Poplar Genomics is Getting Popular: The Impact of the Poplar Genome Project on Tree Research

Plant Biology ◽  
2004 ◽  
Vol 6 (1) ◽  
pp. 2-4 ◽  
Keyword(s):  
Genome Project ◽  
Poplar Genome ◽  
The Impact

scholarly journals The Impact of the Human Genome Project on Complex Disease

Genes ◽  
2014 ◽  
Vol 5 (3) ◽  
pp. 518-535 ◽  
Author(s):  
Jessica Bailey ◽  
Margaret Pericak-Vance ◽  
Jonathan Haines
Keyword(s):  
Human Genome ◽  
Human Genome Project ◽  
Complex Disease ◽  
Genome Project ◽  
The Human Genome Project ◽  
The Impact

scholarly journals Genetics in the 21st Century: Implications for patients, consumers and citizens

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2020 ◽  
Author(s):  
Jonathan Roberts ◽  
Anna Middleton
Keyword(s):  
Human Genome Project ◽  
Personalised Medicine ◽  
Building Blocks ◽  
Healthcare Services ◽  
Genome Project ◽  
Human Response ◽  
Future Health ◽  
Policy Makers ◽  
Human Genes ◽  
The Impact

The first human genome project, completed in 2003, uncovered the genetic building blocks of humankind. Painstakingly cataloguing the basic constituents of our DNA (‘genome sequencing’) took ten years, over three billion dollars and was a multinational collaboration. Since then, our ability to sequence genomes has been finessed so much that by 2017 it is possible to explore the 20,000 or so human genes for under £1000, in a matter of days. Such testing offers clues to our past, present and future health, as well as information about how we respond to medications so that truly ‘personalised medicine’ is now a reality.   The impact of such a ‘genomic era’ is likely to have some level of impact on all of us, even if we are not directly using healthcare services ourselves. We explore how advancements in genetics are likely to be experienced by people, as patients, consumers and citizens; and urge policy makers to take stock of the pervasive nature of the technology as well as the human response to it.

scholarly journals Genetics in the 21st Century: Implications for patients, consumers and citizens

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 2020 ◽  
Author(s):  
Jonathan Roberts ◽  
Anna Middleton
Keyword(s):  
Human Genome Project ◽  
Personalised Medicine ◽  
Building Blocks ◽  
Healthcare Services ◽  
Genome Project ◽  
Human Response ◽  
Future Health ◽  
Policy Makers ◽  
Human Genes ◽  
The Impact

The first human genome project, completed in 2003, uncovered the genetic building blocks of humankind. Painstakingly cataloguing the basic constituents of our DNA (‘genome sequencing’) took ten years, over three billion dollars and was a multinational collaboration. Since then, our ability to sequence genomes has been finessed so much that by 2018 it is possible to explore the 20,000 or so human genes for under £1000, in a matter of days. Such testing offers clues to our past, present and future health, as well as information about how we respond to medications so that truly ‘personalised medicine’ is now moving closer to a reality.The impact of such a ‘genomic era’ is likely to have some level of impact on an increasingly large number of us, even if we are not directly using healthcare services ourselves. We explore how advancements in genetics are likely to be experienced by people, as patients, consumers and citizens; and urge policy makers to take stock of the pervasive nature of the technology as well as the human response to it.

scholarly journals Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

2019 ◽  
Author(s):  
Rui Martiniano ◽  
Erik Garrison ◽  
Eppie R. Jones ◽  
Andrea Manica ◽  
Richard Durbin
Keyword(s):  
Ancient Dna ◽  
Genetic Locus ◽  
Genome Project ◽  
Lower Sensitivity ◽  
Human Populations ◽  
Read Mapping ◽  
Indel Calling ◽  
Alternative Approaches ◽  
Reference Bias ◽  
The Impact

AbstractBackgroundDuring the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA and compare our approach to existing methods.ResultsWe used vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias, but can have lower sensitivity than vg, particularly for indels.ConclusionsOur findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analysing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

scholarly journals The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

2020 ◽  
Vol 10 (9) ◽  
pp. 3337-3346
Author(s):  
Yijia Zhou ◽  
Funan He ◽  
Weilin Pu ◽  
Xun Gu ◽  
Jiucun Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Germline Mutation ◽  
Developmental Stages ◽  
Rare Variants ◽  
Epigenetic Modification ◽  
Genome Project ◽  
Germline Development ◽  
Cpg Sites ◽  
The Impact

