Optimised, 1-day hybridisation-based NGS protocol yields 1% variant detection in MPN samples, as quickly and cost-effectively as multiplex PCR

Tuesday 13 December 2016
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Graham Speight, Ephrem Chin, Lyudmila Georgieva, Nick Cross and David Cook

Presented at the Association For Molecular Pathology (AMP) 2016 annual meeting in Charlotte, NC, USA in November 2016, this poster outlines how the SureSeq™ Core MPN Panel can accurately detect alleles down to 1% variant allele fraction (VAF) in JAK2 (V617F) at a read depth of >1000x, facilitating reliable detection, not only single nucleotide variants, but also 5 bp insertions in JAK2 (exon 12) and deletions of up to 52 bp in CALR (exon 9). 

Introduction

  • Myeloproliferative neoplasms (MPNs) are a group of diseases that affect blood cell production in the bone marrow resulting in the overproduction of one or more cell types. The key MPN driver mutations involve JAK2 (V617F [occurrence of 50-98% depending on the MPN subtype]), JAK2 exon 12, MPL W515K/L and CALR exon 9 insertion and deletions. 
  • Designed for research into the diagnosis, aetiology and prognosis of MPNs, the SureSeq™ Core MPN Panel has been developed by Oxford Gene Technology (OGT) in collaboration with recognised cancer experts to deliver accurate detection (down to a 1% variant allele fraction [VAF]) of somatic variants of these key MPN driver mutations. 
  • The aim of this study is to evaluate the SureSeq Core MPN Panel in conjunction with a new streamlined 1-day hybridisation-based Next Generation Sequencing (NGS) library preparation kit (LPK).

 

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