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.
Organisations
- University of Kent (Lead Research Organisation)
- Digital Scientific UK (Collaboration)
- Pfizer Ltd (Collaboration)
- Central Veterinary Research Laboratory (Collaboration)
- Leica Microsystems GmbH (Collaboration)
- JSR Genetics (Collaboration)
- Hokkaido University (Collaboration)
- Illumina Inc. (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- London Bridge Fertility, Gynaecology and Genetics Centre (Collaboration)
People |
ORCID iD |
| Darren Griffin (Principal Investigator) |
Publications
Balakrishnan CN
(2010)
Gene duplication and fragmentation in the zebra finch major histocompatibility complex.
in BMC biology
Capalbo A
(2016)
Artificial oocyte activation with calcium ionophore does not cause a widespread increase in chromosome segregation errors in the second meiotic division of the oocyte.
in Fertility and sterility
Coates A
(2017)
Differences in pregnancy outcomes in donor egg frozen embryo transfer (FET) cycles following preimplantation genetic screening (PGS): a single center retrospective study.
in Journal of assisted reproduction and genetics
Coates A
(2015)
Use of suboptimal sperm increases the risk of aneuploidy of the sex chromosomes in preimplantation blastocyst embryos.
in Fertility and sterility
Damas J
(2017)
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
in Genome Research
Farré M
(2016)
Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.
in Genome biology and evolution
Finch KA
(2008)
Nuclear organization in human sperm: preliminary evidence for altered sex chromosome centromere position in infertile males.
in Human reproduction (Oxford, England)
Finch KA
(2008)
Nuclear organisation in totipotent human nuclei and its relationship to chromosomal abnormality.
in Journal of cell science
Foster HA
(2010)
Fluorescence in situ hybridization on early porcine embryos.
in Methods in molecular biology (Clifton, N.J.)
Gabriel AS
(2011)
Array comparative genomic hybridisation on first polar bodies suggests that non-disjunction is not the predominant mechanism leading to aneuploidy in humans.
in Journal of medical genetics
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
Griffin D
(2008)
Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution
in BMC Genomics
Griffin DK
(2015)
20th International Chromosome Conference (ICCXX) : 50th Anniversary, University of Kent, Canterbury, 1st-4th September 2014.
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
Griffin DK
(2017)
Continuing to deliver: the evidence base for pre-implantation genetic screening.
in BMJ (Clinical research ed.)
Handyside AH
(2010)
Karyomapping: a universal method for genome wide analysis of genetic disease based on mapping crossovers between parental haplotypes.
in Journal of medical genetics
Ioannou D
(2016)
Impact of sperm DNA chromatin in the clinic.
in Journal of assisted reproduction and genetics
Ioannou D
(2011)
Male fertility, chromosome abnormalities, and nuclear organization.
in Cytogenetic and genome research
Ioannou D
(2011)
Nuclear organisation of sperm remains remarkably unaffected in the presence of defective spermatogenesis.
in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology
McCallie BR
(2016)
Hypomethylation and Genetic Instability in Monosomy Blastocysts May Contribute to Decreased Implantation Potential.
in PloS one
Ottolini CS
(2015)
Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates.
in Nature genetics
Ottolini CS
(2015)
Karyomapping identifies second polar body DNA persisting to the blastocyst stage: implications for embryo biopsy.
in Reproductive biomedicine online
Parks JC
(2016)
Corona cell RNA sequencing from individual oocytes revealed transcripts and pathways linked to euploid oocyte competence and live birth.
in Reproductive biomedicine online
| 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 |
| 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 | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| 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 |
| 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 Inc. |
| Department | Illumina |
| Country | United Kingdom |
| 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 |
| 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 |
| 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 |
| Sector | Academic/University |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |