en News - BIOINFORMATICS BARCELONA News Mon, 23 Apr 2018 12:12:38 +0000 Mon, 23 Apr 2018 12:12:38 +0000 Houdini 2 (http://houdini.antaviana.cat/) http://www.bioinformaticsbarcelona.eu/news The 3rd European Conference on Translational Bioinformatics brings together more than 130 experts

The 3rd European Conference on Translational Bioinformatics (ECTB2018) was held on April 16th-17th at the premises of the Barcelona Biomedical Research Park (PRBB) with the attendance of more than 130 European scientists, developers and entrepreneurs, interested in translating genomics and bioinformatics research into healthcare tools and services. The conference aimed to give the participants a unique experience and a forum for discussing fresh scientific results in the translational domain.

The conference brought together world-leading scientists in the area which highlighted on their presentations the recent advances in information technologies that are facilitating translational research and precision medicine. Some of the topics addressed were Big Data integration and analysis, Personalized Medicine, Genome Sequencing initiatives, etc, delivered by scientists from Europe, Canada and the USA. 

It also had a poster session organised to give participants the opportunity to present individual papers and a round table led by Ferran Sanz, co-chair of the event, to discuss about the main challenges that bioinformatics has to overcome, including the opportunities of the industry in this field.

In his closing remarks, Alfonso Valencia, co-chair of the event, expressed gratitude to all who made the event possible and announced that the 4th European Conference on Translational Bioinformatics will take place next year in Sevilla.

The Conference was organized by the Research Programme on Biomedical Informatics (GRIBIMIM-DCEXS-UPF) and the Barcelona Supercomputing Center (BSC). It was supported by the H2020 MedBioinformatics project coordinated by the GRIB and the INB/ELIXIR-ES project.

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Mon, 23 Apr 2018 12:12:38 +0000 http://www.bioinformaticsbarcelona.eu/news//news/107/the-3rd-european-conference-on-translational-bioinformatics-brings-together-more-than-130-experts http://www.bioinformaticsbarcelona.eu/news/107 0
First internal workshop of the Interuniversitary Doctorate Program in Bioinformatics

The Doctorate Program in Bioinformatics, involving UAB, UPC, UdG, UdL, UOC and UVic-UCC and promoted by the BIB, had its first internal workshop at Casa de Convalescència on April 4th 2018.

A new registration period is open until May 15th, with notification of admission in the first half of June. The registration can be formalized online through any of the participant universities, and you can find all the information in the corresponding web pages: UAB, UPC, UdG, UdL, UOC, UVic-UCC.

You may contact Xavier Daura (xavier.daura@uab.cat) for any additional questions.
 

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Fri, 20 Apr 2018 10:56:15 +0000 http://www.bioinformaticsbarcelona.eu/news//news/105/first-internal-workshop-of-the-interuniversitary-doctorate-program-in-bioinformatics http://www.bioinformaticsbarcelona.eu/news/105 0
Young BSC researcher is co-first author of two PanCancer Atlas articles

The prestigious scientific journal Cell has published a monograph of 26 articles dedicated to the PanCancer Atlas project, a research programme financed by the United States National Institutes of Health (NIH) in which nearly 1,000 scientists from around the world studied 33 types of cancer using genomic data from 11,000 patients.

Among these scientists is Eduard Porta, a researcher currently based in the life sciences department at Barcelona Supercomputing Center (BSC), who is the co-first author of two of the papers and who contributed to a third. Porta began his participation in the project as a postdoctoral research associate at SBP Medical Research Institute and continued working on it after joining BSC in May 2017. Eduard's work has been funded by a Beatriu de Pinós fellowship. He has also recently obtained Junior Leader grant from the Obra Social la Caixa, the not-for-profit arm of CaixaBank, which will allow him to continue in this line of research at BSC.

In one of the papers in which he is named as co-first author, Porta publishes the most up-to-date list of the 299 genes involved in the development of cancer, including 59 genes that have been linked to cancer for the first time.

"This list of cancer genes was obtained thanks to the systematic application of the top bioinformatics tools, providing us with the most comprehensive study undertaken to date. In addition, in this project we used 12 other bioinformatics tools to identify around 3,200 mutations as those most likely to cause the development of tumours. All this new information provides greater precision when suggesting specific therapies for each patient," explains Eduard Porta.

