n.a. not available
aReduced-penetrance alleles have 33–34 repeats and full-penetrance alleles have ≥ 37 repeats