The Experts below are selected from a list of 73440 Experts worldwide ranked by ideXlab platform
Francis S Collins - One of the best experts on this subject based on the ideXlab platform.
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human Genome Project twenty five years of big biology
Nature, 2015Co-Authors: Eric D Green, James D Watson, Francis S CollinsAbstract:The Human Genome Project, which launched a quarter of a century ago this week, still holds lessons for the consortium-based science it ushered in, say Eric D. Green, James D. Watson and Francis S. Collins.
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the human Genome Project lessons from large scale biology
Science, 2003Co-Authors: Francis S Collins, Michael J Morgan, Aristides PatrinosAbstract:The Human Genome Project has been the first major foray of the biological and medical research communities into “big science.” In this Viewpoint, we present some of our experiences in organizing and managing such a complicated, publicly funded, international effort. We believe that many of the lessons we learned will be applicable to future large-scale Projects in biology.
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the human Genome Project
Cancer, 2001Co-Authors: Francis S Collins, Monique K MansouraAbstract:The information derived from the Human Genome Project, an international effort to decode the information embedded in the human Genome, will revolutionize the practice of medicine in the 21st century by providing the tools to determine the hereditary component of virtually all diseases. This will lead to improved approaches to predict increased risk, provide early detection, and promote more effective treatment strategies. To be ultimately successful, these improvements in research and health care must reach everyone. This success will depend on participation from a broad spectrum of the population. such as scientists, clinicians, research participants, and active discussants, in deliberations of ethics and public policy. The Human Genome Project has helped to inform us about how remarkably similar all human beings are—99.9% at the DNA level. Those who wish to draw precise racial boundaries around certain groups will not be able to use science as a legitimate justification. However, studying the 0.1% of human genetic variations, particularly the distribution of single nucleotide polymorphisms, between affected and nonaffected individuals will significantly inform biomedical researchers about the genetic contributions to complex diseases such as cancer, diabetes, and mental illness. We must all work together to ensure that the risks of such research are considered carefully and that the medical benefits are made available to all. Cancer 2001;91:221–225. © 2001 American Cancer Society.
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the human Genome Project revealing the shared inheritance of all humankind
Cancer, 2001Co-Authors: Francis S Collins, Monique K MansouraAbstract:The information derived from the Human Genome Project, an international effort to decode the information embedded in the human Genome, will revolutionize the practice of medicine in the 21st century by providing the tools to determine the hereditary component of virtually all diseases. This will lead to improved approaches to predict increased risk, provide early detection, and promote more effective treatment strategies. To be ultimately successful, these improvements in research and health care must reach everyone. This success will depend on participation from a broad spectrum of the population. such as scientists, clinicians, research participants, and active discussants, in deliberations of ethics and public policy. The Human Genome Project has helped to inform us about how remarkably similar all human beings are--99.9% at the DNA level. Those who wish to draw precise racial boundaries around certain groups will not be able to use science as a legitimate justification. However, studying the 0.1% of human genetic variations, particularly the distribution of single nucleotide polymorphisms, between affected and nonaffected individuals will significantly inform biomedical researchers about the genetic contributions to complex diseases such as cancer, diabetes, and mental illness. We must all work together to ensure that the risks of such research are considered carefully and that the medical benefits are made available to all.
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new goals for the u s human Genome Project 1998 2003
Science, 1998Co-Authors: Francis S Collins, Ari Patrinos, Elke Jordan, Aravinda Chakravarti, Raymond F Gesteland, Leroy WaltersAbstract:The Human Genome Project has successfully completed all the major goals in its current 5-year plan, covering the period 1993–98. A new plan, for 1998–2003, is presented, in which human DNA sequencing will be the major emphasis. An ambitious schedule has been set to complete the full sequence by the end of 2003, 2 years ahead of previous Projections. In the course of completing the sequence, a “working draft” of the human sequence will be produced by the end of 2001. The plan also includes goals for sequencing technology development; for studying human Genome sequence variation; for developing technology for functional genomics; for completing the sequence of Caenorhabditis elegans and Drosophila melanogaster and starting the mouse Genome; for studying the ethical, legal, and social implications of Genome research; for bioinformatics and computational studies; and for training of Genome scientists.
