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 […]
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 […]
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 […]
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 […]
In this post I wanted to highlight the wonderful “Excel vs R: A Brief Introduction to R” by Jesse Sadler. This is full of useful and practical advice on using R in place of Excel (or any other spreadsheet) for simple data analysis. I use […]
My lab has been a long-time user of Illumina’s transposase exomes for the very simple reason that the 50ng input has been the lowest on the market for number of years*. This made it attractive for cancer samples where we are really limited on DNA availability; […]
Because HPV has such a small and relatively simple genome (8,000 bp encoding 8 genes) it is possible to screen for genetic variation that may underly carcinogenesis. A team from the National Cancer Institute (NCI) has just published the sequencing of over 5,570 human cell and tissue samples – […]
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 […]
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 […]
