DRUG DISCOVERY AND DEVELOPMENT 21


Focus on enhanced assays to detect cancer cells


Demand continues to grow for new and improved assays to detect cancer cells. The latest technologies, as Sean Ottewell reports, focus on rare cancer mutations, colorectal cancer recurrence and breast cancer.


La demande de nouveaux dosages améliorés destinés à détecter les cellules cancéreuses est toujours croissante. Comme l’affirme Sean Ottewell, les dernières technologies sont fortement axées sur les mutations de cancers rares, sur la récurrence du cancer colorectal et sur le cancer du sein.


Der Bedarf an neuen und verbesserten Assays zur Erkennung von Krebszellen wächst ständig. Die neuesten Technologien, wie Sean Ottewell berichtet, konzentrieren sich auf seltene Krebsmutationen, das Wiederauftreten von kolorektalen Karzinomen und Brustkrebs.


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ainDance Technologies, the leading provider of microdroplet-based single


molecule and single cell analysis solutions, has launched the DeepSeq formalin-fixed paraffin-embedded (FFPE) solution, an end-to-end workflow for the ultra-deep targeted sequencing of FFPE and fresh frozen tissue samples.


DeepSeq FFPE enables researchers to discover common and rare cancer mutations that represent as little as one per cent of a heterogeneous tumour.


For the first time, researchers can analyse as many as 500 genomic targets at up to 50 000-fold coverage per loci to discover rare cancers and other disease-specific mutations from heterogeneous samples.


Based on the proven RainStorm microdroplet-based single molecule PCR technology, the DeepSeq Solution delivers high specificity, accurate quantitation and unbiased


Fig. 1. DeepSeq FFPE Solution runs on the automated RDT 1000.


allelic representation. Te company says that the ultra-deep resolution of genomic targets represents a significant enhancement over the 10-30 per cent allelic sensitivity achievable with current next- generation sequencing, target capture/hybridisation, or microarray methods.


It is optimised for both fresh frozen and FFPE tissue, which is the standard archival method for nearly all solid tumours.


Degraded DNA Historically, researchers have been limited in applying next-generation sequencing to FFPE samples due to challenges with low yield, degraded DNA, and sample extraction. With an estimated 400 million FFPE samples stored in tissue banks worldwide, cancer researchers and oncologists can now detect specific novel and causative mutations that drive drug resistance, metastasis and progression of different forms of the disease.


“In order to achieve the promise of targeted therapy cocktails optimised for the individual patient, we need cost-effective tools that address the heterogeneous nature of cancers,” said Kelly A Frazer, founding chief of the division of genome information sciences for the department of paediatrics at the UCSD school of medicine. “Technologies, such as those offered by RainDance, will help us identify rare mutations present in as little as one per cent of a tumour biopsy.”


Te DeepSeq FFPE Solution runs on the RDT 1000, an automated instrument that produces two million single molecule microdroplet-PCR reactions per sample in a single tube in less than one hour (Fig. 1).


Te solution also introduces a number of innovative enhancements to simplify customer workflow and lower sequencing costs, including custom primer libraries, tailed primers to eliminate library generation, and multi-sample indexing.


Genome amplification To further enhance the DeepSeq FFPE Solution, RainDance is collaborating with NuGEN Technologies to develop a complementary fast and simple whole genome amplification (WGA) FFPE sample preparation kit.


NuGEN’s Ovation WGA FFPE product delivers accurate and unbiased genomic representation and generates microgram amounts of DNA from 100 nanograms of starting FFPE DNA samples.


“FFPE samples represent a huge repository of clinical information that has remained virtually untapped by next-generation sequencing due to the lack of available high-


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