A recent BioRxiv report from the Gerlinger group at ICR describes a targeted ctDNA sequencing method that uses error correcting UMIs to achieve 100% sensitivity for mutant allele frequencies of >0.15%, and 87% at >0.075%, and reduce false-positive mutation calls by 98.6%, without adversely affecting the […]
My lab has been a long-time user of Illumina’s transposase exomes for the very simple reason that the 50ng input has been the lowest on the market for number of years*. This made it attractive for cancer samples where we are really limited on DNA availability; […]
This was not a planned post but it follows on nicely from today’s other one about exomes. This time I’m writing about Fluidigm’s new single-cell exome-seq protocol. Yup that’s right, whole exomes from 96 single cells! The C1 is an amazing piece of kit (wish […]
I’ve been finding out more about exomes: specifically QC analysis using HS Metrics in Picard. There’s loads of useful metrics and I’m hoping to get to a point that I can explain these to users here and also look at the results to try and […]
I’m continuing my exome posts with a quick observation. There have been several talks recently that I’ve seen where people present genome and exome data and highlight the drop-out of genomic regions primarily due to PCR amplification and hybridisation artefacts. They make a compelling case […]
What’s the right way to sequence an exome? We’ve been looking at Illumina’s v4 chemistry for HiSeq 2500 and wondering whether we should jump to PE125bp or not, or should we try to reconfigure our exome capture for shorter or longer fragments.Exome-seq: Exomes have been […]
Sequencing service providers are popping up everywhere and offering some great deals on genomes, exomes and RNA-seq. How can this sequencing be so cheap I hear some of my users saying? The costs are usually dependent on a certain volume of work and are likely […]
Illumina and Life Technologies are both launching targeted RNA-seq applications which are likely to become standard tools for many labs; if the price is right. The ability to target a portion of the genome has revolutionised next-generation sequencing experiments. The analysis of exomes has exploded, […]
The New York Times recently published an article on Foundation Medicine and their approach to personalised cancer genomics (targeted sequencing of 236 cancer genes). The test costs $5800 and is covered by some insurers in the USA. And the reports from the test have caused […]
Monitoring of cancer patients is an important part of their treatment and this is traditionally done with tests like Computed Tomography imaging (CT) or biomarker analysis. NGS of cancer amplicons, exomes and/or genomes is being discussed as a realistic addition, and possibly an alternative, to […]
