Microarray analysis for studies of genome organisation and evolution plus development of novel diagnostic tools and technologies

Lead Research Organisation: University of Kent
Department Name: Sch of Biosciences

Abstract

A microarray is a series of tiny spots of DNA arranged on a glass slide in a very ordered way. It can represent a whole genome, ordered as it appears in the organism; it can consist of parts of genes that are expressed in certain tissue at certain times or it can contain DNA that represents the sort genetic of variation that would appear in individual organisms such as ourselves. When we perform certain experiments on these arrays we can better understand when genes are switched on and off at certain developmental time-points, how humans and animals vary genetically and how genomes evolve. Previously my research interests have centred around the studies of chromosomes - the structures that form from the DNA (and associated protein) as a cell divides. Notable successes include the first application of a chromosomal technique for diagnosing genetic disease in embryos only three days after they have been conceived, insight in to sperm production and telling all the chromosomes apart in chicken (the first time this had been achieved in a bird). More recently we have been interested in what happens to the chromosomes when the cell is not dividing i.e. when the cell is performing its normal functions. The opportunity to introduce microarray technology into my laboratory is an exciting one. In principle, a lot of the technology is very similar to that used on chromosomes and thus should not present a quantum leap, particularly if I can attend certain training courses to get me up to speed with respect to protocols for analysing the results obtained. These courses are run regularly e.g. at the Sanger Centre in Cambridge. Specifically, I would be interested in developing new microarray-based technologies for genetic diagnosis in early development; investigating genome evolution in birds; and asking how the switching on and off of genes and gene clusters relates to their position in space and time in the nucleus of a cell. Funding is requested therefore to buy out my time from my teaching and administration duties to re-direct my own interests and that of my laboratory towards this novel technology and, more specifically, asking biological questions using it.

Technical Summary

The purpose of this application is to seek funds to establish microarray technology in my laboratory to pump-prime a high-impact research effort with three areas of interest: 1. Development of tools and technologies for preimplantation diagnostics and to provide insight into aneuploidy origin I first reported preimplantation diagnosis by FISH in the early 1990s; since then, diagnosis is still limited to around eight chromosomes per nucleus. Microarray makes it possible to determine copy number for all chromosomes by CGH and exploit high-density SNP arrays, analysing amplified DNA from both parents and fetus to determine the parent and stage of origin and the determination of the degree and position of cross-over events. 2. Correlation of gene expression and nuclear organisation Studies of nuclear organisation concerned with the three and four-dimensional topology of the interphase nucleus, are thought to be key to understanding large-scale transcriptional regulation and mediation of normal/abnormal cellular function. Previous studies have implicated either a gene density or chromosome size determined arrangement for whole chromosomes. Further studies have addressed individual loci in relation to transcriptional activity. There is however a poorly understood meso-scale between these two extremes. The purpose of the proposed programme of research will be to combine transcription profiling with nuclear organisation studies to investigate the degree to which changes in three-dimensional nuclear organisation are responsible for the transcriptional changes in developing cells. Test systems will include mammalian spermatogenesis and avian macrophage activation. 3. Investigation of chromosome rearrangements in birds Here I will apply labelled chromosome paints directly on to the recently developed chicken tiling path microarray. Careful molecular identification of breakpoints/fusion points will shed light into the mechanisms of avian evolution.

Publications

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Gabriel AS (2011) An algorithm for determining the origin of trisomy and the positions of chiasmata from SNP genotype data. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

