This feature simplifies the identification and analysis of FLT3 ITD variants in somatic tumor samples. With automatic detection, clear visualization in the variant table, and comprehensive annotations from reliable databases, you can confidently interpret ITD occurrences and their relevance to your research.
VarSome Clinical now supports the detection of ITDs in the FLT3 gene from tumor-only somatic samples, starting from FASTQ files. For these cases, we will be utilizing the ITDetect tool and the targeted region will comprise the exons 14 and 15 of the gene from positions ranging chr13:26,608,020 - 28,608,360.
This functionality is compatible with both reference genomes (hg19 and hg38) and works seamlessly in both targeted and untargeted modes, supporting all assays, including generic ones.
Viewing ITD variants:
- ITD variants are shown in the main variant table along with SNP and INDEL variants.
- They are labeled as "ITD" in the Variant Type column and in the General Information card.
Additionally, dynamic filters can be applied to these types of variants in order to have them portrayed alone, independently if they come from ITDetect or our Sentieon caller. It is present as a check box during the Variant Type filtering scheme:
Obtaining only said variants
HGVS notation:
- For duplication variants, the system uses the format c.START_ENDdup.
- For insertions longer than 10 characters, the notation will display a shortened version of the sequence with the first and last two nucleotides/amino acids, followed by the length in parentheses (e.g., c.AT…CT (33) or p.Gly…Glu (11)).
- Hover over the notation (c. or p.) to see "Click to view full sequence" and click to view the complete sequence.
Annotations:
- FLT3 ITDs are annotated with information from trusted databases, including JaxCKB, CIViC, COSMIC, DoCM, PMKB, and OncoKB. These annotations are displayed in clickable cards for easy access to additional information.
Variant details:
- Transcripts are shown using both HGVS Coding (e.g., c.) and HGVS Protein (e.g., p.) formats (see: HGVS nomenclature).
- If a variant is not found in the protein viewer, you will be notified with the message "This protein structure does not contain any data related to the variant ..."
VarSome Clinical now detects FLT3 ITD variants in somatic tumor samples from FASTQ files, with clear annotations, HGVS notation, and support for hg19/hg38 genomes and all assays.
