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CAT #: S100004

NPM1 MRD Software

Product Use

The NPM1 MRD Software package provides automated bioinformatic analyses of raw FASTQ files generated by the Illumina® MiSeqTM, NextSeqTM, and Complete Genomics DNBSEQ-G99 systems when used with the NPM1 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.

Product Details

  • Description

    The NPM1 MRD Assay for use with the Illumina® MiSeqTM platform was designed to produce sequencing data that can be analyzed using the NPM1 MRD Software package. This includes detailed README files with instructions for installation and use of the software package (using either the command-line or REST-API execution method).

    The MiSeqTM sequencing run of samples prepared with the NPM1 MRD Assay outputs FASTQ files that can be easily processed by the NPM1 MRD Software to provide NPM1 insertion 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 insertion variant types ‘A’, ‘B’, ‘D’ or ‘Other’ in the  nucleophosmin (NPM1) gene.

    This software reports results as:

    • Positive
    • Not Detected
    • Undetermined

    Variant Read Frequency (VRF) reported for Positive results. Confidence for detection of ‘A’, ‘B’, ‘D’, or ‘Other’ with a Variant Allele Frequency (VAF) of 5×10-5  and minimum VAF detectable with >95% confidence reported for Not Detected results. Indicates insufficient read depth for a ‘Not Detected’ call at a VAF of 5×10-5 for Undetermined results.

    System Requirements:

    • Operating System: Linux (Ubuntu/RedHat with Docker installed)
    • Containerization: Docker
    • Sequencers: Illumina MiSeqTM, NextSeqTM 1000, NextSeqTM 550, and Complete Genomics 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 and NextSeqTM 550 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. 64 GB required for NextSeqTM 550; 128 GB or
      more recommended.

Disclaimer

This product is for Research Use Only; not for use in diagnostic procedures.

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