NGS white papers and application notes
Browse our collection of white papers and application notes for next generation sequencing (NGS).
Greater confidence in calling low-frequency variants – from as little as 10ng of severely formalin-compromised DNA
In this study, carried out in collaboration with Horizon Discovery, formalin-compromised DNA (fcDNA) samples of differing severity were repaired with the SureSeq™ FFPE repair mix and sequenced using a SureSeq custom hybridisation-based panel.
The aim of the study was to investigate the effect of the repair mix and also the performance of the hybridisation-based enrichment method on DNA with varying levels of damage by measuring critical parameters at different points in the sequencing protocol.
Understanding myeloid disorders with next-generation sequencing
In the past decade, the advent of next-generation sequencing (NGS) has revolutionised the world of genetic research and is now beginning to impact on clinical testing. The introduction of targeted sequencing – a technique that specifically focuses on sequencing regions associated with causal mutations – has improved speed and accuracy of genetic analysis.
In this white paper, the team from the Haemato-Oncology section of the West Midlands Regional Genetics Laboratory (WMRGL) of Birmingham Women’s NHS Foundation Trust in the UK discuss the introduction of a SureSeq NGS cancer panel, highlighting the ease of adoption and two occasions where mutations missed by digital droplet PCR (ddPCR) were picked up by the NGS panel.
Selecting the best NGS enrichment assay for your needs
With next generation sequencing (NGS) now in routine use for a broad range of research and clinical applications, this application note details the value of making the correct choice for the initial sequence enrichment step, which, if poorly designed, can be a source of bias and error in the downstream sequencing assay.
The two main enrichment strategies, amplicon (PCR) and hybridisation are compared and contrasted and the paper illustrates how hybridisation-based assays offer greater opportunity for optimisation through probe design and placement, and can offer better uniformity of coverage, fewer false positives, and superior variant detection due to fewer PCR cycles. Hybridisation-based assays also offer greater scope in terms of the number of genes and regions that can be targeted.
Evaluation of enzymatic DNA digestion as an alternative to mechanical DNA fragmentation (sonication) for targeted NGS using the SureSeq Myeloid Panel
DNA fragmentation is a crucial first step in the preparation of libraries for next generation sequencing (NGS).
Mechanical shearing (sonication) is currently the gold-standard for fragmentation but it requires a significant upfront capital investment.
Oxford Gene Technology (OGT) has evaluated an alternative method of fragmentation using the NEBNext® dsDNA Fragmentase®.
The role of NGS in stratified cancer medicine
Cancer is a leading cause of morbidity and mortality worldwide with approximately 14 million new cases and 8.2 million cancer-related deaths per year.1 One challenge to overcome in the treatment of cancer is its high level of inherent genetic complexity and heterogeneity. Characterising the genetic profile of each individual tumour can therefore help guide the delivery of effective treatment strategies, and this approach of stratified or personalised medicine is driven by the latest advances in genetic technologies.
Clinical research laboratories are increasingly adopting Next Generation Sequencing (NGS) assays to assist them in the analysis of cancer samples. Undoubtedly, NGS has an extremely important role to play in personalised medicine; however, with advances in technology come new challenges. In this white paper, two Clinical Scientists, Dr Matthew Smith and Dr George Burghel, share their views on the use of NGS in cancer genomics and its integration into the laboratory.
1. Cancer, 2015. Available from: http://www.who.int/en/news-room/fact-sheets/detail/cancer. [11 February 2015]
SureSeq™: For research use only; not for use in diagnostic procedures.