H A E Zwart - One of the best experts on this subject based on the ideXlab platform.
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understanding the human Genome Project a biographical approach
New Genetics and Society, 2008Co-Authors: H A E ZwartAbstract:This article analyzes a number of recently published autobiographies by leading participants in the Human Genome Project (HGP), in order to determine to what extent they may further our understanding of the history, scientific significance and societal impact of this major research endeavor. Notably, I will focus on three publications that fall under this heading, namely The common thread by John Sulston (2002/2003), The language of God (2006) by Francis Collins and A life decoded by Craig Venter (2007).1 What may we learn from these autobiographical sources about the dynamics of scientific change? What is their added value in understanding science in general and the HGP in particular? These questions will be elaborated in three directions: on the level of knowledge (epistemology), power (politics) and the Self (ethics). On the epistemological level, genomics is often presented as a paradigm shift in the life sciences, a tremendous up-scaling of research, an “informatization” of life. Autobiographies may ...
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understanding the human Genome Project a biographical approach
Social Science Research Network, 2008Co-Authors: H A E ZwartAbstract:This article analyzes a number of recently published autobiographies by leading participants in the Human Genome Project (HGP), in order to determine to what extent they may further our understanding of the history, scientific significance and societal impact of this major research endeavor. Notably, I will focus on three publications that fall under this heading, namely The Common Thread by John Sulston (2002/2003), The Language of God (2006) by Francis Collins and A Life Decoded by Craig Venter (2007). What may we learn from these autobiographical sources about the dynamics of scientific change? What is their added value in understanding science in general and the HGP in particular? These questions will be elaborated in three directions: on the level of knowledge (epistemology), power (politics) and the Self (ethics). On the epistemological level, genomics is often presented as a paradigm shift in the life sciences, a tremendous up-scaling of research, an “informatization” of life. Autobiographies may reveal how this shift – usually discussed in more general terms from a philosophy of science or science studies perspective – manifests itself on an individual scale, on a microepistemological level. On the political level, autobiographies may inform us about the micro-politics of scientific change. Finally, on the level of Self, autobiographies may allow us to analyze how researchers, through practices of Self, are actively engaged in constituting themselves as responsible subjects in the face of unpredictable dynamics and unforeseen dilemmas.
Olga Chervova - One of the best experts on this subject based on the ideXlab platform.
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Genomechronicler the personal Genome Project uk genomic report generator pipeline
Frontiers in Genetics, 2020Co-Authors: Jose Afonso Guerraassuncao, Olga Chervova, Lucia Conde, Ismail Moghul, Amy P Webster, Simone Ecker, Christina Chatzipantsiou, Pablo P Prieto, Stephan Beck, Javier HerreroAbstract:In recent years, there has been a significant increase in whole Genome sequencing data of individual Genomes produced by research Projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole Genome or whole exome sequencing, producing a Genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalGenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence, and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype. The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party Project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.
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the personal Genome Project uk an open access resource of human multi omics data
Scientific Data, 2019Co-Authors: Olga Chervova, Lucia Conde, Jose Afonso Guerraassuncao, Ismail Moghul, Amy P Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan TianAbstract:Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.
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personal Genome Project uk pgp uk a research and citizen science hybrid Project in support of personalized medicine
BMC Medical Genomics, 2018Co-Authors: Stephan Beck, Olga Chervova, Lucia Conde, Alison Berner, Simone Ecker, Graham R Bignell, Maggie Bond, Martin J Callanan, Manuel Corpas, Hannah R ElliottAbstract:Background: Molecular analyses such as whole-Genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Methods: Defined as a research Project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Results: Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal Genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the Project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present Genome, a free, open-source educational app suitable for the lay public to allow exploration of personal Genomes. Conclusions: Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.
George M Church - One of the best experts on this subject based on the ideXlab platform.
