A novel approach for selective enrichment of custom gene targets for oncology research

Bjoern Textor 1, Andrew Barry2, Daniel Kraushaar3, Sarah Bowman3, Lynne Apone2, Kruti Patel3, Noa Henig3, Amy Emerman3, Theodore Davis2, Salvaltore Russello2, Cynthia Hendrickson3
1 New England Biolabs GmbH, Germany
2 New England Biolabs Inc., USA
3 Directed Genomics Inc., USA

Target enrichment of selected exonic regions for deep sequence analysis is a widely used practice for the discovery of novel vari- ants, identification and phenotypic association of known variants for a wide range of practical applications, including somatic variant detection in human cancer.
Deep sequencing of tumor material is required to effectively detect mutations that may be present at low frequencies, or in sam- ples that contain a mixture of malignant and stromal cells. Due to these challenges, highly focused gene panels are used to narrow the regions being studied, reducing overall sequencing costs while providing the necessary coverage for variant detection. Challenges pertaining to selecting the appropriate genes for inclusion are fur- ther confounded by the high costs and time required to develop custom gene panels.
The NEBNext DirectTM technology utilizes a novel approach to selectively enrich nucleic acid targets ranging from a single gene to several hundred genes, without sacrificing specificity. Further- more, intrinsic properties of the approach improve sensitivity and have proven amenable to challenging sample types including FFPE tissue and circulating tumor DNA (ctDNA). The result is a 1-day protocol that enables the preparation of sequence-ready libraries with high specificity, uniformity, and sensitivity for the discovery and identification of nucleic acid variants.
Here, we will discuss the NEBNext Direct approach to target enrichment, specifically with regard to identification of somatic variants in clinically relevant samples, as well as content strategies to efficiently customize content for genes involved in cancer research.

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