STR calling and interpretation

Calling methodology

Emedgene uses ExpansionHunter by DRAGEN to call short tandem repeats (STR), also known as repeats expansions.

Thirty clinical genes associated with diseases caused by repeat expansion are called in DRAGEN version 3.9 and presented in the platform. Those genes are: AFF2, AR, ATN1, ATXN1, ATXN10, ATXN2, ATXN3, ATXN7, ATXN8OS, C9ORF72, CACNA1A, CBL, CNBP, CSTB, DIP2B, DMPK, FMR1, FXN, GIPC1, GLS, HTT, JPH3, NIPA1, NOP56, PABPN1, PHOX2B, PPP2R2B, RFC1, TBP, TCF4.

STR calling with ExpansionHunter

Spanning reads

Exact sizes of short repeats are identified from spanning reads that completely contain the repeat sequence.

Flanking reads

When the repeat length is close to the read length, the size of the repeat is approximated from the flanking reads that partially overlap the repeat and one of the repeat flanks.

In-repeat reads (IRRs)

If the repeat is longer than the read length, its size is estimated from reads completely contained inside the repeat (in-repeat reads). In-repeat reads anchored by their mate to the repeat region are used to estimate the size of the repeat up to the fragment length. When there is no evidence of long repeats with the same repeat motif elsewhere in the genome, pairs of in-repeat reads can also be used to estimate the size of long (greater-than-fragment-length) repeats.

Note: ExpansionHunter for STR calling is designed for use in PCR-free WGS only. While STR variants might be called in exome cases, the limitations are currently unknown and it is therefore not recommended for use.

Recommendation for interpretation

In light of our recent experience and an internal investigation by the Illumina’s scientific team, we believe it is appropriate to enable prioritization for a subset of STR loci, but not all loci typed by DRAGEN. This is due to technical genotyping challenges and/or lack of scientific evidence of pathogenicity for the remaining loci. Current list of genes where STR may be tagged when appropriate is provided below:

Gene	Associated Condition	Mode of Inheritance	Repeat Unit
ATXN10	Spinocerebellar ataxia 10 (SCA10)	Autosomal Dominant	ATTCT
ATXN8OS	Spinocerebellar ataxia 8 (SCA8)	Autosomal Dominant	CTG
ATN1	Dentatorubral-pallidoluysian atrophy (DRPLA)	Autosomal Dominant	CAG
ATXN1	Spinocerebellar ataxia 1 (SCA1)	Autosomal Dominant	CAG
ATXN2	Spinocerebellar ataxia 2 (SCA2)	Semi-dominant	CAG
ATXN3	Spinocerebellar ataxia 3 (SCA3)	Autosomal Dominant	CAG
ATXN7	Spinocerebellar ataxia 7 (SCA7)	Autosomal Dominant	CAG
CACNA1A	Spinocerebellar ataxia 6 (SCA6)	Autosomal Dominant	CAG
DMPK	Myotonic dystrophy 1 (DM1)	Autosomal Dominant	CTG
DMPK	Myotonic dystrophy 1, mild	Autosomal Dominant	CTG
FMR1	Fragile X tremor/ataxia syndrome (FXTAS) or Premature Ovarian Failure (POF)	X-linked	CGG
FMR1	Fragile X Syndrome (FXS)	X-linked	CGG
HTT	Huntington's disease (HD)	Autosomal Dominant	CAG
PPP2R2B	Spinocerebellar ataxia 12 (SCA12)	Autosomal Dominant	CAG
TBP	Spinocerebellar ataxia 17 (SCA17)	Autosomal Dominant	CAG
C9orf72	Amyotrophic lateral sclerosis and/or frontotemporal dementia (FTDALS1)	Autosomal Dominant	GGGGCC
AR	Spinal and bulbar muscular atrophy (SBMA)	X-linked	CAG
FXN	Friedreich ataxia (FRDA)	Autosomal Recessive	GAA
CNBP	Myotonic dystrophy 2 (DM2)	Autosomal Dominant	CCTG
JPH3	Huntington disease-like 2 (HDL2)	Autosomal Dominant	CTG
NOP56	Spinocerebellar ataxia 36 (SCA36)	Autosomal Dominant	GGCCTG