In the second publication where Porta is named as co-first author, the BSC researcher goes into further depth on the role of these genes in certain immune responses of the organism in fighting tumours and suggests routes towards the use of personalised immunology therapies.

"We have seen that the immune system has six main different types of response against tumours. These responses are, to a certain extent, independent of the type of cancer. We have also shown that some specific cancer genes are associated with a specific type of immune response. This information will allow new drug combinations to be put forward which, by attacking these genes, could prompt the patient's immune system to attack cancerous cells," Porta concludes.

Expanding the study of cancer

In October 2013, researchers involved in the creation of The Cancer Genome Atlas (TCGA) published the first 'pancancer' analysis, in which the cell and genome patterns of 12 different cancers were identified. Building on the success of this programme, in 2016 it was agreed to expand the study and include additional genomic information, such as ADN mutations, epigenetic data and gene expression data obtained systematically for 33 different cancers in 11,000 oncology patients.

The publication of this article series completes the second phase of the PanCancer Atlas project, concluding with the identification of genetic patterns providing a unified view of the commonalities and differences of the myriad types of cancer analysed. This information is the foundation for the development of strategies in personalized medicine, in which treatments are adapted to the genetic characteristics of each patient.

About Eduard Porta

Having obtained his PhD in bioinformatics from the University of Barcelona, Eduard Porta spent four years as a postdoctoral research associate at the Sanford Burnham Prebys Medical Discovery Institute under Adam Godzik, director of the centre's Bioinformatics and Biology Systems Programme. During this time, he began working on the PanCancer Atlas project. Thanks to a Beatriu de Pinós postdoctoral grant, he joined BSC in May 2017 to continue participating in this project, as part of which he has contributed to various publications, including two as first author of the consortium. Porta has also been awarded a 'Junior Leader' grant by the Obra Social de la Caixa, the not-for-profit arm of CaixaBank, which is reserved for postdoctoral researchers at the most prestigious Spanish research centres.

Authors

Along with the BSC, other leading institutions around the world have contributed to this programme, including the SBP Medical Discovery Institute, the Washington University St. Louis, the Johns Hopkins University, the BROAD Institute, the Institute for Systems Biology and the MD Anderson Cancer Center among others.

This manuscript is part of The Cancer Genome Atlas (TCGA) Program, a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI).

Reference of the study

For the article Comprehensive Characterization of Cancer Driver Genes and Mutations

Matthew H. Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta,Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C. Wendl, Jaegil Kim, Brendan Reardon, Patrick Kwok-Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, Jianjiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio-Perez, Niranjan Nagarajan, Isidro Cortés-Ciriano, Daniel Cui Zhou, Wen-Wei Liang, Julian M. Hess, Venkata D. Yellapantula, David Tamborero, Abel Gonzalez-Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J. Park, Eliezer M. Van Allen, Han Liang, The MC3 Working Group, The Ccer Genome Atlas Research Network, Michael S. Lawrence, Aam Godzik, Nuria Lopez-Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J. Lazar, Gordon B. Mills, Rachel Karchin and Li Ding.

DOI: 10.1016/j.cell.2018.02.060

For the article Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Li Ding, Matthew H. Bailey, Eduard Porta-Pardo, Vesteinn Thorsson, Antonio Colaprico, Denis Bertrand, David L. Gibbs, Amila Weerasinghe, Kuan-lin Huang, Collin Tokheim, Isidro Cortés-Ciriano, Reyka Jayasinghe, Feng Chen, Lihua Yu, Sam Sun, Catharina Olsen, Jaegil Kim, Alison M. Taylor, Andrew D. Cherniack, Rehan Akbani, Chayaporn Suphavilai, Niranjan Nagarajan, Joshua M. Stuart, Gordon B. Mills, Matthew A. Wyczalkowski, Benjamin G. Vincent, Carolyn M. Hutter, Jean Claude Zenklusen, Katherine A. Hoadley, Michael C. Wendl, llya Shmulevich, Alexander J. Lazar, David Wheeler, Gad Getz and The Cancer Genome Atlas Research Network.

