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 […]

7 11, 2017

R vs Excel by @vivalosburros

By | November 7th, 2017|Categories: I am not a Bioinformatician, Methods and applications, Other stuff|0 Comments

In this post I wanted to highlight the wonderful “Excel vs R: A Brief Introduction to R”  by Jesse Sadler. This is full of useful and practical advice on using R in place of Excel (or any other spreadsheet) for simple data analysis. I use […]

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 – […]

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 […]

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