21 04, 2017

Update on @illumina index-swapping

By | April 21st, 2017|Categories: "Experimental design controls etc", Core facilities, Design, Methods and applications, Next-generation sequencing|0 Comments

Illumina released a white paper this week describing their efforts to understand the index-swapping issues with the ExAmp chemistry. This story has been covered many times and got lots of Tweets in the days since the BioRxiv paper from Stanford was uploaded. Megan Molteni at Wired wrote a lengthy […]

7 04, 2017

@qiagene GeneReader data published

By | April 7th, 2017|Categories: I am not a clinician, Next-generation sequencing|Tags: , |0 Comments

The Qiagen GeneReader is an NGS platform developed for the clinic and aims to deliver a sample-to-answer solution. I covered the “launch” of the instrument at the end of 2016 and summarised some of the details but there was no public data to take a […]

28 03, 2017

What does RNA-Seq mean to you

By | March 28th, 2017|Categories: Core facilities, Methods and applications, Next-generation sequencing|1 Comment

This post is a follow on from my ABRF2017 presentation this morning. Slides are available on SlideShare. RNA-Seq is the most widely published NGS method, but what do researchers mean by the term “RNA-Seq”? Virtually none of them mean sequencing of RNA. Most are talking […]

28 03, 2017

HMW DNA extraction for long-reads on @nanopore or @10XGenomics

By | March 28th, 2017|Categories: 10X Genomics, Methods and applications, Next-generation sequencing|8 Comments

Long-reads require long DNA molecules which require high molecular weight (and undamaged) DNA. Extraction with your standard column is unlikely to be optimal. I’m starting to look at the best methods for HMW DNA extraction for long-read applications as my lab is supporting a couple of […]

28 03, 2017

Single-cell analysis improved with consensus clustering

By | March 28th, 2017|Categories: Next-generation sequencing, Single-cell sequencing|0 Comments

Anyone interested in single-cell RNA-Seq analysis is likely to be interested in a paper published today by the Sanger in Nature Methods: Kiselev et al. (2017) SC3: consensus clustering of single-cell RNA-seq data. The new single-cell clustering tool performs better than 5 other methods: tSNE + k-means […]

22 03, 2017

10X Genomics 10x cheaper…and better too!

By | March 22nd, 2017|Categories: "Experimental design controls etc", 10X Genomics, Methods and applications, Next-generation sequencing, Single-cell sequencing, Uncategorized|0 Comments

Confession: this post may not actually make your 10X Genomics experiments ten times cheaper…but implement Demuxlet in your workflow and with the right sort of experiment you might just get there! Single-cell RNA-Seq might just have got a whole lot cheaper, thanks to a method […]

17 03, 2017

The cost of an NGS cancer test in the NHS – £339

By | March 17th, 2017|Categories: I am not a clinician, Next-generation sequencing|0 Comments

In 2013 researchers from Oxford’s Molecular Diagnostics Centre, NIHR BRC, WTCHG and Department of Oncology led by Anna Schuh and Jenny Taylor sequenced 351 lung, melanoma and colorectal tumours from patients using an NGS 46-gene hotspot cancer panel. Results were delivered with a median turnaround of 7 days […]

15 03, 2017

Cas9 CATCH-seq and lego-brick microfludics

By | March 15th, 2017|Categories: Methods and applications, Nanopore sequencing, Next-generation sequencing, Other stuff|Tags: , , |0 Comments

Two publications presenting really cool technologies recently caught my attention: “Lego for molecular biology” and “CATCH-Seq: CRISPR for target enrichment sequencing”. Both are technologies I’d like to play with, and my son can join in the Lego modelling if we build some here in Cambridge! Lego […]

13 03, 2017

smMIP technology and, quality of statistical review reviewed

By | March 13th, 2017|Categories: Methods and applications, Next-generation sequencing|Tags: |0 Comments

A paper published one month ago in Nature Genetics: Stessman et al 2017, by Evan Eichler’s group at HHMI, reported finding 91 genes associated with neuro-developmental disorders. 25 of these were enriched in autism probands and the authors reported a “network associated with high-functioning autism (full-scale IQ >100)”. […]

2 03, 2017

APOBEC-Seq for DNA methylation without the bisuflite

By | March 2nd, 2017|Categories: Methods and applications, Next-generation sequencing|Tags: , |1 Comment

For me one of the top talks at #AGBT17 was in a concurrent session. Theodore Davis from New England Biolabs presented “APOBEC-Seq: An enzymatic method for methylome analysis at single-base resolution without bisulfite treatment.” His talk focused on some of the cons of using sodium bisulfite sequencing for methylation in epigenetic […]

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