11 10, 2016

Clinical trials using ctDNA

By | October 11th, 2016|Categories: Uncategorized|0 Comments

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 […]

23 05, 2016

Increased read duplication on patterned flowcells- understanding the impact of Exclusion Amplification

By | May 23rd, 2016|Categories: Uncategorized|5 Comments

Next-generation sequencing is fantastic technology and its use has revolutionised our understanding of biology, but it is not perfect, multiple issues occur in every lab from sample extraction through to the actual sequencing. Not all of these are well enough understood to be safely ignored […]

3 05, 2016

How many reads to sequence a genome?

By | May 3rd, 2016|Categories: Uncategorized|2 Comments

Last year I posted about the Lander-Waterman equation used to calculate the number of reads needed to sequence a sample. I explained that this general equation (C = LN/G) can be rearranged to allow you to compute the number of reads (N) to sequence a […]

29 04, 2016

SPRI alternatives for NGS

By | April 29th, 2016|Categories: Uncategorized|5 Comments

SPRI beads, generally in the form of AMPureXP beads, are almost ubiquitous in genomics applications such as library prep for NGS. The most popular thing I’ve ever written was a post on this blog four years ago: “How do SPRI beads work?” with almost 100,000 […]

11 04, 2016

WGS versus Exome: what’s best for cancer?

By | April 11th, 2016|Categories: Uncategorized|1 Comment

I’ve just started using Twitter polls and kicked things off with a couple asking followers whether they thought Cancer research (or diagnostics) is best investigated using whole genome sequencing, higher depth exomes, much higher depth amplicomes, or even long-reads. Please do take the poll and […]

17 03, 2016

How much is a 2nd hand HiSeq?

By | March 17th, 2016|Categories: Uncategorized|5 Comments

We recently bought two HiSeq 4000 instruments to run larger RNA-seq and exome projects on. Over the next few months we’ll be transitioning other library types where we can, and think perhaps 65-85% of the work we do can be ported over from the 2500. […]

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