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

Contributors

Jacqueline Chan¹ , Lyudmila Georgieva¹ , Sabine Eckert¹ , Faidra Partheniou¹ and Graham Speight¹

¹OGT, Oxford, UK

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 BRCA1, BRCA2, TP53, PTEN, and PIK3CA, as well as more moderate risk genes such as PALB2, BRIP1, RAD51C 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).

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.