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James Hadfield

James received a Biology degree from the University of East Anglia in 1995, and his PhD in 2014. His career so far has leant towards technology development or implementation. In 1995 he developed a differential PCR test for ErbB2 copy number and over the last 16 years he's worked at; the Norfolk & Norwich Hospital, Royal London on Diabetes genetics, the Cambridge Uni Department of Pathology and the John Innes Centre on Wheat disease resistance gene cloning and arrays. In 2000 he set up an Affy and spotted microarray facility at JIC, he co-founded the UK Affy user group, which is still going strong. Whilst at JIC he also won a Biotech competition, and hopes one-day to start a business although none of his ideas have come to anything yet! In 2006 James moved to set up the genomics facility at the CRUK Cambridge Institute, a department of the University of Cambridge. The lab offers broad spectrum genomic services for scientists at CRI and Illumina next-gen sequencing for CRI, Gurdon, LMB, IMS, Stem Cell, Obs & Gynae and Haematology. His interests today are firmly in next generation sequencing and development of the technology for personalised medicine. He also writes the Core Genomics blog, commenting on the exciting and fast moving world of Genomics. With a focus on next-generation sequencing and microarray technologies, although it is does go off on tangents from time-to-time. Publications by James Hadfield

Articles by James Hadfield:

Nanopore Sequencing: An Update

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.

09 Jul 2016 Genomics & Epigenetics

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

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…

09 Jul 2016 Genomics & Epigenetics

Why Is It Important To Run Your NGS Gels Consistently?

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…

16 Jul 2015 Genomics & Epigenetics

Quantifying Your NGS Libraries

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…

20 Feb 2015 Genomics & Epigenetics

Top 10 Tips for NGS Library Preparation

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…

02 Jan 2015 Genomics & Epigenetics

The Real Cost of Sequencing in 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…

05 Dec 2014 Genomics & Epigenetics

The Birth Of The Epitranscriptome: RNA Gets Methylated Too!

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…

17 Oct 2013 Genomics & Epigenetics

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

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…

20 Jun 2013 Genomics & Epigenetics

Why Is It Important To Run Your NGS Gels Consistently?

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…

02 May 2013 Genomics & Epigenetics

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

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…

11 Apr 2013 Genomics & Epigenetics

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

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.…

21 Feb 2013 Genomics & Epigenetics

Some Sanger Sequencing Tips and Tricks

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…

17 Jan 2013 Genomics & Epigenetics

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

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…

11 Oct 2012 Genomics & Epigenetics

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

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…

04 Oct 2012 Genomics & Epigenetics

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

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.…

27 Sep 2012 Genomics & Epigenetics

Next Generation Sequencing: The Three Main Technologies

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…

16 Aug 2012 Genomics & Epigenetics

An Introduction To ChIP-seq

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…

04 Nov 2011 Genomics & Epigenetics