DOI: 10.1016/j.cell.2018.03.033

For the article The Immune Landscape of Cancer

Vésteinn Thorsson, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen Gao, Christopher L. Plaisier, James A. Eddy, Elad Ziv, Aedin C. Culhane, Evan O. Paull, I.K. Ashok Sivakumar, Andrew J. Gentles, Raunaq Malhotra, Farshad Farshidfar, Antonio Colaprico, Joel S. Parker, Lisle E. Mose, Nam Sy Vo, Jianfang Liu, Yuexin Liu, Janet Rader, Varsha Dhankani, Sheila M. Reynolds, Reanne Bowlby, Andrea Califano, Andrew D. Cherniack, Dimitris Anastassiou, Davide Bedognetti, Arvind Rao, Ken Chen, Alexander Krasnitz, Hai Hu, Tathiane M. Malta, Houtan Noushmehr, Chandra Sekhar Pedamallu, Susan Bullman, Akinyemi I. Ojesina, Andrew Lamb, Wanding Zhou, Hui Shen, Toni K. Choueiri, John N. Weinstein, Justin Guinney, Joel Saltz, Robert A. Holt, Charles E. Rabkin, The Cancer Genome Atlas Research Network, Alex J. Lazar, Jonathan S. Serody, Elizabeth G. Demicco, Mary L. Disis, Benjamin G. Vincent and llya Shmulevich.

DOI: 10.1016/j.immuni.2018.03.023

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Fri, 06 Apr 2018 09:07:52 +0000 http://www.bioinformaticsbarcelona.eu/news//news/103/young-bsc-researcher-is-co-first-author-of-two-pancancer-atlas-articles http://www.bioinformaticsbarcelona.eu/news/103 0
I FORUM BIB - "Bioinformatics: solutions to complex challenges"

 

 

 

Since its creation, BIB has become the meeting point in the field of bioinformatics, promoting and stimulating different initiatives:

  • Creating quality education and training programmes responding to the sector needs
  • Stimulating the research and knowledge transfer among different stakeholders
  • Boosting the industrial sector through competitiveness and innovation
  • Giving visibility to the sector, both nationally and internationally
  • Favouring internal and external collaboration with the involved actors
     

On Wednesday, October 24, Bioinformatics Barcelona organizes the first Forum BIB, under the theme of "Bioinformatics: solutions to complex challenges" with the aim of highlighting the role of Bioinformatics in the fields of health and agri-food, and showing the successes achieved in the ecosystem through BIB since its creation.


The conference will include the most relevant speakers in the Bioinformatics field, as well as Bioinsformatics Barcelona partners (universities, research centres, hospital research institutes, large scientific infrastructures, companies, start ups, etc.). Through them, some of the Bioinformatics applications will be addressed, cases of success in the ecosystem will be showed, and the conclusions of the BIB working groups will be presented.


Ana Ripoll
BIB President

 

I FORUM BIB - "Bioinformatics: solutions to complex challenges"
When: Wednesday October 24, 2018
Where: CosmoCaixa Barcelona (c/ Isaac Newton, 26, Barcelona)
Spread the word: #ForumBIB

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Wed, 21 Mar 2018 11:21:44 +0000 http://www.bioinformaticsbarcelona.eu/news//news/101/i-forum-bib-bioinformatics-solutions-to-complex-challenges http://www.bioinformaticsbarcelona.eu/news/101 0
New portal allows users to navigate thousands of data on human genetic diversity

The international project 1000 genomes provides information on 2504 complete genomic sequences from 26 populations around the world. It is the most extensive global human genetic variation data set to date, with more than 84 million genetic differences catalogued. In order to make this information available and help with navigating through such a large amount of data, researchers from the Bioinformatics of Genomic Diversity group at the Universitat Autònoma de Barcelona (UAB), in collaboration with scientists from the Institute of Evolutionary Biology (IBE), a centre belonging to the CSIC and the Pompeu Fabra University (UPF), created the PopHuman browser, the largest available inventory of measures of genetic diversity along the human genome. This resource allows the exhaustive search of episodes of natural selection which have taken place in the human lineage and have left their print on the genome.

Human genetic variation is the set of genetic differences which distinguish our genomes, either among individuals within a population or between populations. There are no two genetically identical humans. On average, each of us is more than 99% genetically identical to any other person, while the less than 1% of genetic variants distinguishing our genomes are present in different frequencies in different human populations. The geographically and ancestrally more distant populations tend to differ more, although it is the differences between individuals within populations, especially in the African ones, the most important quantitatively in the set of the human genetic variation.