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the Genome Project write
Science, 2016Co-Authors: Jef D Boeke, George M Church, Aravinda Chakravarti, Andrew Hessel, Nancy J Kelley, Adam P Arkin, Yizhi Cai, Robert E Carlson, Virginia W Cornish, Liam J HoltAbstract:The Human Genome Project (“HGP-read”), nominally completed in 2004, aimed to sequence the human Genome and to improve the technology, cost, and quality of DNA sequencing ( 1 , 2 ). It was biology's first Genome-scale Project and at the time was considered controversial by some. Now, it is recognized as one of the great feats of exploration, one that has revolutionized science and medicine.
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Harvard Personal Genome Project: lessons from participatory public research
Genome Medicine, 2014Co-Authors: Madeleine P Ball, Jason R Bobe, Michael F Chou, Tom Clegg, Preston W Estep, Jeantine E Lunshof, Ward Vandewege, Alexander Wait Zaranek, George M ChurchAbstract:Background Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their Genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public Genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole Genome data to participants. We also observe some of the community growth and discussion that has occurred related to our Project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants.
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the personal Genome Project
Molecular Systems Biology, 2005Co-Authors: George M ChurchAbstract:Mol Syst Biol. 1: 2005.0030 Large potential benefits for systems biology reside in applications to human health and identity. To develop our community's skills in these directions, ready access to highly integrated and comprehensive human Genome and phenome data sets is extremely important and increasingly feasible technically. The few human 'functional genomics' data sets available today tend to be isolated from one another. Some of the tools needed to break through this impasse are addressed below in the context of a Personal Genome Project (PGP) as a natural successor to the Human Genome Project (HGP)—two recent buds in the ancient field of genetics. From my first interaction with Wally Gilbert in 1976, it seemed that a large (but appealing) leap would be to go from his new method for sequencing 30 bp segments to a method to get everyone's full Genome sequenced. Six billion base pairs for six billion people had a nice ring to it. This was still merely a fantasy when we published a paper called 'Genomic Sequencing' in 1984 (Church and Gilbert, 1984) and conspired to create a 3 billion dollar HGP later that year (Cook‐Deegan, 1989). For the subsequent 16 years, radical technology development (while kept alive in a few 'back‐rooms') was clearly a minor funding priority relative to 'production' sequencing. However, by 2001, the criticisms of the old technology grew and the call for affordable personal Genomes became irresistible (Jonietz, 2001). In early 2004, the NIH‐NHGRI posted a request for applications, and in October 2004 and August 2005, announced grant awards totaling $70 million for technology leading to human Genome sequences for $100 000 in 5 years and $1000 in 10 years (http://www.nih.gov/news/pr/aug2005/nhgri‐08.htm). As if the motivation were not already high enough, at the recent Genome Sequencing & Analysis Conference in Hilton Head (October …
Lucia Conde - One of the best experts on this subject based on the ideXlab platform.
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Genomechronicler the personal Genome Project uk genomic report generator pipeline
Frontiers in Genetics, 2020Co-Authors: Jose Afonso Guerraassuncao, Olga Chervova, Lucia Conde, Ismail Moghul, Amy P Webster, Simone Ecker, Christina Chatzipantsiou, Pablo P Prieto, Stephan Beck, Javier HerreroAbstract:In recent years, there has been a significant increase in whole Genome sequencing data of individual Genomes produced by research Projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole Genome or whole exome sequencing, producing a Genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalGenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence, and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype. The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party Project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.
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the personal Genome Project uk an open access resource of human multi omics data
Scientific Data, 2019Co-Authors: Olga Chervova, Lucia Conde, Jose Afonso Guerraassuncao, Ismail Moghul, Amy P Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan TianAbstract:Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.
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personal Genome Project uk pgp uk a research and citizen science hybrid Project in support of personalized medicine
BMC Medical Genomics, 2018Co-Authors: Stephan Beck, Olga Chervova, Lucia Conde, Alison Berner, Simone Ecker, Graham R Bignell, Maggie Bond, Martin J Callanan, Manuel Corpas, Hannah R ElliottAbstract:Background: Molecular analyses such as whole-Genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Methods: Defined as a research Project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Results: Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal Genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited 10 participants willing to actively engage as citizen scientists with the Project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present Genome, a free, open-source educational app suitable for the lay public to allow exploration of personal Genomes. Conclusions: Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.