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|0 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; […]

16 10, 2017

WGS of HPV reveals the finer details of HPV genetic variation

By | October 16th, 2017|Categories: Methods and applications, Next-generation sequencing, Uncategorized|0 Comments

Because HPV has such a small  and relatively simple genome (8,000 bp encoding 8 genes) it is possible to screen for genetic variation that may underly carcinogenesis. A team from the National Cancer Institute (NCI) has just published the sequencing of over 5,570 human cell and tissue samples – […]

3 10, 2017

DNA in vellum proves authenticity of paintings

By | October 3rd, 2017|Categories: Next-generation sequencing, Other stuff|0 Comments

A short article in todays Times quotes William Cowley parchment makers as saying velum provides the only foolproof way for detecting art forgery. Very simply an artist creates their work on vellum and retains a sample for genetic comparison should a suspected forgery come to […]

21 07, 2017

DAP-Seq for higher-throughput transcription factor analysis

By | July 21st, 2017|Categories: Methods and applications, Next-generation sequencing|0 Comments

The Ecker lab at the Salk Institute published a method for very high-throuphut transcription factor analysis in Nature Protocols yesterday: Mapping genome-wide transcription-factor binding sites using DAP-seq. The method is elegantly simple in its concept; PCR-free libraries from native gDNA are hybridised with affinity-tagged in vitro-expressed transcription factors, […]

12 07, 2017

ctDNA analysis from 250pg

By | July 12th, 2017|Categories: Methods and applications, Next-generation sequencing|2 Comments

A recent paper in Nature Scientific Reports from Maurice Jansen’s group at the Erasmus Medical Centre in Rotterdam presents ctDNA analysis by targeted NGS from just 250pg of input cfDNA . This is a very small amount of material, and although the authors do discuss […]

11 05, 2017

Update on @illumina index-swapping: better libraries

By | May 11th, 2017|Categories: Methods and applications, Next-generation sequencing|Tags: |3 Comments

Index-swapping appears to be driven by excess adapter/primer (Illumina whitepaper). The take-home messages are 1) to use UDIs (unique dual-indexes), and 2) clean-up your libraries to remove left-over adapter/primer. Later in this post I’m going to work through one solution for getting rid of any remaining adapter/primer in an NGS library; but […]

5 05, 2017

Inflection points for @nanopore sequencing

By | May 5th, 2017|Categories: Methods and applications, Nanopore sequencing, Next-generation sequencing|6 Comments

When will nanopore sequencing push short-reads (i.e. Illumina) off their pedestal? According to Clive PromethION is the Illumina killer…but this same conversation was going on many times at London Calling. I wanted to highlight two areas that might be about to flip to ONTs advantage […]

24 04, 2017

Update on @illumina index-swapping: better barcode design

By | April 24th, 2017|Categories: "Experimental design controls etc", Core facilities, Methods and applications, Next-generation sequencing|Tags: , , |2 Comments

Last week I followed up on the index-swapping issue after Illumina released their white paper and also covered what Ethan Linck at The Molecular Ecologist had posted about the Sinha et al BioRxiv paper. In that post I said I’d write a follow-up post about index design over the weekend – here it is! […]

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