The study of the human genetic variation has significant evolutionary and medical applications. It has allowed to determine the origin of humanity in sub-Saharan Africa hundreds of thousands of years ago and subsequent human migrations, and it also helps in understanding how certain genetic variants have contributed to the adaptation of human populations to their environment in the whole planet. The description and explanation of the evolutionary forces controlling human genetic variation within and between populations is thus a fundamental goal of population genetics.

In an article published recently in the prestigious journal Nucleic Acids Research, the UAB and IBE researchers presented an exhaustive inventory of genetic diversity measures along the human genome from the data of the project 1000 genomes. This inventory captures the evolutionary properties of the sequences, and it is available to researchers through the PopHuman genome browser, an online portal allowing users to navigate the results through a graphical interface. PopHuman offers the most complete catalogue of estimates of human genetic variation so far in terms of number of genomes and populations analysed, and incorporates the genetic changes between the human and the chimpanzee genomes. 

In this way, PopHuman allows to detect from relatively recent selective episodes, such as those related to the establishment of agriculture in European and Asian populations some 10,000 years ago, to older episodes which have recurrently occurred throughout the past million years, such as the one observed in the region of the PRM1 gene, involved in the compaction of sperm DNA. Researchers are convinced that PopHuman will become the starting point for any exhaustive analysis of the different selective episodes which have taken place in the human lineage and have left their mark on the genome.

 

Contact researchers:

Sònia Casillas and Antonio Barbadilla
Institute of Biotechnology and Biomedicine (IBB)
Department of Genetics and Microbiology
Universitat Autònoma de Barcelona (UAB)
Tel: +34 93 586 8958
sonia.casillas@uab.cat
 

Original article:

Sònia Casillas, Roger Mulet, Pablo Villegas-Mirón, Sergi Hervas, Esteve Sanz, Daniel Velasco, Jaume Bertranpetit, Hafid Laayouni, Antonio Barbadilla. "PopHuman: the human population genomics browser." 2018. Nucleic Acids Research, 46(D1):D1003-D1010. https://doi.org/10.1093/nar/gkx943. Impact Factor: 10.162.

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Thu, 08 Feb 2018 11:01:24 +0000 http://www.bioinformaticsbarcelona.eu/news//news/97/new-portal-allows-users-to-navigate-thousands-of-data-on-human-genetic-diversity http://www.bioinformaticsbarcelona.eu/news/97 0
Bioinformatics firm Mind the Byte acquires Intelligent Pharma

Bioinformatics firm Mind the Byte, a pioneer in the development of technologies based on artificial intelligence, cloud and big data for computational drug design, has acquired 100% of Intelligent Pharma, one of the leaders in Spain in chemoinformatics services for the pharmaceutical and biotechnology industry.

Since they were established in 2011 and 2007 respectively, both firms which are based in the Barcelona Science Park have managed to raise €5.8 million in public and private capital and position themselves at the forefront of the sector.

This deal is the largest corporate operation to date in the emerging Spanish bioinformatics market and makes Mind the Byte the leading company in Spain and one of the largest companies in Europe in artificial intelligence applied to medicine discovery and development.

The terms of the agreement have not yet been made public but they include one part in cash and the other as a share swap. Mind the Byte is to finance the integration and growth of both firms with a capital increase, the third in its history, coming to €3 million.

"This transaction is part of Mind the Byte's business plan for the company's growth and internationalisation through strategic acquisitions," said Alfons Nonell-Canals, founder and CEO of the company. "The integration of Intelligent Pharma will mean we can benefit from its valuable network of contacts, equipment, technology and offices while also increasing our market share straight away. Our forecast for 2019 is to reach €2 million in turnover."

Mind the Byte, an Amazon Web Services technology partner since 2013, delivers its technology through a SaaS (Software as a Service) platform and high added value scientific services. In 2015 it opened its first European subsidiary in the Copenhagen Bio Science Park (Denmark) while in 2016 it moved into the Japanese market with local firm Filgen where it expects to achieve €1.2 million in turnover by 2020.

The acquisition of Intelligent Pharma, which has offices in Munich and Heidelberg (Germany), London (United Kingdom) and Alberta (Canada) and clients in over 20 countries worldwide, will enable the Catalan bioinformatics firm to expand its local and global footprint while also extending its range of services and speeding up its product innovation in the geographical areas where it has a presence.

"The integration will allow us to round off our portfolio of tools for designing drugs with the knowhow built up by Intelligent Pharma over more than 10 years in the market and technologies which add to those of Mind the Byte, something that will be very handy when it comes to enhancing our line of business," affirmed Nonell-Canals.


