Horizon Diagnostics Blog

Recent developments in targeting NTRK fusions for cancer therapeutics

Apr 27, 2018 3:24:21 PM No Comments

The NTRK Gene Family

Since the mid-80s, evidence has shown that gene fusions are implicated in cancer. With advances in Next Generation Sequencing (NGS) technology, the impact of gene fusions on driving cancers and how they act as potential therapeutic targets is quickly being revealed.

Read More Oncology Panels, NGS, Reference Standards, RNA, RNA fusions

Why You Should Use Cell Line-Derived Reference Material for NGS Oncology Assays

Apr 12, 2018 2:12:47 PM 1 Comment

 

We all know NGS analysis can be difficult to navigate. Not only is the human genome complex, but technical errors can occur throughout the entire workflow – from sample preparation, through sequencing and during analysis.

Thankfully, these technical errors can be mitigated by using high-quality reference material. Using the best standards for your assay will help both calibrate your NGS measurements and evaluate your diagnostic performance.

With advances in affordable technologies, there is now a multitude of reference types to choose from including patient material, cell line-derived standards and synthetic spike-ins. In this blog, we shine the spotlight on cell line-derived standards and the distinct advantages these have when used for NGS oncology assays.

Read More Oncology Panels, NGS, Reference Standards

Our Top 5 Quality Control (QC) Metrics Every NGS User Should Know

Feb 20, 2018 3:03:09 PM No Comments Comment

We all know how vital quality control is for our samples. A lot of research has gone in to developing useful QC metrics for genomics experiments – primarily due to their high cost. Skipping this step will waste both time and money.

There are 3 main areas where QC can be applied to NGS:

  • On the starting nucleic acids
  • After Library preparation
  • Post-Sequencing
Ultimately the best QC of your NGS experiments is likely to come from the sequence data and, because of this, many labs will run a QC lane first.
Read More NGS

10 Top Tips for Validating your NGS Assay

Feb 6, 2018 11:32:46 AM No Comments Comment

With new advances in technology, we’re now moving more towards large panel Next-Generation Sequencing (NGS) assays and whole exome (WES) and genome sequencing. NGS is gaining popularity thanks to the high-throughput capability and lower cost per sample.

However, validating these complex assays can be tricky, so we’ve compiled some top tips from industry guidelines* to help you...

Read More Oncology Panels, NGS, Reference Standards

The growing impact of liquid biopsies on precision medicine

Oct 11, 2017 10:30:20 AM No Comments Comment

 Liquid biopsies are becoming increasingly popular in cancer research. We take a look at their potential impact in the clinic and how current technologies can help us keep pushing the boundaries of precision medicine. 

Read More NGS, cfDNA, Reference Standards

Detecting RNA Fusions in cancer - the benefits, the challenges and the solution

Aug 25, 2017 4:28:37 PM No Comments Comment

 

RNA-Sequencing (RNA-seq) of oncogenic fusions is becoming increasingly popular in cancer research and diagnosis. Here, we talk about the benefits of using RNA in fusion detection workflows, the challenge of workflow variability and how to be confident of your assay results.
Read More Reference Standards, RNA, RNA fusions

SHERLOCK: The case of the disruptive diagnostic

May 10, 2017 2:07:05 PM No Comments Comment

“SHERLOCK is exciting because it represents a sensitive approach to detect mutations, much like PCR, but it does not require a thermocycler and could work as a bedside test.” - Dr Tilmann Buerckstuemmer, Global Head of Innovation at Horizon Discovery

Read More CRISPR, cfDNA

Top 10 RNA-Seq Publications of All Time

Jan 9, 2017 2:07:51 PM No Comments Comment
"RNA-Seq is the most likely NGS technique to be used by researchers in 2017 due to its versatility"

RNA-seq has become a ubiquitous tool in both biological and medical research. Much of the RNA-seq analysis done is still for differential gene expression from poly-adenylated mRNAs; but the success of RNA-seq can also be seen in the rapid increase in knowledge about biological systems and the large number of distinct variants of the method.  The combination of these factors allow us to go much further than the 'simple' 3’ gene expression microarrays and now opens up the possiblities of: splicing analysis, differential allele expression, variant detection, alternative start/stop, gene fusion detection, RNA editing and eQTL mapping to name but a few...

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The Evolution of Sequencing and Quality Control

Oct 20, 2016 5:00:54 PM No Comments Comment

Do you remember when…?

Do you remember when Frederick Sanger and his colleagues invented dideoxynucleotide chain termination sequencing back in 1977? Technology has come on a long way, and the recent advancements now means that we're doing more sequencing now than ever before.

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Why you should be pushing your assay's limit of detection

Sep 21, 2016 10:18:54 AM No Comments Comment

 

Next Generation Sequencing

Next Generation Sequencing (NGS), has become a universal tool in diverse industries; most recently moving into the clinic for patient diagnosis. However, if labs wish to analyze patient-derived materials they must first face a hurdles labs to optimize and validate their workflow including determining the exact test limitations.

It is due to the unequivical interest and increasing popularity of NGS based tumor testing that specific guidelines for detecting tumor variants have been established, including by the State of New York Health Department1 advizing on how to determine an assay’s limit of detection to name but one parameter. Based on the recommendations, they state that samples should have enough sequence data for a minimum average coverage of 500x so that minor allele frequencies of 5% can be reliably detected. However, with newer technologies bestoying increasing importance on low allelic frequencies and coverage bias issues (more below about this), should we be aspiring to push this limit of detection even further?

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