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 […]

10 04, 2017

Index-swapping with @illumina ExAmp clustering

By | April 10th, 2017|Categories: Uncategorized|8 Comments

A paper uploaded to BioRxiv yesterday is the first (almost) published report of index-swapping on Illumina’s Exclusion-Amplification (ExAmp) chemistry. The paper: Index Switching Causes “Spreading-Of-Signal” Among Multiplexed Samples In Illumina HiSeq 4000 DNA Sequencing, by a group from Stanford Functional Genomics Facility published a re-analysis of single-cell […]

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 […]

31 03, 2017

Mass-cytometry webinars from @Fluidigm

By | March 31st, 2017|Categories: Methods and applications, Other stuff|0 Comments

The Helios/CyToF mass-cytometry technology is making waves here in our Flow Core and is likely to be a useful addition to multi-omic studies. Fluidigm have a series of webinars that I thought readers of Core-Genomics might be interested in: Decoding human tumors and healthy tissue […]

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 […]

17 03, 2017

MinION or GridION for your core lab

By | March 17th, 2017|Categories: Core facilities, Nanopore sequencing|2 Comments

Clive Brown presented a webinar on Tuesday with multiple updates on Oxford Nanopore technology, Keith Robison covered them all over at OmicsOmics, but I’ll just be focussing on the launch of GridION X5. If you want to know more about GridION, PromethION, Throughput, 1D^2 Chemistry, Basecalling, the FPGA Basecalling Accelerator, and a […]

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