Abstract DNA methylation is a dynamic epigenetic modification found in most eukaryotic genomes. It is known to lead to a high CpG to TpG mutation rate. However, the relationship between the methylation dynamics in germline development and the germline mutation rate remains unexplored. In this study, we used whole genome bisulfite sequencing (WGBS) data of cells at 13 stages of human germline development and rare variants from the 1000 Genome Project as proxies for germline mutations to investigate the correlation between dynamic methylation levels and germline mutation rates at different scales. At the single-site level, we found a significant correlation between methylation and the germline point mutation rate at CpG sites during germline developmental stages. Then we explored the mutability of methylation dynamics in all stages. Our results also showed a broad correlation between the regional methylation level and the rate of C > T mutation at CpG sites in all genomic regions, especially in intronic regions; a similar link was also seen at all chromosomal levels. Our findings indicate that the dynamic DNA methylome during human germline development has a broader mutational impact than is commonly assumed.

scholarly journals Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Rui Martiniano ◽  
Erik Garrison ◽  
Eppie R. Jones ◽  
Andrea Manica ◽  
Richard Durbin
Keyword(s):  
Ancient Dna ◽  
Genetic Locus ◽  
Genome Project ◽  
Lower Sensitivity ◽  
Human Populations ◽  
Mapping Accuracy ◽  
Indel Calling ◽  
Alternative Approaches ◽  
Reference Bias ◽  
The Impact

Abstract Background During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software to avoid reference bias for aDNA and compare with existing methods. Results We use to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with to the human linear reference genome. Using leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with , especially for insertions and deletions (indels). Alternative approaches that use relaxed parameter settings or filter alignments can also reduce bias but can have lower sensitivity than , particularly for indels. Conclusions Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.

Discovery and Integrative Neuroscience

2005 ◽  
Vol 36 (2) ◽  
pp. 55-63 ◽  
Author(s):  
Stephen H. Koslow
Keyword(s):  
Information Technologies ◽  
Public Funding ◽  
Genome Project ◽  
Added Value ◽  
Simulation Tools ◽  
Discovery Research ◽  
Private And Public ◽  
System Data ◽  
Primary Focus ◽  
The Impact

Hypothesis driven research has been shown to be an excellent model for pursuing investigations in neuroscience. The Human Genome Project demonstrated the added value of discovery research, especially in areas where large amounts of data are produced. Neuroscience has become a data rich field, and one that would be enhanced by incorporating the discovery approach. Databases, as well as analytical, modeling and simulation tools, will have to be developed, and they will need to be interoperable and federated. This paper presents an overview of the development of the field of neuroscience databases and associate tools: Neuroinformatics. The primary focus is on the impact of NIH funding of this process. The important issues of data sharing, as viewed from the perspective of the scientist and private and public funding organizations, are discussed. Neuroinformatics will provide more than just a sophisticated array of information technologies to help scientists understand and integrate nervous system data. It will make available powerful models of neural functions and facilitate discovery, hypothesis formulation and electronic collaboration.

Genetic testing and the moral dynamics of family life

1999 ◽  
Vol 8 (3) ◽  
pp. 193-205 ◽  
Author(s):  
Eric T. Juengst
Keyword(s):  
Genetic Testing ◽  
Genome Project ◽  
Blended Families ◽  
Genetic Risk Assessment ◽  
Ethical Problems ◽  
The Public ◽  
Extended Families ◽  
Genetic Risks ◽  
The Human Genome Project ◽  
The Impact

American families are a segment of the public that will feel the impact of the Human Genome Project most acutely: but they are also one of the least well studied segments with regard to that impact. Three sets of ethical problems, in particular, deserve more scrutiny: the effect of increased genetic risk assessment on family members' willingness to assist their kin discover mutually incriminating genetic risks, its impact on the candor with which extended families communicate within themselves about their genetic health risks, and its influence on the ways that families seek to protect the interests of their most vulnerable members. In each of these areas, anecdotal experience already shows how genetic testing can undermine a family's commitment to its own interdependence in these ways, and that traditional, multigenerational, sessile families are likely to experience more disruption than either blended families or “virtual families” linked primarily through electronic communication.

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