International Human Epigenome Consortium

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The International Human Epigenome Consortium (IHEC) is a scientific organization, founded in 2010, that helps to coordinate global efforts in the field of Epigenomics. [1] [2] [3] [4] The initial goal was to generate at least 1,000 reference (baseline) human epigenomes from different types of normal and disease-related human cell types. [5] [6] [7]

Contents

Structure and funding

IHEC's operations are funded by its full members (national and regional scientific funding agencies), and staffed largely on a volunteer basis by scientists and other experts from participating funding agencies and epigenome mapping projects. [8]

Current IHEC Member Countries

In addition, countries and agencies supportive of IHEC goals are organizations that have not yet made a full financial contribution to the project, but whose members provide time and expertise: [22]

Oversight of IHEC is provided by an executive committee, whose members are nominated by Full Member organizations. [23] This committee works closely with an International Scientific Steering Committee, whose members are the scientific leaders of participating projects and other leaders in the field of epigenetics, as well as a Data Coordination Center. Additional expertise is contributed by workgroups composed of members of participating research projects.

IHEC interacts and coordinates its efforts with other large-scale international genomics projects, such as the International Cancer Genome Consortium (ICGC), [24] ENCODE., [25] [26] and the Global Alliance for Genomics and Health. [27] Committee and workgroup members, as well as other individuals involved in IHEC, meet annually at an event hosted by member countries on a rotating basis. [28] Most meetings are hosted in conjunction with a scientific symposium, some of which are open to non-IHEC scientists and sometimes members of the public.

Goals

The ultimate objective of IHEC is to determine how the Epigenome has shaped human populations over generations and in response to the environment. [25] [29] The first phase of IHEC's operations involves coordinating the production of at least 1,000 reference epigenomes from healthy and diseased human cells, as well as a limited number of model organisms relevant to specific human diseases. The initial focus is on cellular states including stemness, immortality, proliferation, differentiation, senescence, and stress. The reference epigenome for each sample comprises high resolution maps of DNA methylation and key regulatory histone modifications, with corresponding information about the type and expression level of all transcribed genes (protein coding as well as non-coding / small RNAs). [30] The data produced are made freely available to the research community via the IHEC Data Portal, [31] [32] European Genome-phenome Archive (EGA), [33] and other venues. [34] [25] [35]

In addition, participating research projects are engaged in developing new epigenomics and associated bioinformatics methods.

In November 2016 IHEC members from Canada, the European Union's BLUEPRINT Consortium, the German Epigenome Program “DEEP”, Japan, Singapore, and the United States published a group of 41 coordinated papers in Cell Press and other journals. [36] [37] [38] [39] The papers included descriptions of molecular biology and computational methods as well as new research on normal and disease biology. [40] [41] [42] [43]

See also

Related Research Articles

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An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome can result in changes to the structure of chromatin and changes to the function of the genome.

<span class="mw-page-title-main">ENCODE</span> Research consortium investigating functional elements in human and model organism DNA

The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims "to build a comprehensive parts list of functional elements in the human genome."

<span class="mw-page-title-main">Computational epigenetics</span>

Computational epigenetics uses statistical methods and mathematical modelling in epigenetic research. Due to the recent explosion of epigenome datasets, computational methods play an increasing role in all areas of epigenetic research.

The International Cancer Genome Consortium (ICGC) is a voluntary scientific organization that provides a forum for collaboration among the world's leading cancer and genomic researchers. The ICGC was launched in 2008 to coordinate large-scale cancer genome studies in tumours from 50 cancer types and/or subtypes that are of main importance across the globe.

Cancer genome sequencing is the whole genome sequencing of a single, homogeneous or heterogeneous group of cancer cells. It is a biochemical laboratory method for the characterization and identification of the DNA or RNA sequences of cancer cell(s).

The Epigenomics database at the National Center for Biotechnology Information was a database for whole-genome epigenetics data sets. It was retired on 1 June 2016.

<span class="mw-page-title-main">Randy Jirtle</span> American geneticist

Randy Jirtle is an American biologist noted for his research in epigenetics, the branch of biology that deals with inherited information that does not reside in the nucleotide sequence of DNA. Jirtle retired from Duke University, Durham, NC in 2012. He is Professor of Epigenetics in the Department of Biological Sciences at North Carolina State University, Raleigh, NC, and Senior Visiting Scientist at the McArdle Laboratory of Cancer Research, University of Wisconsin, Madison, WI. Jirtle is noted for his research on genomic imprinting, and for his use of the Agouti mouse model to investigate the effect of environmental agents on the mammalian epigenome and disease susceptibility.

The International Human Epigenomics Consortium (IHEC) was launched in 2010 to coordinate global efforts in the field of epigenomics. IHEC aims to generate at least 1,000 reference baseline human epigenomes from different types of normal and disease-related human cell types.

