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Table 3 FMR1 and FMR2 full-mutations detected by ExpansionHunter, GangSTR, and TREDPARSE with lowered repeat length threshold

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

Aligner Isaac BWA
Locus FMR1 (n = 18) FMR2 (n = 3) FMR1 (n = 18) FMR2 (n = 3)
FM threshold 54 repeats 60 repeats 54 repeats 60 repeats
Allelic classification FM IM NL FP FM NL FP FM IM NL FP FM NL FP
EH_v2 18 . . 20 3 . 0 18 . . 16 3 . 0
EH_v3 18 . . 22 3 . 0 18 . . 22 3 . 0
GangSTR 4 . 14 7 0 3 0 3 . 15 0 0 3 0
TREDPARSE 15 1 2 8 0 3 0 16 . 2 13 0 3 0
  1. The number of full-mutations (FMs) misclassified as normal (NL; < 45 repeats for FMR1 and < 31 repeats for FMR2) or intermediate (IM; 45–54 repeats for FMR1) allele are shown. The true number (n) of known FM alleles in the FMR1 and FMR2 genes is indicated in parenthesis. False-positive (FP) calls made by the tools are also reported