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Table 2 Full-mutation samples detected in the EGA and simulated genomes using the default implementation of STR analysis tools

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

Gene AR (n = 1) ATN1 (n = 2) ATXN1 (n = 3) ATXN3 (n = 1) C9orf72 (n = 3) DMPK (n = 17) FMR1 (n = 18) FMR2 (n = 3) FXN (n = 25) HTT (n = 13) FPs Total FM detected Sensitivity
FM threshold (rpts) 37 47 38 59 60 50 200 200 65 39
Allelic classification FM FM FM FM FM FM FM FM NL/FM or FM/FM NL/FM or FM/FM
Isaac
 EH_v2 1 2 2 1 3 17 1 0 25 13 6 65 0.75581395
 EH_v3 1 2 3 0 3 17 0 0 25 13 5 64 0.74418605
 GangSTR 0 2 2 0 0 16 0 0 16 11 8 47 0.54651163
 TRED 1 2 1 0 3 17 0 0 25 13 3 62 0.72093023
 STRetch 1 2 3 1 3 17 2 3 20 13 26 65 0.75581395
 exSTRa 1 2 3 0 3 17 1 3 5 13 33 48 0.55813953
BWA
 EH_v2 1 2 2 1 3 17 0 0 25 13 6 64 0.74418605
 EH_v3 1 2 3 0 3 17 0 0 25 13 5 64 0.74418605
 GangSTR 1 2 2 1 1 16 0 0 0 10 8 33 0.38372093
 TRED 1 2 1 0 3 17 0 0 25 13 10 62 0.72093023
 STRetch 1 2 3 1 3 17 2 3 20 13 26 65 0.75581395
 exSTRa 1 2 3 1 3 16 9 3 25 13 35 76 0.88372093
  1. The analyzed dataset had 86 samples with at least one known full-mutation allele. The number of true-positives detected by the tools, sensitivity, and the number of false positives identified in our default analysis of the Isaac- (top panel) and BWA-aligned (bottom panel) genomes are shown. NL normal, FM full-mutation, FPs false-positives, rpts repeats, EH_v2 ExpansionHunter version 2, EH_v3 ExpansionHunter version 3, TRED TREDPARSE