I had the very real pleasure of introducing Prof Lucy Raymond at Biotexcel’s Genomic Medicine 2017 in Cambridge last week. She was speaking in a session that included Dr David Bentley (Illumina Inc – Genomes for Medicine), Prof Stephan Beck (UCL Cancer Institute – Towards Personal Epigenomics), and Prof Sadaf Farooqi (University […]
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 […]
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, […]
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 […]
Prof Yutaka Suzuki’s lab at the University of Tokyo published a paper last week in DNA research: Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer. In the paper they described their work detecting SNVs in EGFR, KRAS, NRAS and NF1, and EML4-ALK, […]
I recently had a days training at Oxford Nanopore’s labs on their new cDNA-Seq kit and ran the resulting libraries on the GridION (one of the first customers to do so). A lot of people are watching RNA-Seq developments at ONT very closely. The London […]
Iain Macaulay organised a #singlecell meeting at Norwich’s Earlham Institute earlier this month. The meeting was fun and there were some great presentations during a day of talks and discussion on the development and application of single cell technologies. 100+ #singlecell analysis methods at www.tinyurl.com/mqabyur One that […]
The Genomics England project (a.k.a. UK100k genomes) is known as a whole genome sequencing project. It aims to sequence 100,000 genomes from UK NHS patients with Rare Disease or Cancer. But Genomics England have a very nice tool for people interested in targeted sequencing via […]
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 […]
This is a first for me as I’ve not finished this post at all! Instead I’m going to use this as a space to document my ideas, and experiences, in bringing Oxford Nanopore’s RNA-seq into my core lab at the CRUK Cambridge Institute. I’m hoping […]