 
Title YouNome - your personalised genome in 24 self portraits 
Description We exhibited a unique science-art collaboration (YouNome) to engage, educate and inspire the general public about 'personalized genomics': the study of someone's genetic code in its entirety. Keith Robinson (the artist) in collaboration with Prof Griffin has produced 25 self-portraits, each representing a section of the human genome (chromosome) by altering his own image (self portrait). The collection (accompanied by explanatory notes), chosen to be exhibited at the Canterbury Festival in October 2016, aims to promote scientific understanding, reference art history, and reflect popular culture. We have recently, in collaboration with the English department, extended YouNome to the generation of 25 poems (selected or generated de-novo by University of Kent poets) to reflect the portraits. To increase public engagement, in collaboration with digital artists we will (based in Invicta House) invite the public to use simple iPad-based face alteration software to output self portraits in similar styles as the original artwork. The follwing questions form the inspiration for the 'YouNome' exhibition: Who knows what genomic information means? How can (personalized) genomics be presented to an audience in an informative, memorable, challenging way? How can we raise awareness of the concept of personalized genomics and what it means to society through portraiture? Historically artists have created self-portraits, for vanity, self-scrutiny or cultural commentary. Public response to the artist's self-vision differs to that of other portraits. Why is this? What makes up and informs 'the self?' What do we see when a self-portrait is informed with contemporary genomic understanding? Addressing some of the above questions through portraiture brings an added dimension to the overall impact and engagement of the YouNome project. 
Type Of Art Artwork 
Year Produced 2016 
Impact Exhibited at Canterbury Festival 
URL http://www.keithrobinsonpainting.com/Younome
 
Description I am pleased to report the successful completion of the specific aims outlined, more or less as stated. In addition I have embarked on a radical programme of publication, science communication and outreach. The key achievements of the past three years have been as follows:

• 28 publications since 2008, the majority as lead author and original research (as opposed to reviews)
• Contribution to leading journals such as Genome Research, Nature, Journal of Cell Science
• These papers collectively already have over 200 citations already
• Total career tally has now exceeded 100 papers
• H-index has now exceeded 30
• Promoted to Professor of Genetics
• Elected Vice President of International Chromosome and Genome Society
• Increased media profile
• Significant public engagement and outreach
• 5 plenary/keynote lecture invitations
• 6 PhD graduations
• Industrial funding and CASE studentships
• Short listed for Times Higher Education Research Project of the Year 2010

All of the stated aims in the application have been fulfilled as follows:

Developing novel tools and technologies that will replace standard FISH-based approaches for diagnosing genetic diseases at the preimplantation stage.
Products of conception, human oocytes and human embryos were all investigated in this project. Most notably, the project led to the development of "Karyomapping" a Universal approach for the diagnosis of genetic disease in human preimplantation embryos (this was dubbed "the Genetic MOT by the press). Both array CGH and SNP arrays have been used and we have both developed new technologies to determine the origins of chromosome copy number in oocytes and embryos. (Handyside et al. 2010; Gabriel et al. 2010, 2011). The first Karyomapping clinical case has been performed and led to a live birth of twins.

Investigating the relationship between three and four dimensional nuclear organisation and global gene expression in a number of model cell types
Transcriptomic studies in spermatogenesis (both human and mouse) have been investigated (Ellis et al. 2008, Griffin et al. 2010) providing further insight into the process. In this case there was a slight deviation from the aims, as attempts to correlate genome organisation and gene expression were not realised. Nonetheless there have been several publications on nuclear organisation (Finch et al 2008a,b; Skinner et al. 2009b; Ioannou and Griffin 2011). The avian macrophage work mentioned in the application was largely unfrtuitful.

Gaining a further insight into avian evolution through the hybridisation of whole genomic DNA and individual chromosome specific libraries to avian tiling path arrays.
This part of the project has led to several publications in high quality journals. CNVs (copy number variants) have been detected in many species using the chicken tiling path arrays and the presence of CNVs has been correlated to chromosome breakage and recombination during evolution (Griffin et al. 2008; Skinner et al. 2009a; Volker et al. 2010). Several further manuscripts were subsequently published
Exploitation Route The development of Karyomapping has led to the release of a commercial product by Illlumina Inc that is being used for preimplantation diagnosis.

