18 12, 2017

Why are @illumina flowcell names so similar (but only occasionally rude)

By | December 18th, 2017|Categories: Next-generation sequencing, Other stuff|2 Comments

Anyone who’s run Illumina instruments over the years is likely to have noticed how flowcells can have remarkably similar (and occasionally amusing) names. This can create a real headache when looking for a specific run as a single mismatch can cause you to spend some time […]

24 11, 2017

SPLiT-Seq: single-cell RNA-Seq without the hardware

By | November 24th, 2017|Categories: Methods and applications, Next-generation sequencing, Single-cell sequencing|Tags: , , |0 Comments

I’ve been meaning to write up a post on a BioRxiv report from earlier this year: “Scaling single cell transcriptomics through split pool barcoding”1. The Seelig Lab at the University of Washington have developed a single-cell RNA sequencing method to enable labelling RNA molecules with cell-of-origin information using […]

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; […]

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 […]

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