CoreGenomics has moved
CoreGenomics
by James@cancer
3y ago
Follow this link to Enseqlopedia/coregenomics... "CoreGenomics is dead...long live CoreGenomics"...the CoreGenomics blog has moved to its new home: http://enseqlopedia.com/coregenomics. Please update your bookmarks and register to follow the new blog, for updates on the NGS map (coming soon), and to access the new Enseqlopedia (coming soon)! Enseqlopedia: Last year I started the process of building the new Enseqlopedia site, after five years of blogging here on Blogger. Whilst Enseqlopedia is still being developed the CoreGenomics blog has moved over and you can also find all the ..read more
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10X Genomics updates
CoreGenomics
by James@cancer
3y ago
We had a seminar form 10X Genomics today to present some of the most recent updates on their systems and chemistry. The new chemistry for single-cell gene expression and the release of a specific single-cell controller show how much effort 10X have placed on single-cell analysis as a driver for the company. Phasing is looking very much the poor cousin right now, but still represents an important method to understand genome organisation, regulation and epigenetics. Single cell 3'mRNA-seq V2:  the most important update from my perspective was that 10X libraries can now be run on H ..read more
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MinION: 500kb reads and counting
CoreGenomics
by James@cancer
3y ago
A couple of Tweets today point to the amazing lengths Oxford Nanopores MinION sequencer is capable of generating - over 400kb! Dominik Handler Tweeted a plot showing read distribution from a run . In replies following the Tweet he describes the DNA handling as involving "no tricks, just very careful DNA isolation and no, really no pipetting (ok 2x pipetting required)". and Martin Smith Tweeted an even longer read, almost 500kb in length... Exactly how easily we'll all see similar read lengths is unclear, but it is going to be hugely dependant on the sample and probably having ..read more
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Unintended consequences of NGS-base NIPT?
CoreGenomics
by James@cancer
3y ago
The UK recently approved an NIPT test to screen high risk pregnancies for foetal trisomy 21, 13, or 18 after the current primary screening test, and in place of amniocentesis (following on from the results of the RAPID study). I am 100% in favour of this kind of testing and 100% in favour of individuals, or couples, making the choice of what to do with the results. But what are the consequences of this kind of testing and where do we go in a world where cfDNA foetal genomes are possible? I decided to write this post after watching "A world Without Downs", a documentary on BBC2 that was pre ..read more
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Does the world have too many HiSeq X Tens?
CoreGenomics
by James@cancer
3y ago
Illumina stock dropped 25% after a hammering by the stock market with their recent announcements that Q3 revenues would be 3.4% lower than expected at just $607 million. This makes Illumina a much more attractive acquisition (although I doubt this summers rumours of a Thermo bid had any substance), and also makes a lot of people ask the question "why?" The reasons given for the shortfall were "a larger than anticipated year-over-year decline in high-throughput sequencing instruments" i.e. Illumina sold fewer sequencers than it expected to. It is difficult to turn these revenue figu ..read more
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Controlling for bisulfite conversion efficiency with a 1% Lamda spike-in
CoreGenomics
by James@cancer
3y ago
The use of DNA methylation analysis by NGS has become a standard tool in many labs. In a project design discussion we had today somebody mentioned the use of a control for bisulfite conversion efficiency that I'd missed, as its such a simple one I thought I'd briefly mention it here. In their PLoS Genet 2013 paper, Shirane et al from Kyushu University spiked-in unmethylated lambda phage DNA (Promega) to control for, and check, the C/T conversion rate was greater than 99%. The bisulfite conversion of cytosine bases to uracils, by deamination of unmethylated cytosine (as s ..read more
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SIRVs: RNA-seq controls from @Lexogen
CoreGenomics
by James@cancer
3y ago
This article was commissioned by Lexogen GmbH. My lab has been performing RNA-seq for many years, and is currently building new services around single-cell RNA-seq. Fluidigm’s C1, academic efforts such as Drop-seq and inDrop, and commercial platforms from 10X Genomics, Dolomite Bio, Wafergen, Illumina/BioRad, RainDance and others makes establishing the technology in your lab relatively simple. However the data being generated can be difficult to analyse and so we’ve been looking carefully at the controls we use, or should be using, for single-cell, and standard, RNA-seq e ..read more
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Batch effects in scRNA-seq: to E or not to E(RCC spike-in)
CoreGenomics
by James@cancer
3y ago
At the recent Wellcome Trust conference on Single Cell Genomics (Twitter #scgen16) there was a great talk (her slides are online) from Stephanie Hicks in the @irrizarry group (Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute). Stephanie was talking about the recent work she's been doing looking at batch effects in single-cell data, all of which you can read about in her paper is on the BioRxiv: On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data. You can also read about this paper over ..read more
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Clinical trials using ctDNA
CoreGenomics
by James@cancer
3y ago
DeciBio have a great interactive Tableau dashboard which you can use to browse and filter their analysis of 97 “laboratory biomarker analysis” ImmunOncolgy clinical trials; see: Diagnostic Biomarkers for Cancer Immunotherapy – Moving Beyond PD-L1. The raw data comes from ClinicalTrials.gov where you can specify a "ctDNA" search and get back 50 trials, 40 of which are open. Two of these trails are happening in the UK. Investigators at The Royal Marsden are looking to measure the presence or absence of ctDNA post CRT in EMVI-positive rectal cancer. And Astra Zeneca are looking for ctDNA a ..read more
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Index mis-assignment to Illumina's PhiX control
CoreGenomics
by James@cancer
3y ago
Multiplexing is the default option for most of the work being carried out in my lab, and it is one of the reasons Illumina has been so successful. Rather than the one-sample-per-lane we used to run when a GA1 generated only a few million reads per lane, we can now run a 24 sample RNA-seq experiment in one HiSeq 4000 lane and expect to get back 10-20M reads per sample. For almost anything other than genomes multiplexed sequencing is the norm. But index sequencing can go wrong, and this can and does happen even before anything gets on the sequencer. We noticed that PhiX has been turning u ..read more
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