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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

From: STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

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

  1. Novel STR disease loci (not in the reference genome) are indicated in bold/underline
  2. AD Autosomal dominant, AR Autosomal recessive, XD X-linked dominant, XR X-linked recessive
  3. aNo spanning reads, spanning pairs only