An emerging market with great potential

Bioinformatics is an emerging science in which computer science and information technology are applied to processing biological data. Chemoinformatics used for drug discovery is a key technology in this strategic area and one of the essential tools for R&D in the pharmaceutical industry since it enables reducing the time and cost of drug discovery and shortening the time to market for new medicines.

 "It can take 10 or 15 years and extremely long-term investment coming to hundreds of millions of euro to develop a drug," pointed out Nonell-Canals.  "With the help of bioinformatics, we can help cut that time, and the cost and risk of investment by streamlining the molecule discovery phase. Moreover, under our recent agreement with the Swedish firm Prosilico, we now also advise companies in the preclinical studies phase."

Data in the most recent report by international consultants Transparency Market Research (TMR) show that the world bioinformatics market is growing exponentially and the $2.3 billion valuation in 2012 is expected to reach $9.1 billion by the end of 2018.

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Tue, 16 Jan 2018 12:23:49 +0000 http://www.bioinformaticsbarcelona.eu/news//news/95/bioinformatics-firm-mind-the-byte-acquires-intelligent-pharma http://www.bioinformaticsbarcelona.eu/news/95 0
Genes identified that distinguish mammals from other animals

What distinguishes Homo sapiens from other living beings? And the group of mammals? What makes them different? These are the questions that researchers from GRIB (IMIM-UPF) together with researchers of the Department of Experimental and Health Sciences from the UPF have been trying to answer. To do this, they analysed the already-sequenced genomes of 68 mammals and identified 6,000 families of genes that are only found in these animals. These are genes with no homologues outside mammals, in other words, they are not present in other hairless species. In humans, it is estimated that they represent 2.5% of the genes that code for proteins. The work was led by Dr. José Luis Villanueva-Cañas, a member of the Evolutionary Genomics group of GRIB and currently a researcher at the Evolutionary Biology Institute (UPF-CSIC), and Dr. Mar Albà, ICREA researcher and head of the Evolutionay Genomics group of GRIB. The study also involved Dr. David Andreu's group from the UPF. It has been published in the journal Genome Biology and Evolution.

Dr. Villanueva-Cañas explains that the aim of the work was to "understand which genes define mammals as a class, in other words, which genes are only found in this group". To do this, he designed a set of programs that made it possible to compare the genomes of 68 mammals. These included Homo sapiens, as well as other primates and representatives of the main orders of this class of animals, including the Iberian lynx. With this data he generated a catalogue of genes exclusive to the mammals, of around 6,000 families of genes. At the same time, he assigned them a possible age of origin according to the species in which they are present. He also tried to figure out what these genes do, using expression data (RNA sequencing) from different tissues, to see where and how they are expressed, and proteomic data to check if they are translated, in other words, produce proteins.

Some of these genes have a de novo origin, and do not come from the duplication of pre-existing genes. De novo genes are important for acquiring new functions during evolution, as was demonstrated by another study led by Dr. Albà (Origins of de novo genes in human and chimpanzee, published in Plos Genetics). The new study has managed to identify the functions of some of these genes, related to how the skin is structured and why it is different from that of, for example, reptiles, as well as other genes involved in the mammary glands characteristic of mammals. They have also identified antimicrobial peptides, which participate in the body's defence against pathogens.

The researchers also stress that the genes they have found are short and usually only expressed in one, or just a few tissues. Dr. Albà wants to highlight that "Studies like this help us understand how new genes form during evolution and whether they play an important role in the adaptation of organisms to their environment". For this reason, "cataloguing mammal genes is the first step in understanding their functions" and "brings us closer to defining a set of pieces that originated at the start of their evolution and which are common to all of them, or some of their subgroups". Dr. Villanueva-Cañas explains that "We still we do not know the function of an important part of our genes, so it is necessary to make an effort to characterise them." This is the case of one that was identified during the study (neuronatin), which plays a so-far-unknown role in brain development.

