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: , |0 Comments

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 […]

22 02, 2017

NeoPrep is dead….what does this mean for Illumina

By | February 22nd, 2017|Categories: Core facilities, Nanopore sequencing, Next-generation sequencing|Tags: |0 Comments

Illumina have finally dropped the NeoPrep from their lineup after a short but pretty rocky road. Launched at AGBT15 the instrument promised hassle free library prep automation for users that did not require full 96well plate production-scale solutions. Early access users I spoke to at […]

22 02, 2017

Hydroxymethylation (hmC) papers from CEGX

By | February 22nd, 2017|Categories: Methods and applications, Next-generation sequencing|Tags: , , |0 Comments

Cambridge Epigenetix (@CEGX_news) have a list of almost 50 papers on their website using their technology for DNA methylation and hydroxymethylation analysis, which I thought readers of CoreGenomics might be interested in. They also have a list of Epigenetics Conferences coming up….enjoy! The papers: Chen et […]

21 02, 2017

#AGBT17

By | February 21st, 2017|Categories: Conferences, Next-generation sequencing, Single-cell sequencing|0 Comments

This years #AGBT17 did not look as exciting as previous years have done, especially with all the major announcements being made at JP Morgan. In fact Illumina even went as far as to say they’d have no news at all during the conference! However there was […]

15 02, 2017

Nanostring Hyb&Seq

By | February 15th, 2017|Categories: Conferences, Methods and applications, Next-generation sequencing, Other stuff|Tags: , , |4 Comments

Nanostring had an interesting poster presented by Joe Beecham at last years AGBT describing their novel single-molecule hybridization-based sequencing chemistry (see AGBT and JPMorgan 2016 coverage from GenomeWeb). This utilizes the Nanostring optical barcodes in a new configuration to deliver Hyb&Seq: no amplification, no enzymes, and no […]

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