<span class="mw-page-title-main">Christoph Bock</span>

Christoph Bock is a German bioinformatician and principal investigator at the Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences and a visiting professor at the Medical University of Vienna.

<span class="mw-page-title-main">Bradley Bernstein</span> Biologist

Bradley E. Bernstein is a biologist and Professor of Cell Biology at Harvard Medical School. He is Chair of the Department of Cancer Biology at the Dana–Farber Cancer Institute and the Director of the Broad Institute's Gene Regulation Observatory. He is known for contributions to the fields of epigenetics and cancer biology.

Azim Surani is a Kenyan-British developmental biologist who has been Marshall–Walton Professor at the Wellcome Trust/Cancer Research UK Gurdon Institute at the University of Cambridge since 1992, and Director of Germline and Epigenomics Research since 2013.

<span class="mw-page-title-main">Manolis Kellis</span> Greek-born computational biologist

Manolis Kellis is a professor of Computer Science at the Massachusetts Institute of Technology (MIT) in the area of Computational Biology and a member of the Broad Institute of MIT and Harvard. He is the head of the Computational Biology Group at MIT and is a Principal Investigator in the Computer Science and Artificial Intelligence Lab (CSAIL) at MIT.

<span class="mw-page-title-main">Nicole Soranzo</span> Italian British geneticist

Nicole Soranzo is an Italian-British senior group leader in human genetics at the Wellcome Sanger Institute, Professor of Human Genetics at the University of Cambridge. She is an internationally recognised Human Geneticist who has focused on the application of cutting edge genomic technologies to study the spectrum of human genetic variation associated with cardio-metabolic and immune diseases. She has led many large-scale discovery efforts including more than 1,000 novel genetic variants associated with cardio-metabolic diseases and their risk factors as well as establishing the HaemGen consortium, which is a worldwide effort to discover genetic determinants of blood cell formation and also interpretation of the downstream consequences of sequence variation through a host of integrative analyses and functional approaches.

The Global Alliance for Genomics and Health (GA4GH) is an international consortium that is developing standards for responsibly collecting, storing, analyzing, and sharing genomic data in order to enable an "internet of genomics". GA4GH was founded in 2013.

Professor Susan J. Clark is an Australian biomedical researcher in epigenetics of development and cancer. She was elected a Fellow of the Australian Academy of Science in 2015, and is a National Health and Medical Research Council (NHMRC) Senior Principal Research Fellow and Research Director and Head of Genomics and Epigenetics Division at the Garvan Institute of Medical Research. Clark developed the first method for bisulphite sequencing for DNA methylation analysis and used it to establish that the methylation machinery of mammalian cells is capable of both maintenance and de novo methylation at CpNpG sites and showed is inheritable. Clark's research has advanced understanding of the role of DNA methylation, non-coding RNA and microRNA in embryogenesis, reprogramming, stem cell development and cancer and has led to the identification of epigenomic biomarkers in cancer. Clark is a founding member of the International Human Epigenome Consortium (IHEC) and President of the Australian Epigenetics Alliance (AEpiA).

Human epigenome is the complete set of structural modifications of chromatin and chemical modifications of histones and nucleotides. These modifications affect according to cellular type and development status. Various studies show that epigenome depends on exogenous factors.

H3K4me1 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the mono-methylation at the 4th lysine residue of the histone H3 protein and often associated with gene enhancers.

H4K20me is an epigenetic modification to the DNA packaging protein Histone H4. It is a mark that indicates the mono-methylation at the 20th lysine residue of the histone H4 protein. This mark can be di- and tri-methylated. It is critical for genome integrity including DNA damage repair, DNA replication and chromatin compaction.

H3K9ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 9th lysine residue of the histone H3 protein.

John A. Stamatoyannopoulos a Greek-American physician-scientist in molecular biology and epigenomics. He is a professor of genome sciences and medicine at the University of Washington, where he heads the Stam Lab and led UW Medicine's participation in the ENCODE project. John is the son of Greek geneticist George Stamatoyannopoulos. Stamatoyannopoulos currently serves as scientific director at the Altius Institute for Biomedical Sciences.

References

[44]

