Table 1.

Current catalog of targeted mutations for AML.

GeneExpected type of variantGene locationTarget sequence length (bp)Average running timea (s/sample)
Reference target
 IDH1SNP (R132)Exon 4650.008
 DNMT3ASNP (R882)Exon 23650.01
 NPM14-bp insertionExon 10–11 + UTR800.017
 FLT3ITDExon 13–153450.107
 FLT3TKDExon 20680.019
 MYCSNP (T58A/P59R)Exon 2680.018
Variant target
 NUP98–NSD1FusionExon 11 + 7620.07
 NSD1–NUP98FusionExon 6 + 13620.061
 KMT2APTDExon 8 + 2620.067
  • a Average computation times are reported for Leucegene samples and assume that k-mer count tables are cached in RAM before running km. The performance of the caching step is highly dependent on I/O architecture, taking around 25 s on a typical system. The approaches used to prepare each target sequence for detecting the expected mutations are presented in the Materials and Methods section.