Reference article: Villanueva-Cañas JL, Ruiz-Orera J, Agea MI, Gallo M, Andreu D; Alba MM. New Genes and Functional Innovation in Mammals. Genome Biology and Evolution, 2017; 9, 1886-1900. DOI: 10.1093/gbe/evx136

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Tue, 05 Dec 2017 11:04:24 +0000 http://www.bioinformaticsbarcelona.eu/news//news/93/genes-identified-that-distinguish-mammals-from-other-animals http://www.bioinformaticsbarcelona.eu/news/93 0
Mind the Byte and Prosilico sign a strategic partnership agreement
  • Together, the two companies will provide a broad portfolio of in silico models covering most aspects of virtual drug discovery and development.
  • Prosilico software will now be included in Mind the Byte's SaaS platform and both firms will promote each other's technologies.
  • This agreement fits with Mind the Byte's plans to expand internationally through strategic alliances and increase its range of services.

Mind the Byte, a bioinformatics company located at the Barcelona Science Park (PCB) and at Copenhagen BioScience Park (COBIS), announces that it has just signed an agreement to share technology with the Swedish-based company Prosilico. Within this partnership, Mind the Byte adds to its in silico drug discovery platform the capacity of doing some virtual predictions of human clinical ADME/PK and covers now a wider range of expertise and know-how.

The platform, which uses Cloud Computing, already allows studying the mechanism of action of drugs and conducting computational screenings for hit finding or drug repurposing. Now, it will be complemented with some Prosilico tools to predict relevant human in vivo ADME/PK properties in models independently validated by pharma companies.

The CEO of Mind the Byte Alfons Nonell-Canals says, "We have selected Prosilico as a partner because they have been able to utilize human clinical data to develop predictive models covering a wide range of ADME/PK applications and diminishing a lot of the otherwise common in vitro and in vivo experiments."

"Prosilico founding partners have documented their innovative work by a number of publications over the years and they bring a long big pharma experience from AstraZenca which makes Prosilico a very attractive partner for us," says Thomas Högberg, Chief Strategic Officer also from Mind the Byte.

On the other side, the CEO of Prosilico, Urban Fagerholm, concludes, "Mind the Byte is at the forefront of computational drug discovery providing a unique Software as a Service platform allowing also midsize pharma, biotechs and institutions an affordable and flexible access to High Performance Computing. We hope that being on this platform will advance the use of our human-based in silico ADME/PK tools and we look forward to the collaboration."

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Thu, 30 Nov 2017 12:13:02 +0000 http://www.bioinformaticsbarcelona.eu/news//news/91/mind-the-byte-and-prosilico-sign-a-strategic-partnership-agreement http://www.bioinformaticsbarcelona.eu/news/91 0
Genomics prepares to jump to three dimensions

Genomics is one of the most rapidly evolving areas of biology. Over the last 15 years, the challenge of biologists has been to obtain the sequence of genes (one-dimensional information) in order to understand, for example, how changes in DNA fragments give rise to disease. "The great number of 1D genomics studies over the years has shown that the analysis of gene sequences, although providing important information, is not enough to understand the origin of complex diseases. Connections remain hidden and this is probably because they depend on a 3D signal that determines how genes are folded within the nucleus, and how and when they are made accessible to the cell," explains Modesto Orozco, a world expert in 3D genomics and head of the Bioinformatics and Molecular Modelling Lab at the Institute for Research in Biomedicine (IRB Barcelona).

Modesto Orozco, also Professor at the University of Barcelona, is co-organizing the Barcelona BioMed Conference: "Multidimensional Genomics: The 3D/4D organization of chromatin" together with Marc Martí-Renom from the CNAG/CRG in Barcelona and Giacomo Cavalli from the Institut de Génétique Humain/CNRS in France. The event, which begins today and runs until 15 November, will gather 20 world experts in 3D genomics from the US and Europe at the Institut d'Estudis Catalans in Barcelona. The initiative is organized by the Institute for Research in Biomedicine (IRB Barcelona) with the collaboration of the BBVA Foundation.

"Google Earth" applied to genomics

The invited speakers and 150 attendees share a common goal: to move from a one-dimensional vision of the genome to understand how chromatin, the DNA inside the cell's nucleus, is folded and how the structure of this folding can offer insight into how DNA works. "What we are shooting for is a sort of "Google Earth" applied to genomics," Orozco describes graphically. "A platform where we can see the two metres of the folded DNA molecule, and at the same time zoom in to atomic detail on a region that interests us in order to see the changes accumulated over time - 4D- due to external conditions, or to needs of the cells," he explains.

Is 3D/4D genomics a reality?

3D/4D genomics is a reality, although it is still at a very basic level of scientific research, far from clinical application, with several initiatives underway in the US and Europe. Within Europe, the three conference co-organizers are leading a Horizon 2020 project that aims to standardize the way in which 3D genomics projects are conducted, and how data are stored and exploited.

