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Final Report Summary - INTERCROSSING (Innotive Training Environment for Researchers Combining the Resources of Statistical Science, Informatics & Genetics)

The INTERCROSSING project has received funding from the EU's 7th Framework Programme for research, technological development and demonstration under grant agreement no.289974.
THE ADDRESS OF THE PROJECT PUBLIC WEBSITE http://intercrossing.wikispaces.com/
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SUMMARY DESCRIPTION OF THE PROJECT OBJECTIVES
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The principal strategic objective of INTERCROSSING was the cultivation of a new type of early stage researcher (ESR) to deal with challenges of exploiting the latest Next Generation Sequencing (NGS) technologies. Each ESR received rigorous training in three disciplines hardly ever found together any one young scientist: i) population genetics, ii) informatics and iii) statistics. The OVERARCHING OBJECTIVE of the project was to provide TRAINING COURSES so that ESRs, recruited with a background in one of the three disciplines, would develop expertise across the full range, and to provide TRAINING BY RESEARCH, and INTER-SECTORIAL research experience. Research training took place in seven sub-projects pairing a university with an SME/museum. The objective was to overcome a barrier to progress identified by the latter. The ESRs worked alongside each other in reciprocal placements – giving each ESR experience of research in two sectors. The topics span from medicine to agriculture, and from genomics to epigenetics.

THE WORK PERFORMED SINCE THE BEGINNING OF THE PROJECT
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The consortium appointed 13 Early Stage researchers, employed for 3 years each with PhD-level training. The team was 6 female ESRs and 7 male, originating from 5 EU countries and 4 others.

All the planned training courses were successfully delivered, plus 2 extra proposed by the ESRs:
INTERCROSSING ESR START WORKSHOP (QMUL 9-12 Dec. 2012). Training on team building, 'Your Project and Entrepreneurship', ESRs personal development plans started. The ESRs initiated their committees.
STRATEGY WORKSHOP & CONFERENCE (Giessen/Munich 24-28 Feb. 2013). Modern agriculture, plant breeding and genomics, workshop on NGS-based transcriptomics. Modern multivariate statistics and QTL analysis in R.
HORIZON-SCAN WORKSHOP (CLC Aarhus 15 June 2013). NGS data analysis in the CLC workbench, Perl scripting and Software development, industry perspective on career objectives and recruitment . Outreach: ESRs posted videos as part of the ESRs journal http://goo.gl/HmMXRp .
CLOUD COMPUTING TRAINING (GRANADA Era7 26-30 Aug. 2013). Cloud computing for bioinformatics, advanced management of Cloud computing projects and stateless parallel computation in the cloud. Group projects, analysing data from a disease outbreak.
MOLECULAR POPULATION GENETICS (VIENNA 21-26 Oct. 2013). ESR initiative: all joined the Vienna Graduate School of Population Genetics, plus network-strengthening session in which each ESR identified software or support they could provide to other members of the network.
MID-TERM MEETING AND WORKSHOPS (GRENOBLE 24-28 March 2014). Formal mid-term review plus ESR training on Bayesian inference and model-based analysis.
PUBLIC COMMUNICATION & PUBLICATION PLANNING (NHM, London 8-15 Oct. 2014)
Modelling species distributions and Science communication (with press, scientific and general public). Outreach: the ESRs’ presentations, delivered jointly with the Museum’s professional interlocutors between scientists & public).
ACHIEVEMENTS CONFERENCE AND WORKSHOP ON EUROPEAN POLICY AND CAREER PLANNING (26 April - 02 May 2015, Bayer CropScience Ghent).
Courses on career planning, entrepreneurship and the future of European research. ESRs presented their achievements to three invited experts, followed by 2 days of reciprocal presentations at Bayer.
ESR CAREER-PLANNING FOLLOW-UP (4 Nov. 2015, QMUL video-conferencing studio). The ESR committee implemented a virtual event following up the career training session (at Ghent)

MAIN RESULTS & ACHIEVEMENTS
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Each subproject (A1-A7: pairings of university with an SME/museum) met their milestones: completing the inter-sectorial placements, presenting reports on time (Milestones 1-4), and publication plans (5) and achievements (6) to the relevant meetings (NHM London & Ghent).

