The application of a hybridisation-based NGS enrichment panel for the analysis of somatic variants in tumour samples and reference standards

Friday 23 June 2017
Applications:

Jacqueline Chan , Lyudmila Georgieva , Sabine Eckert , Faidra Partheniou and Graham Speight

Presented at the 42nd Association of Genetic Technologists (AGT) 2017 annual meeting in St Louis, USA, this poster outlines the application of a hybridisation-based next-generation sequencing enrichment panel for the analysis of solid tumour somatic variants, demonstrating 100% concordance in variant detection in both genomic and formalin-compromised DNA and superior uniformity of coverage from hybridisation-based enrichment when compared to an amplicon-based method in key exons of BRCA1 and BRCA2.

Introduction

  • Breast and Ovarian cancers are some of the most common cancers in women. 
  • Next-generation sequencing (NGS) has enabled the simultaneous study of mutations in high penetrance breast cancer predisposition genes. 
  • These include BRCA1BRCA2TP53PTEN, and PIK3CA, as well as more moderate risk genes such as PALB2BRIP1RAD51C and RAD51D.

Using OGT’s extensive background in bait design we have developed a range of fully tested and optimised baits targeting all coding exons of a range of key cancer-related genes (Table 1).

APC BRCA2 CHECK2 GATA3 PIK3CA RB1
ATM BRIP1 EGFR MSH6 PTEN SF3B1
BARD1 CDH1 ERBB2 NBN RAD51C STK11
BRCA1 CDK12 ESR1 PALB2 RAD51D TP53

Table 1: Key breast and ovarian cancer-related genes with empirically tested bait sets available in the SureSeq myPanel™ range.

To evaluate the application of a hybridisation-based approach we:

  • Compared the uniformity of coverage between a PCR amplification-based and the SureSeq™ hybridisation-based enrichment approach for BRCA1 and BRCA2 in solid tumour samples. 
  • Assessed the performance of a custom panel (ALK, KIT, EGFR, KRAS, and TP53) from the SureSeq myPanel NGS Custom Cancer Panel range using the Quantitative Multiplex Reference Standard – gDNA and formalin-compromised DNA, from Horizon.

 

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