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James Hadfield

James has a PhD in Genomics from the University of East Anglia. An experienced life-sciences researcher and senior operational manager with over 20 years’ experience in Genomics technologies. Track record of scientific leadership, innovation, leading a lab team and managing significant annual budgets. Skilled in Genomics, Transcriptomics and single-cell technologies with a focus on cancer biology; excels at identifying and applying disruptive scientific innovation. An adaptive collaborator, innovator and entrepreneur. A thought leader in genomics with a broad network across academia and industry who works across effectively at all levels.

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Articles by James Hadfield

RNA-seq

An Introduction to RNA-seq

By James Hadfield | July 9, 2016

RNA sequencing (Wang 2009) is rapidly replacing gene expression microarrays in many labs. RNA-seq lets you quantify, discover and profile RNAs. For this technique, mRNA (and other RNAs) are first converted to cDNA.   The cDNA is then used as the input for a next-generation sequencing library preparation. In this article, I’ll give a brief…

Where Did It All Go Wrong?! Quality Control For Your NGS Data

Where Did It All Go Wrong?! Quality Control For Your NGS Data

By James Hadfield | July 9, 2016

You’ve carefully collected your samples, extracted nucleic acids and made your first set of next-generation sequencing libraries. How are you going to know if the data you get back is any good and whether it will be worth the effort in learning how to do the analysis? Who is to blame? Fortunately, there are several…

Nanopore sequencing

Nanopore Sequencing: An Update

By James Hadfield | July 9, 2016

People would have said that a USB sequencer not much bigger than a memory stick which could sequence genomes in 50kb+ read-lengths was impossible “’Star Trek’ technology!” Now, that futuristic technology is here.

Why Is It Important To Run Your NGS Gels Consistently?

Why Is It Important To Run Your NGS Gels Consistently?

By James Hadfield | July 16, 2015

This article discusses some of the important things to consider if you are using agarose gel electrophoresis for size-selection of your NGS libraries. Gel electrophoresis is a simple and very commonly used technique in most labs. Careful! It’s a critical step However this simplicity means people can often overlook the fact that there are applications where…

Quantifying Your NGS Libraries

Quantifying Your NGS Libraries

By James Hadfield | February 20, 2015

If you want to get the maximum yield and quality from your next-generation sequencing experiment then you are going to need to make sure each of the libraries you produce is carefully quantified ready for pooling and/or loading onto a flow cell. If the quantification goes wrong you’ll get a bad balance of samples within…

Top 10 Tips for NGS Library Preparation

Top 10 Tips for NGS Library Preparation

By James Hadfield | January 2, 2015

Making a Next Generation Sequencing (NGS) library can seem a bit daunting to the new user, as failures can be expensive. But don’t be put off, as NGS library preparation is relatively simple molecular biology, and can be very easy if you choose to use a commercial kit from one of the many suppliers. Take…

The Real Cost of Sequencing in 2014

The Real Cost of Sequencing in 2014

By James Hadfield | December 5, 2014

We are now living in the era of the $1000 genome. Unfortunately, most of us are still paying significantly more than this for a genome, or an equivalent amount of data in the form of exomes or RNA-seq reads. There are several reasons for this higher-than-expected price and this post aims to highlight where the…

The Birth Of The Epitranscriptome: RNA Gets Methylated Too!

By James Hadfield | October 17, 2013

Most biologists are aware of chemical modification of DNA in the form of 5-methylcytosine (mC), the eponymous ‘5th base’. Moving to the 6th base The fields of epigenetics and epigenomics are increasingly having an impact on our understanding of biology and a subsequent impact on medicine. Some biologists are aware of the wider range of DNA…

DNA shearing

Shearing DNA For Next Generation Sequencing: Which Method Should I Choose?

By James Hadfield | June 20, 2013

Next-generation sequencing (NGS) really has taken the world by storm! In NGS, millions of short ‘read’s are sequenced in a short space of time, leaving you with vast amounts of data to analyze! For all NGS platforms, the input sample (i.e. your cell free DNA) must be cleaved into short sections or fragments prior to…

Why Is It Important To Run Your NGS Gels Consistently?

By James Hadfield | May 2, 2013

Size Selection via Gel Electrophoresis Whether you are using NGS for whole genome sequencing, SNP variant analysis, HLA typing, HLA matching, or even transcriptome or miRNA analysis by RNA-seq, size selection is an extremely important consideration for optimum results. Precise size selection can increase sequencing efficiency, save money and improve genome assemblies, as well as…

Where Did It All Go Wrong?! Quality Control For Your NGS Data

By James Hadfield | April 11, 2013

You’ve carefully collected your samples, extracted nucleic acids and made your first set of next-generation sequencing libraries. How are you going to know if the data you get back is any good and whether it will be worth the effort in learning how to do the analysis? Who is to blame? Fortunately, there are several…

Too good to be true?! What can Nextera do for you?

By James Hadfield | February 21, 2013

Read on… Nextera is an Illumina NGS library preparation system that works very differently from the standard fragment library preps being used in most labs. Instead of the usual Illumina fragmentation, end-repair and adapter ligation, the Nextera enzyme mix is simply added to DNA for five minutes and a library is ready for PCR amplification.…

Some Sanger Sequencing Tips and Tricks

By James Hadfield | January 17, 2013

Sanger sequencing is still a workhorse of most molecular biology labs. Even with the advent of next-generation sequencing we still need to sequence our clones and PCR products. In this article I have listed some of the tips and tricks we used in our Sanger services. (1)Dilution of BigDye: I’d expect this to be a…

A Short History of Sequencing Part 3: personal NGS, disposable sequencers and what the future holds.

By James Hadfield | October 11, 2012

Personalizing NGS Due to the relative ease of whole human genome sequencing, clinical researchers became interested in how they might use this technology to help their patients. There were, and still are, obstacles to overcome- but the promise is so great! The Ion Torrent technology came in a small box which could easily sit in…

A Short History of Sequencing Part 2: the first of the next.

By James Hadfield | October 4, 2012

The Human Genome Project was successful, but hard work. The major improvements to the technology were the increases in parallelization and automation. In 2003, just as the HGP completion papers were published in Nature and Science, ABI launched the‘3730XL’. It could run 24 96-well plates per day and generate around 2 MB of sequence. Some…

A Short History of Sequencing Part 1: from the first proteins to the Human Genome

By James Hadfield | September 27, 2012

It all started with proteins The earliest methods for sequencing were developed for proteins. In 1950, Pehr Edman published a paper demonstrating a label-cleavage method for protein sequencing which was later termed “Edman degradation”. Around the same time Fred Sanger was developing his own labelling and separation method which led to the sequencing of insulin.…

Next Generation Sequencing: The Three Main Technologies

By James Hadfield | August 16, 2012

A paradigm shift by the Big Three As we learned last week, the Human Genome Project was accomplished using the improved Sanger method and technology from Applied Biosystems (ABI). Despite the significant technical improvements to this ‘first-generation’ technology, sequencing multiple human genomes was never going to be easy without a paradigm shift. Over the last…

An Introduction To ChIP-seq

An Introduction To ChIP-seq

By James Hadfield | November 4, 2011

ChIP-seq is a wonderful technique that allows us to interrogate the physical binding interactions between protein and DNA using next-generation sequencing. In this article, I’ll give a brief review of ChIP and introduce the chromatin immunoprecipitation sequencing technique (ChIP-seq), which combines ChIP with next-generation sequencing. What is chromatin immunoprecipitation? Chromatin immunoprecipitation (ChIP) allows us to…

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