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Table 4 Short tandem repeat candidates identified in our patient cohort

From: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

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)
  1. 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
  2. aReduced-penetrance alleles have 33–34 repeats and full-penetrance alleles have ≥ 37 repeats