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Haematology OncoKit HS2

Description

Analysis of the main molecular markers related to ALL, AML, CML, MDS, MPN and other hematological neoplasms by NGS sequencing

Format

32 rx

Technology

paired-end NGS

Reference

IMG-427

Compatible equipment

NextSeq 500/550Dx and NextSeq 1000/2000 System

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  • NGS panel for the study of the following oncohematological diseases: acute myeloid leukemia (AML), chronic myeloid leukemia (CML), myeloproliferative neoplasms (MPN), acute lymphoid leukemia (ALL), and myelodysplastic syndromes (MDS).
  • Complete exon sequencing of 89 genes and 26 fusion genes.
  • Detects SNVs, indels, structural variants (SVs) including gene fusions, CNVs throughout the whole genome, and pharmacogenetic variants via a single DNA analysis.
  • Bioinformatics analysis using the Datagenomics software and semiautomated generation of reports, including functional and clinical classification of the identified variants.
  • STIDs can be included: integrated sample identification and tracking system.
  • Based on high sensitivity RNA-probe technology with dual UMI (unique molecular identifiers) Barcoding.
  • Mean coverage: > 690X in a NextSeq 500/550Dx and 1170X in a NextSeq 1000/2000.
  • Mean coverage after UMI analysis (removal of duplicates): > 600X in a NextSeq 500/550Dx and > 865X in a NextSeq 1000/2000.
  • Coverage at 200X: > 93% in a NextSeq 500/550Dx and 97% in a NextSeq 1000/2000.
  • Uniformity at 20X: > 97%.
  • Specificity and sensitivity for all type of variants: > 99%.

Haematology OncoKit HS2 utilizes a fully automated library preparation technology, involving enzymatic fragmentation and enrichment of regions of interest through capture probes hybridization. This kit employs Agilent’s HS2 technology, which integrates dual Unique Molecular Identifiers (UMIs). The use of dual UMIs enhances the sensitivity and accuracy of variant calling while reducing potential index-hopping during sequencing on Illumina platforms.

  • Lab workflow: fully automated panel for Magnis NGS Prep System Dx equipment.
  • Sample type: DNA from peripheral blood and bone marrow.
  • Number of samples per run:
    • NextSeq 500/550Dx System: 16 samples in a High-Output v2.5 kit (150 cycles) or 6 samples in a Mid-Output v2.5 kit (150 cycles).
    • NextSeq 1000/2000 System: 16 samples in a P2 flow cell (200 cycles).
  • Sequencing: paired-end NGS (2-x-75 cycles in a NextSeq 500/550Dx System and 2-x-100 cycles in a NextSeq 1000/2000 System).
  • Input of DNA required: 100 ng.
  • Detection limits:
    • SNVs and indels: 2%.
    • SVs: 5% for high-confidence detection and 2% for detection with medium reliability.
    • CNVs: 4 copies for gains and a complete deletion for losses at 25% tumor representation.
  • Targeted genes: ANKRD26, ARID5B, ASXL1, ASXL2, ATRX, BCOR, BCORL1, BLNK, BRAF, CALR, CBL, CDKN2A, CDKN2B, CEBPA, CHIC2, CREBBP, CRLF2, CSF3R, CSNK1A1, CUX1, DDX3X, DDX41, DNMT3A, EP300, ETNK1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GATA3, GNAS (exon 8), GNB1, HAVCR2, IDH1, IDH2, IKZF1, IL7R, JAK1, JAK2, JAK3, KIT, KMT2A, KMT2D, KRAS, MAP2K1 (exons 1 to 11), MPL, MSH2 (exons 1 to 16), NF1, NFE2, NOTCH1, NPM1, NR3C1, NRAS, NSD2 (exons 18 and 19), NT5C2 (exons 2 and 13), PAX5, PHF6, PIGA, PPM1D, PRPF8, PTEN, PTK2B, PTPN11, RAD21, RB1, RUNX1, SETBP1, SF3B1, SH2B3, SMAD9, SAMD9L, SMC1A, SMC3, SRP72, SRSF2, STAG1, STAG2, STAT5B, TERT, TET2, TPMT, TP53, TYK2, UBA1, U2AF1, WT1 and ZRSR2.
  • Non-coding regions: Non-coding gene TERC, intron 4 of GATA2, complete UTRs of TP53 and ANKRD26, 3 hotspots in the 5’UTR and promoter region of TERT (chr5:1295228, chr5:1295250 and chr5:1295161).
  • Fusion genes: ABL1 (5’UTR region, introns 1, 2 and 3), ABL2 (introns 1, 2, 3, 4, 5 and 6), BCR (introns 1, 3, 6, 8, 12, 13, 14, 15, 19 and 20), CBFA2T3 (introns 9, 10 and 11 and 3’UTR region), CBFB (introns and exons 4 and 5), CREBBP (introns 1, 2, 3 and 4), CSF1R (introns 11 and 12), EPOR (intron 7 and CDS exon 8), ETV6 (introns 2, 3, 4, 5, 6 and 7), FGFR1 (introns 7, 8, 9 and 10), FUS (introns 5, 6, 7, 8, 9), IL3 (5’UTR), JAK2 (introns 8, 9, 10, 11, 12, 14, 15, 16, 17, 18 and 19), KMT2A (introns 1, 2, 6, 7, 8, 9, 10, 11, 15, 20, 22, 24, 29 and 30), MEF2D (introns 5, 6, 7, 8 and exon 6), MNX1 (intron 1), NPM1 (introns 3, 4 and 5), NUP214 (introns 16 and 17), NUP98 (introns 8, 10, 11, 12, 13, 14, 15 and 16 and exon 10), PDGFRA (introns 11 and 12 and exon 12), PDGFRB (introns 8, 9, 10, 11 and 12), RARA (intron 2), RBM15 (intron 1), RUNX1 (introns 5, 6 and 7), TAL1 (intron 3) and TCF3 (introns 15, 16 and 17).
  • CNVs: detection of copy number variations (CNVs) across the entire genome.
Haematology OncoKit HS2:
Haematology OncoKit HS2: Instructions for use
Analysis certificate

Haematology OncoKit HS2

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