8 11, 2017

Error-corrected ctDNA sequencing for mutation and CNV using UMIs

By | November 8th, 2017|Categories: ctDNA, Exomes and amplicons, Methods and applications, Next-generation sequencing|2 Comments

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 […]

19 10, 2017

@Illumina Nextera Flex

By | October 19th, 2017|Categories: Exomes and amplicons, Library Prep, Methods and applications, Next-generation sequencing|1 Comment

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; […]

2 10, 2014

More on exomes

By | October 2nd, 2014|Categories: Exomes and amplicons|0 Comments

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 […]

15 09, 2014

Are PCR-free exomes the answer

By | September 15th, 2014|Categories: Exomes and amplicons|3 Comments

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 […]

14 07, 2014

Sequencing exomes: what sort of read to use?

By | July 14th, 2014|Categories: Exomes and amplicons|0 Comments

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 […]

13 11, 2013

Dr Evil’s exome seqeuncing services

By | November 13th, 2013|Categories: Exomes and amplicons|1 Comment

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 […]

29 08, 2013

Targeted RNA-seq methods are here

By | August 29th, 2013|Categories: Exomes and amplicons, Methods and applications, Next-generation sequencing|2 Comments

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, […]

7 04, 2013

ctExome-seq: Circulating tumour exomes as a non-invasive method to track tumour evolution during treatment

By | April 7th, 2013|Categories: Exomes and amplicons, Methods and applications, Next-generation sequencing|3 Comments

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 […]

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