  1. ↑ "Time for the epigenome : Article : Nature".
  2. ↑ Project set to map marks on genome: Nature 463: 596-597 (2010) doi:10.1038/463596b
  3. ↑ Bae, JB (2013). "Perspectives of international human epigenome consortium". Genomics Inform. 11 (1): 7–14. doi:10.5808/GI.2013.11.1.7. PMC   3630389 . PMID   23613677.
  4. ↑ "BioNews - Human Epigenome project launched" Archived 2010-12-28 at the Wayback Machine .
  5. ↑ "France: Human epigenome consortium takes first steps" Archived 2015-07-08 at the Wayback Machine . 5 March 2010.
  6. ↑ "Frontiers | Multilayer-omics analyses of human cancers: exploration of biomarkers and drug targets based on the activities of the International Human Epigenome Consortium | Epigenomics and Epigenetics". Frontiers.
  7. ↑ GmbH, Eurice. "About IHEC · IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  8. ↑ GmbH, Eurice. "IHEC Countries · IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  9. ↑ "Canadian Epigenetics, Environment and Health Research Consortium Overview".
  10. ↑ "The EU invests €30 million to map new territory in health research".
  11. ↑ "Journey from stem cell to blood cell uncovered: BLUEPRINT study catalogues events that regulate blood cell creation".
  12. ↑ "Catalogue of how white cells are formed by the blood stem cell".
  13. ↑ "Europe to map the human epigenome".
  14. ↑ GmbH, Eurice. "IHEC welcomes two new European member projects | IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  15. ↑ "Deutsche Beteiligung am International Human Epigenome Consortium (IHEC)" Archived 2015-07-08 at the Wayback Machine .
  16. ↑ "DEEP (Deutsches Epigenom Programm) Project".
  17. ↑ GmbH, Eurice. "Singapore · IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  18. ↑ GmbH, Eurice. "IHEC welcomes the Hong Kong Epigenomics Project as new member to the consortium | IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  19. ↑ "The Hong Kong Epigenomics Project". epihk.org. Retrieved 2017-06-23.
  20. ↑ "The International Human Epigenome Consortium (IHEC) | Collaboration/cooperation with external institutions | Japan Agency for Medical Research and Development". www.amed.go.jp. Retrieved 2017-06-23.
  21. ↑ "Roadmap Epigenomics Project - Home". www.roadmapepigenomics.org. Archived from the original on 2021-04-08. Retrieved 2017-07-18.
  22. ↑ Eurice GmbH. "IHEC Members · IHEC" Archived 2013-10-08 at the Wayback Machine .
  23. ↑ GmbH, Eurice. "IHEC Working Groups · IHEC". ihec-epigenomes.org. Retrieved 2017-06-23.
  24. ↑ "Genome Medicine | Authorisation | Synergy and competition between cancer genome sequencing and epigenome mapping projects".
  25. 1 2 3 Eurice GmbH. "Objectives".
  26. ↑ "Delving deeper into the animal genome".
  27. ↑ "Home | Global Alliance for Genomics and Health". genomicsandhealth.org. Retrieved 2017-07-18.
  28. ↑ Eurice GmbH. "News+Events · IHEC".
  29. ↑ Stunnenberg, Hendrik G.; Abrignani, Sergio; Adams, David; Almeida, Melanie de; Altucci, Lucia; Amin, Viren; Amit, Ido; Antonarakis, Stylianos E.; Aparicio, Samuel (2016-11-17). "The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery". Cell. 167 (5): 1145–1149. doi: 10.1016/j.cell.2016.11.007 . hdl: 2445/124834 . ISSN   0092-8674. PMID   27863232.
  30. ↑ Protocols and Standards’
  31. ↑ "Data Portal | IHEC". epigenomesportal.ca. Retrieved 2017-06-23.
  32. ↑ Bujold, David; Morais, David Anderson de Lima; Gauthier, Carol; Côté, Catherine; Caron, Maxime; Kwan, Tony; Chen, Kuang Chung; Laperle, Jonathan; Markovits, Alexei Nordell (2016-11-23). "The International Human Epigenome Consortium Data Portal". Cell Systems. 3 (5): 496–499.e2. doi: 10.1016/j.cels.2016.10.019 . ISSN   2405-4712. PMID   27863956.
  33. ↑ "IHEC coordinated paper release". EGA Blog. Retrieved 2017-06-23.
  34. ↑ Eurice GmbH. "About IHEC".
  35. ↑ "IHEC Data Portal".
  36. ↑ "Consortium: IHEC: Cell Press" . Retrieved 2017-06-23.{{cite journal}}: Cite journal requires |journal= (help)
  37. ↑ Cell editorial team (2016-11-17). "A Cornucopia of Advances in Human Epigenomics". Cell. 167 (5): 1139. doi: 10.1016/j.cell.2016.11.001 . ISSN   0092-8674. PMID   27863229.
  38. ↑ "Epigenetics Around the Web: Top epigenetics stories from 2016 - Epigenetics". Epigenetics. Retrieved 2017-06-23.
  39. ↑ "More than 40 New Papers on Epigenetics Published | The Scientist Magazine®". The Scientist. Retrieved 2017-06-23.
  40. ↑ "Singapore scientists part of breakthrough in autism research" . Retrieved 2017-06-23.
  41. ↑ "Cancer Epigenomic Insights Reported by International Consortia Members". GenomeWeb. Retrieved 2017-06-23.
  42. ↑ "Epigenome Consortium Research Teams Tackle Immune Response Epigenetics". GenomeWeb. Retrieved 2017-06-23.
  43. ↑ "How blood cell genetic variations impact on common diseases" . Retrieved 2017-06-23.
  44. ↑ "Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus".
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