They aim to create a package of protocols, methodologies and processes that put order in a field that so far has none. "Techniques for 3D genomics are very new and there are gaps in how we process data, and this causes a sense of fragility, especially because results are difficult to reproduce," explains Orozco, coordinator of the European project.

During the conference, the developments made so far in the MuG (Multiscale Complex Genomics*) platform will be presented in a dedicated practical session with 70 participants. "The Barcelona BioMed Conference is a great opportunity to launch the platform internationally. It is based on a disruptive technology that allows scientists to connect to the platform from anywhere in the world and process their genomic data, switching very easily from one technique to another, with higher or lower resolution," describes Orozco.

For scientists, 3D genomic promises to afford a leap forward in personalized medicine and the treatment of diseases. "We are still far from using 3D genomics in applications for patients, but we will get there. Advances in this field will allow us to understand how the genome really works and how it is regulated, how we can impact this regulation, and the hidden reasons behind several diseases that today we simply can't understand," concludes the scientist.

"MuG has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 676556"

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Fri, 17 Nov 2017 12:17:34 +0000 http://www.bioinformaticsbarcelona.eu/news//news/89/genomics-prepares-to-jump-to-three-dimensions http://www.bioinformaticsbarcelona.eu/news/89 0
The “DNA corrector” is more efficient in the most important regions of the genome

Error surveillance and repair mechanisms during DNA replication do not show the same competence in all regions of the human genome. Scientists headed by ICREA researcher Núria López-Bigas at the Institute for Research in Biomedicine (IRB Barcelona) reveal that the mechanism that repairs errors in DNA is more efficient in the regions of genes that hold information for the production of proteins.

The basic structure of genes is divided into exons and introns. The former hold the genetic sequences required to synthesise proteins, while most of the sequence of the latter hold less important information. Exons do not vary much between species, that is to say, they are similar between humans, mice and worms, for example. The accepted scientific explanation for this similarity is that exons are critical regions for the viability of an organism and therefore many mutations lead to lethal phenotypes and are therefore not observed.

"Negative selection is a key factor responsible for conserving exons between species, but we now know it is not the only factor. We demonstrate for the first time that exons hold fewer mutations than other regions because these regions are repaired more effectively" explains Núria López-Bigas, head of the Biomedical Genomics lab.

When DNA is copied, the molecule called polymerase-responsible for replication-places one nucleotide after the other in the sister sequence following the original sequence, but from time to time the wrong nucleotide is incorporated, thus causing an error. These errors can be corrected by the DNA mismatch repair machinery.

The researchers analysed colorectal tumours in which the polymerase carries a mutation, converting it to an error-prone polymerase. For this reason, these tumours contain a large number of mutations. By comparing the proportion of mutations in exons and introns, these scientists revealed that the former carry far fewer than what would be expected.

So they then went on to study the genomes of a type of paediatric brain cancer characterised not only by a mutated polymerase-like in the tumours previously examined-but also by an inactivated repair system. They observed that the number of mutations in the exons of these tumours was as high as that expected.

"The repair mechanism ensures that mutations do not accumulate in the genome, particularly in exons," explains Joan Frigola, PhD student and first author of the article together with postdoc Sabarinathan Radhakrishnan.

The scientists now have a clue as to the mechanism that makes the repair machinery in exons more efficient than in introns. This higher efficiency, they say, lies in exons having a very high content of a specific mark, H3K36me3, which allows greater recruitment of repair proteins to exons, thus making the repair process more efficient.

"Our repair machinery "knows" that it must focus on the most important regions of the genome. This point should be taken into consideration when studying DNA mutation and repair processes and in studies on evolution, whether in tumours or species," López-Bigas says.

The lab headed by López-Bigas began this research at the Pompeu Fabra University and completed it at IRB Barcelona. The study has been funded by the European Research Council (ERC), the UE's H2020 Programme, the Ministry of Economy and Competitiveness/European Regional Development Funds, and the Fundació La Marató de TV3.

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Thu, 16 Nov 2017 14:14:15 +0000 http://www.bioinformaticsbarcelona.eu/news//news/87/the-dna-corrector-is-more-efficient-in-the-most-important-regions-of-the-genome http://www.bioinformaticsbarcelona.eu/news/87 0