View Oncomine™ Myeloid Research Assay analysis results

The dedicated Myeloid_FLT3_LongITD algorithm in Ion Reporter™ Software Oncomine™ Myeloid Research Assay analysis workflows identify large internal tandem duplications (ITD) in exons 14 and 15 of the FLT3 gene.

The analysis workflow is for use with Oncomine™ Myeloid Research Assay DNA sequencing results.

In-frame insertions in exons 14 and 15 are detected by both the FLT3 Long ITD algorithm, and the variant calling algorithms in Ion Reporter™ Software. Therefore FLT3-ITD variants can be called by one or both types of variant calling. We recommend obtaining the results from the Myeloid_FLT3_LongITD algorithm for ITDs of 8 bases or larger. For smaller variants review the Ion Reporter™ Software variant calling results. The Ion Reporter™ Software variant calling module can sometimes call ITDs larger than 8 base pairs, but its sensitivity to variants in that size range is lower than the Myeloid_FLT3_LongITD algorithm.

See the following table for guidelines in obtaining FLT3 ITD calls from the Oncomine™ Myeloid Research Assay analysis workflows.

FLT3- ITD variant Length

Called by Myeloid_FLT3_LongITD algorithm

Called by variant calling module in Ion Reporter™ Software

Annotated by Oncomine™ Reporter

≥8 bp

Yes

Yes (with lower sensitivity than the FLT3 algorithm)

Yes

<8 bp

No

Yes

Yes

Algorithm description: For standard INDEL detection, long inserts at the ends of reads can cause a partial alignment, resulting in soft-clipping of the alignment. Since this can soft-clip the FLT3-ITD sequence, and eliminate downstream anchoring sequence, the standard INDEL parameters might not detect all FLT3-ITD calls. The Myeloid_FLT3_LongITD algorithm analyzes 3' regions of trimmed reads for presence of anchor sequences, and determines the likely position and size of the duplication by looking for copies of sequence in the mapped and trimmed regions.

To view the analysis results:

  1. In the Ion Reporter™ Software Home tab, click View analyses or click the Analyses tab. Search, filter, or scroll to find the analysis of interest in the list of Analyses, then click the analysis link.

    The Analysis Results table opens to the list of Oncomine variants.

    • Variants that are called by the Myeloid_FLT3_LongITD algorithm appear in the default Oncomine view, and are identified as FLT3ITD Oncomine Variant Class and Type in the Analysis Results table and as SVTYPE in the output VCF file.

    • Both the variant calling module in Ion Reporter™ Software and the Myeloid_FLT3_LongITD algorithm can detect the same variant, which appear adjacent in the Ion Reporter™ Software Analysis Results as SNV or Indel and FLT3ITD variant types, respectively.

    • Mut/WT is the ratio of mutant FLT3-ITD variants to the number of the wild type FLT3 read count.

  2. (Optional) In the Classification column, classify variants by selecting a classification from the dropdown list.
  3. Click Pharmacogenomics.
  4. In the ClinVar column, click the ClinVar link to open the NCBI ClinVar variant website where information about the ClinVar variant annotation is maintained.
  5. In the variant-specific ClinVar website, click the Variation Report link to view more information about the variant.