The CNV information is of general use to the avian genomics community
Sectors Agriculture, Food and Drink,Education,Healthcare

URL http://www.kent.ac.uk/bio/profiles/staff/griffin.html
 
Description Invited academic lectures since 2008 Plenary/keynote lecture invitations 2008 - European Colloquium on Animal Cytogenetics and Genome Mapping - Bucharest, Romania 2010 - International colloquium on Animal Cytogenetics and Gene Mapping. Krakow, Poland: given special award medal for services to the conference 2011 - World DNA Day, Dailan, China. 2011 - International Symposium on Industrial Biotechnology, Dailan, China. 2012 - International Colloquium on Animal Cytogenetics and Gene Mapping. Cordoba, Spain: Session/meeting chair invitations 2008 - Digital Scientific User Group Meeting, Cambridge 2008/2009/2011 - Pig Breeders' Round Table. Canterbury (meeting host) 2010 - European Society for Human Reproduction and Embryology, Rome, Italy. 2011 - 18th International Chromosome Conference (ICCXVIII). Manchester (meeting host, session chair & speaker). Invitations to speak at scientific meetings (not inc. Plenaries and session chairs above) 2009 - 17th International Chromosome Conference - Boone, USA 2009 - BBSRC Fellows' Conference (near Coventry) 2010 - Course on use of the DT40 Cell Line, Galway, Ireland 2010 - Preimplantation Diagnosis International Society, Montpellier, France 2011 - International Symposium on the Conservation of Wild Birds, Abu Dhabi, UAE 2011 - British Andrology Society, Bristol Departmental seminars 2008/2009/2010/2011 Central Veterinary Research Laboratory, Dubai, UAE 2009 University of Oxford, Wellcome Trust 2009 University of Birmingham 2009 University of Leeds 2010 University of Bologna 2010 Roslin Institute, University of Edinburgh Current collaborators include: 1. The London Bridge Fertility, Gynaecology and Genetics Centre 2. Pfizer 3. JSR Genetics 4. Digital Scientific UK 5. Central Veterinary Research Laboratory, Dubai 6. University of Cambridge, Department of Pathology 7. University of Cambridge, Department of Clinical and Veterinary Medicine 8. Roslin Institute, Edinburgh 9. University of Hokkaido 10. Kreatech Diagnostics 11. BlueGnome Cambridge PhD graduations 1. Katie A Finch. "Molecular cytogenetic studies of human sperm and pre-implantation embryos with specific reference to genome organisation: Future applications for fertility treatment and diagnosis." Graduated November 2008 2. Nicholas D Temperley. "Evolution and Genetic Variation of Avian Toll-like Receptor Genes." Graduated November 2008 3. Abdulmawla M Abogrein. "Numerical chromosome abnormalities in human sperm and embryos: Correlations and mechanisms." Graduated June 2009. 4. Benjamin M Skinner. "Comparative cytogenomics between chicken and duck: wider insights into genome evolution and organisation." Graduated 2009 5. Dimitris Ioannou. "Multicolour interphase cytogenetics in human sperm and embryos: Chromosome copy number and the relevance of nuclear address". To graduate June 2011 6. Alem S Gabriel. "Cytogenomics of human oocytes and embryos: Application of microarrays for the study of the incidence of origin of chromosome copy number errors." To graduate June 2011. All students submitted within 4 years of registration. Post-graduate examination 1. Examiner for MSc in Human Genetics (University of Leeds) and Prenatal Diagnosis/Fetal Medicine (UCL) 2. Examined an MPhil at the University of Cambridge and an MD at the University of London 3. Examined PhDs at the Universities of Cambridge, London (UCL) Stirling and Stellenbosch (South Africa) Media activity 1) Appeared on BBC1: "The Big Questions." On two occasions (invited for a 3rd time but had to decline) 2) BBC1: News broadcasts on Karyomapping work 3) BBC South East: News Broadcast 4) ITV Meridian: News Broadcast 5) BBC Radio Kent: News Broadcast 6) KMFM: Feature 7) New Scientist: 4 occasions 8) Newswire: Medwire news (UK) 9) Podcast: The Times 10) Through the Science Media Centre, numerous comments in national press (approx. 300) 11) "10 commandments for being a successful scientist" presentation given at Royal Society, Appeared on blog in "Nature" magazine and formed part of American Chemical Society webinar programme. Outreach 1) Numerous Café Scientifique (Kent, London, Beijing) - Designer Babies 2) Becket Medical Society - Canterbury 3) Rotary Club of Canterbury 4) Outreach Activity to Schools (STEMnet ambassador) 5) Numerous science fairs including BBC's "Bang Goes the Theory Roadshow 6) Symposium at Royal Society: 10 commandments for being a successful scientist. Appeared on Nature blog and formed part of American Chemical Society webinar programme (1100 registrants) 7) Chair of Darwin 200 committee, this involved coordinating a range of research-related events celebrating Darwin's 200th birthday
First Year Of Impact 2008
Sector Agriculture, Food and Drink,Education,Healthcare
Impact Types Cultural,Societal,Economic,Policy & public services

