14 02, 2018

New products from @10XGenomics #AGBT18 workshop

By | February 14th, 2018|Categories: 10X Genomics, Conferences, Methods and applications, Next-generation sequencing|0 Comments

The 10XGenomics workshop just closed at AGBT and they announced some truly revolutionary new applications: single-cell feature barcoding, single-cell ATAC-Seq and single-cell CNV (feat CBGB). I’ll go through each of these in more detail below but I wanted to start by highlighting the success of single-cell analysis […]

7 02, 2018

Transplant patients may help to unlock the secrets of ctDNA

By | February 7th, 2018|Categories: ctDNA, Next-generation sequencing|0 Comments

Can transplant genomics help better understand ctDNA? Circulating cell free (cfDNA) of tumour (ctDNA) is released by apoptotic and necrotic cells into blood and other bodily fluids. It has transformed NIPT and is transforming Cancer medicine. However the biology behind it’s release is still not […]

16 01, 2018

Illumina index sequencing – where is my sample?

By | January 16th, 2018|Categories: Core facilities, Next-generation sequencing|0 Comments

Indexed sequencing is vital to the delivering cost-effective, and statistically robust, experiments. Nearly all non-WGS projects are indexed to some degree so understanding how the indexing works is useful; fortunately Illumina produced this handy guide for users: Indexed sequencing overview. After indexed sequencing our reads […]

9 01, 2018

JP Morgan – Illumina and iSeq

By | January 9th, 2018|Categories: Next-generation sequencing|0 Comments

iSeq! Illumina’s newest sequencer is the iSeq 100 and costs just $19.5k. Expect 4 million reads, up to 1.2 Gb, in 9-17 hours (approximately 2-3 minute cycle times estimated from the iSeq specifications). This is the deliverable from Project Firefly first mentioned by Jay Flatley at […]

8 01, 2018

JP Morgan 2018

By | January 8th, 2018|Categories: Next-generation sequencing|0 Comments

JP Morgan kicks off today and there are sure to be lots of exciting announcements by many of the life science companies we’re all using. I’m particularly interested to hear about new developments in the diagnostics space as my new job is going to be […]

4 01, 2018

Enseqlopedia maps updated

By | January 4th, 2018|Categories: Next-generation sequencing|0 Comments

There have been several map updates which I’d not published (apologies to you all). Unfortunately the map was broken yesterday morning and I’m figuring out what’s wrong. Hopefully we’re back to normal service now, while the issues get dealt with in the back end! New […]

3 01, 2018

NGS methods naming discussed in Nature Methods

By | January 3rd, 2018|Categories: Methods and applications, Next-generation sequencing|0 Comments

I’m really pleased to have a commentary article published in Nature Methods today: A profusion of confusion in NGS methods naming. My colleague Jaques Retief and I have been talking about NGS methods for many years and decided to write this article to highlight some of […]

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 […]

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