Welcome to Enseqlopedia
This website was started as the Core-Genomics blog in 2010 by James Hadfield as a place to collect his thoughts about all things NGS and to share these with anyone who cared to read them. After over 1 million page views James decided to formalise his blog and to bring together a few other ideas to create Enseqlopedia.
Enseqlopedia is meant to be an encylopedia for NGS. Over time it will be added to so it holds a comprehensive summary of NGS information including: technology providers, methods and applications, people and papers. I hope this helps to educate and inform the NGS community, particularly new users. The blog content will focus on commentary around recent NGS news, new product information and will have an emphasis on technology, advances in NGS and NGS R&D.
The views expressed by James in this blog are his own. Any similarity to the views of anyone, or any organisation, alive, dead or undead are entirely accidental.
Dr. Hadfield lives in Wymondham, Norfolk, UK. He completed a BSc in Molecular Biology (2.2) in 1995, and obtained his PhD in Genomics in 2015; both at the University of East Anglia. His research interests include Genomics and NGS technology, transcriptome analysis, circulating tumor DNA “liquid biopsy” and the use of NGS. He has authored 20ish peer-reviewed scientific articles and book chapters, has written over 500 blog posts, and lectures at both national and international meetings on topics related to NGS.
Dr. Hadfield is the Head of the Genomics Core facility at Cancer Research UK’s Cambridge Institute, a department of the University of Cambridge. His lab offers NGS services on Illumina HiSeq, MiSeq & NextSeq for scientists at CRUK-CI and ten other collaborating University departments or Institutes, as well as single-cell analysis on Fluidigm C1 and 10X Genomics systems. He is also currently seconded part-time at Genomics England as a sequencing expert and chairs the Sequencing Advisory Group and “Other Omics” working group. He is on the Scientific Advisory Board of Rubicon Genomics, and the Liverpool Centre for Genomic Research.
Dr Hadfield’s career so far has leant towards technology development or implementation. Over the last 16 years he’s worked at; the Norfolk & Norwich Hospital on ErbB2, Royal London on Diabetes genetics, the Cambridge University Department of Pathology on Immunology, and the John Innes Centre on Wheat disease resistance gene cloning. In 2000 he set up an Affy and spotted microarray facility at JIC, and co-founded the UK Affy user group. At JIC he also won a Biotech competition, and has had a strong interest in the commercialisation of research ever since. In 2006 James moved to set up the genomics facility at CRUK’s new Cambridge Institute.
Conflicts of Interest
My conflicts of interest statement is copied almost verbatim from Michael Eisen’s blog which I happily acknowledge. If everyone was as open as he is, the world would be a little better…“Like everybody, I have a series of interests, financial and otherwise, that could be affected by things I do and opine on. I endeavour not to let these influence my actions as a scientist or commentator. But I am not naive enough to think that I can always do this, and feel it is important that people know the things that might be influencing me.”
Financial: I have been rewarded for speaking at events by commercial sponsors, either as a paid speaker or by the covering of travel expenses and/or registration fees. I serve on the Scientific Advisory Board of Rubicon Genomics, a company that develops and provides nucleic acid library preparation molecular biology reagents and kits – and was the first company to deliver a fast 3 step NGS library-prep protocol. I meet with the company approximately once a year, and received renumeration for this. I got involved in the company because I thought the technology was really cool and we used it to great effect in the first reported circulating tumour exomes (Murtaza et al: Nature 2012). I am paid for a small amount of content on the Core Genomics blog (clearly indicated). I am also a paid consultant in the NGS space for variety of groups – no confidential information is shared as part of these discussions.
Professional: I currently receive virtually all of my lab’s funding from Cancer Research UK’s core award to the Cambridge Institute, and thus clearly have a professional conflict when talking about CRUK, or the University of Cambridge.
Under Creative Commons License: Attribution
Publications by James Hadfield
Davies, Denyer & Hadfield. Bioanalyzer chips can be used interchangably for many analyses of DNA or RNA. Biotechniques 2016.
Mohammad et al. Progesterone receptor modulates ERα action in breast cancer. Nature 2015.
Hadfield & Eldridge. Multi-genome alignment for quality control and contamination screening of next-generation sequencing data. Frontiers in Genetics 2013.
Azizan et al. Somatic mutations in ATP1A1 and CACNA1D underlie a common subtype of adrenal hypertension. Nat Genet. 2013
Murtaza et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 2013
Idris et al. The role of high-throughput technologies in clinical cancer genomics. Expert Rev Mol Diagn 2013
Forshew et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012
Curtis et al. The genomic and transcriptomic architecture of 2000 breast tumours reveals novel subgroups. Nature 2012.
Holmes et al. Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. PNAS 2012
Aldridge and Hadfield. Introduction to miRNA profiling technologies and cross-platform comparison. Methods Mol Biol 2012.
Massie et al. The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J. 2011
Katsnelson et al. Genomes by the thousand. Nature 2010
Lynch et al. The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment. Bioinformatics BMC Genomics 2010
Git et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010
Curtis et al. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 2009
Schmidt et al. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009
Das et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular Cell 2008
Smith et al. STS markers for the wheat yellow rust resistance gene Yr5 suggest a NBS-LRR-type resistance gene cluster. Genome 2007
Marquardt et al. Additional targets of the Arabidopsis autonomous pathway members, FCA and FY. J Exp Bot 2006
Mitra et al. A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. Proc Natl Acad Sci USA. 2004
Koebner et al. Large-scale mutagenesis directed at specific chromosomes in wheat. Genome 2001
Jennings et al. A differential PCR assay for the detection of c-erbB 2 amplification used in a prospective study of breast cancer. Mol Pathol. 1997