 
Description Karyomapping discussed by HFEA
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Karyomapping is now a product marketed by Illumina and is in clinical practice
URL http://clinical.illumina.com/clinical/reproductive-genetic-health/clinical-labs/preimplantation-gene...
 
Description Sustainable agriculture
Amount £996,720 (GBP)
Organisation Technology Strategy Board (TSB) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 12/2011 
End 12/2015
 
Description List of collaborators 
Organisation Central Veterinary Research Laboratory
Country United Arab Emirates 
Sector Public 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Digital Scientific UK
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Hokkaido University
Country Japan 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Illumina
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation JSR Genetics
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Leica Microsystems GmbH
Department Kreatech Diagnostics
Country Netherlands, Kingdom of the 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation London Bridge Fertility, Gynaecology and Genetics Centre
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Hospitals 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation Pfizer Ltd
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation University of Cambridge
Department Department of Pathology
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation University of Cambridge
Department Department of Veterinary Medicine
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Description List of collaborators 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution A number of collaborations formed part of this project (see list)
Start Year 2006
 
Title Karyomapping 
Description Universal test for preimplantation genetic diagnosis 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Wide-scale adoption
Year Development Stage Completed 2013
Development Status Under active development/distribution
Impact Babies born free of genetic disease 
URL http://clinical.illumina.com/clinical/reproductive-genetic-health/clinical-labs/preimplantation-gene...
 
Description Media and outreach 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Media activity

1) Appeared on BBC1: "The Big Questions." On two occasions (invited for a 3rd time but had to decline)

2) BBC1: News broadcasts on Karyomapping work

3) BBC South East: News Broadcast

4) ITV Meridian: News Broadcast

5) BBC Radio Kent: News Broadcast

6) KMFM: Feature

7) New Scientist: 4 occasions

8) Newswire: Medwire news (UK)

9) Podcast: The Times

10) Through the Science Media Centre, numerous comments in national press (approx. 300)

11) "10 commandments for being a successful scientist" presentation given at Royal Society, Appeared on blog

in "Nature" magazine and formed part of American Chemical Society webinar programme.



Outreach

1) Numerous Café Scientifique (Kent, London, Beijing) - Designer Babies

2) Becket Medical Society - Canterbury

3) Rotary Club of Canterbury

4) Outreach Activity to Schools (STEMnet ambassador)

5) Numerous science fairs including BBC's "Bang Goes the Theory Roadshow

6) Symposium at Royal Society: 10 commandments for being a successful scientist. Appeared on Nature blog

and formed part of American Chemical Society webinar programme (1100 registrants)

7) Chair of Darwin 200 committee, this involved coordinating a range of research-related events celebrating

Darwin's 200th birthday

My efforts on "10 commandments on being a successful scientist" has one of the first hits on Google when entering the term "successful scientist"
I am regularly asked to comment on local news events
The work led to 2 Technology strategy board awards and 1 Knowledge transfer partnerships
I regularly give public presentations and now have 4 different ones (Designer babies, Are our genetic male bits disappearing, being a successful scientist, and the genome of dinosaurs). I must have given about 100-200 of these at schools, science fairs etc and they are always well received.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012
URL http://www.kent.ac.uk/bio/profiles/staff/griffin.html