RESULTS & ACHIEVEMENTS BY SUBPROJECT
A1 (Era7, Granada; JF University, Grenoble) The ESRs collaborated on resources for gene-set enrichment for key pathways, released as OLOPath.db. Kovach also released obe.SNP for obesity-related genomic information, plus two packages now in use by Era7. Vatsiou published 3 papers on detecting selection, including evidence of positive selection on human metabolic pathways.

A2 (PopGenTech & Eagle Genomic Cambridge; JF University Grenoble) Kulkarni, the 2nd JFU ESR, released the VirEst pipeline developed with the industrial partners to analyse viral sequence, and published a paper on the analysis of hepatitis C sequence to detect drug-resistance mutations.

A3 (CLCbio, Aarhus; QMUL University London) The ESRs collaborated to assemble, annotate and release the first draft of the Ash Genome. Zohren has released a tool for genotyping polyploids and a paper on introgression in the birch tree genome. Sollars has released a pipeline for polyploid genome analysis and published a paper on genomic markers for ash dieback tolerance.

A4 (NPZ & JMU Giessen; QMUL University of London) The combination of practical work at NPZ/JMU with analysis at QMUL led to the release of miRcounts, software for quantifying miRNA expression (Hatlen), a thesis on genomic prediction in oilseed rape, and a paper on the effects of population subdivision (Jan). Hatlen also published a phylogenetic analysis of epigenetic pathways.

A5 (NHM_London; University of Vienna) The ESRs jointly studied the bluebell hybrid zone and released introgression-analysis tools in R. Marquart has released MarkerDev, a workflow to develop markers for such analyses from RNAseq data, published a note on hybridisation and a paper on genome size. Blanckaert published a paper on intra genomic interactions and genetic load.

A6 (Genetwister, Wageningen; LMU University, Munich) The ESRs worked together to overcome the challenge of developing Bioinformatic Tools for Polyploid Crops, of interest to the commercial partner. They have published a joint paper on the tools. Grandke has released an R package PERGOLA for linkage mapping in polyploids, and Raganathan has released Polyphase, a complementary polyploid haplotyping method with an R-interface for phase-validation.

A7 (Era7, Granada; LMU University, Munich) The ESRs worked on the development and deployment of bespoke Era7 packages to the statistical correlation of key allele frequencies with environmental variables, an approach used in Bozicevic's paper on adaptation of flies to different climates. Alekhin has released Nispero, bioinformatics cloud computation tool, Metapasta, a tool for 16S metagenomics analysis and published a paper on Bacteria Genome Annotation.

THE EXPECTED FINAL RESULTS AND THEIR POTENTIAL IMPACT AND USE
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The explicit main objective of INTERCROSSING to produce young researchers with a rarely-found set of interdisciplinary training. One clear measure of impact is that over half of the ESRs have already been successful in job applications across two sectors: three in commercial/applied research (Elekhin, Era7 software engineer; Kovach, Zalando retail informatics; Sollars, NHS diagnostic bioinformatics), five in bioinformatics/genetics at research institutes or universities (Blanckaert, Gulbenkian Inst.; Grandke, Giessen Uni; Hatlen, Essex Uni, Vatsiou, Inst. of Cancer Research, Zohren, Crick Inst.). The others have just graduated (Jan) or are writing up PhD theses. In a more informal validation of the repertoire of INTERCROSSING training, one of the successful candidates was told at interview 'with your combination of skills you could walk into a bioinformatics job anywhere in the country'.
The main results have been outlined above by project, in summary the project has so far produced 16 publications 18 instances of foreground which have been publicly distributed (GNU/MIT/open commons/AGPLv3 licenses). The publication plans indicate a doubling of outputs over the next three years. Highlights of the current impact are the suite of bioinformatics resources that are in day-to day use at the commercial partners (above) and the assembly and annotation Ash Genome (http://www.ashgenome.org/tools) which will continue to be used to be used as an online resource in the battle against the emergent ash dieback disease.

Contact

Richard Alan Nichols, (Director of Research)
Tel.: +44 207 882 3055
E-mail
Record Number: 191424 / Last updated on: 2016-11-10
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