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Invivoscribe - FLT3 ITD MRD Software for Illumina MiSeq Platform

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The FLT3 ITD MRD Software is designed for bioinformatic analysis of RAW FASTQ files generated by Illumina MiSeq and other platforms like DNBSEQ-G99 and NextSeq 1000 sequencers. It is specifically used with the FLT3 ITD MRD Assay to identify internal tandem duplications (ITDs) in the FLT3 gene, providing enhanced diagnostic insights into hematolymphoid malignancies. This software generates variant read frequency and confidence data for ITD detection with a particular focus on variant allele frequencies. The output is customizable to integrate into downstream Laboratory Information Management Systems (LIMS) and compatible reporting systems. Data output is provided as .tsv files, allowing for detailed analysis of individual and aggregate sample data. This dockerized Linux-based software is streamlined for flexibility and adaptation, although it is intended solely for research purposes and not for diagnostic use.

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The FLT3 ITD MRD Software package provides automated bioinformatic analyses of raw FASTQ files generated by the Illumina® MiSeqTM, when used with the FLT3 ITD MRD Assay. The dockerized Linux-based software is built for portability, flexibility and can be easily integrated into down-stream reporting systems and/or LIMS.

The FLT3 ITD MRD Software is now compatible with FASTQ files generated by the DNBSEQ-G99 and NextSeqTM 1000 sequencers.

The FLT3 ITD MRD Assay for use with the Illumina® MiSeqTM platform was designed to produce sequencing data that can be analyzed using the FLT3 ITD MRD Software package. This includes detailed README files with instructions for installation and use of the software (using either the command-line or REST-API execution method).

The MiSeqTM sequencing run of samples prepared with the FLT3 ITD MRD Assay outputs FASTQ files that can be easily processed by the FLT3 ITD MRD Software to provide FLT3 ITD variant calls. Individual sample and aggregate sample data output is generated in the form of .tsv (tab-separated value) files. This software package allows for the identification and tracking of internal tandem duplications (ITD) in the fms-like tyrosine kinase 3 (FLT3) gene and provides the length of the ITD up to 252 base pairs.

This software reports ITD results as:

  • Positive
  • Not Detected
  • Undetermined

Variant Read Frequency (VRF) and confidence for the detection of an ITD with an input Variant Allele Frequency (VAF) of 5×10-5 is reported for Positive and Not Detected results.

System Requirements:

  • Operating System: Linux (Ubuntu/RedHat with Docker installed).
  • Containerization: Docker.
  • Sequencers: Illumina (MiSeqTM, NextSeqTM 1000), CompleteGenomics DNBSEQ-G99.
  • Processor: Minimum of 16 processors for processing MiSeqTM and DNBSEQ-G99 datasets. 64 or more recommended for NextSeqTM 1000.
  • Disk: 12 GB for installation of the software. 50 GB of available empty space for processing a set of MiseqTM FASTQ files, and 100 GB for NextSeqTM 1000 and DNBSEQ-G99.
  • RAM: 16 GB required; 32 GB or more recommended for MiSeqTM. 128 GB required; 256 GB or more recommended for DNBSEQ-G99 datasets and NextSeqTM 1000.