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

Rajan-Babu, Indhu-Shree; Peng, Junran J.; Chiu, Readman; Li, Chenkai; Mohajeri, Arezoo; Dolzhenko, Egor; Eberle, Michael A.; Birol, Inanc; Friedman, Jan M.

doi:10.1186/s13073-021-00932-9

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	Borderline^a	n.a.
821-M	ATXN2	.	ES	.	.	Borderline^a	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

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ISSN: 1756-994X

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