Genotype–phenotype databases: challenges and solutions for the post-genomic era

Þórisson, Guðmundur Á.; Muilu, Juha; Brookes, Anthony J.

doi:10.1038/nrg2483

Cited by 88 publications

(59 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The latter is one of the major components of the IBP initiative after it was realized that there were few information systems (IS) in breeding that integrated a database of germplasm information, phenotypic data and a complete analytical pipeline (Ribaut et al, 2013). This kind of database is widely used in human disease as reviewed by (Thorisson et al, 2009). Central databases for breeding exist for each of the crops of interest for CGIAR centers.…”

Section: Discussionmentioning

confidence: 99%

Evaluating Human Resource Capacity for Crop Breeding in National Programs in Africa and South and Southeast Asia

Diop¹,

Okono²,

Ribaut³

2013

View full text Add to dashboard Cite

Plant breeders must keep abreast of the rapid evolution of new technologies, and also implement information management strategies that efficaciously handle the ever growing amount of data required for efficient integrated breeding. Updated training for breeders is critical to build relevant human resource capacity, particularly in developing countries whose breeding programs suffer a lack of staff with diverse expertise. The CGIAR Generation Challenge Programme is leading such a capacity-building initiative. A survey was conducted among course nominees to establish a baseline of breeder level of education, knowledge and skills in analyzing data and their involvement in molecular breeding programs. The breeders were mainly from three regions: West and Central Africa, East and Southern Africa, and South and Southeast Asia, and also included a few participants from North Africa. Many of the breeders from all the regions held or were working towards a PhD. Gender balance was low, principally in West and Central Africa, where less than 15% of the breeders were women. Between 57% and 73% of the breeders surveyed in the different regions were involved in molecular breeding projects at regional or international level. The Use of multiple software tools by individual breeders for data analysis was low for breeders from all the regions, with most using 1 -3 packages. A lack of high data-analysis capacity will be a problem in an era where integration of genomics and phenotypic data in breeding programs is essential to efficiently deliver improved cultivars.

show abstract

Section: Discussionmentioning

confidence: 99%

Evaluating Human Resource Capacity for Crop Breeding in National Programs in Africa and South and Southeast Asia

Diop¹,

Okono²,

Ribaut³

2013

View full text Add to dashboard Cite

show abstract

“…The Human Variome Project (HVP) and Genotype-2-Phenotype Project (GEN2PHEN) are global efforts to catalog all mutations associated with human disease [Ring et al, 2006;Thorisson et al, 2009]. These projects continue to address the resource, technical, and policy challenges in creation of an infrastructure for linkage of Locus Specific Databases (LSDBs) and other knowledgebases containing information on mutations associated with human disease.…”

Section: Knowledgebases and Educational Resourcesmentioning

confidence: 99%

“…All of this needs to be conducted within an overarching framework of ethical practice, policy guidelines, and data governance. However, if these challenges can be addressed, this would enable an integrated view of genotypic and/or phenotypic knowledgebases, across multiple institutions worldwide [Mitropoulou et al, 2010;Olivier et al, 2009;Thorisson et al, 2009].…”

Section: Knowledgebases and Educational Resourcesmentioning

confidence: 99%

Emerging landscape of genomics in the electronic health record for personalized medicine

Ullman-Culleré

Mathew

2011

Hum. Mutat.

View full text Add to dashboard Cite

The Information Technology (IT) roadmap for personalized medicine requires Electronic Health Records (EHRs), extension of Healthcare IT (HIT) standards, and understanding of how genetics/genomics should be integrated into the clinical applications. For reduced overall costs and development times, these three initiatives should run in parallel. EHRs must contain structured data and infrastructure that enables quality analysis, Clinical Decision Support (CDS) and messaging within the healthcare information network. Fortunately, as a result of sustained financial commitment to nongenetic-based healthcare, the industry has HIT data standards and understanding of EHR functionality that improves patient safety and outcomes while reducing overall healthcare costs. However, the HIT standards and EHR functional requirements, needed for personalized medicine, are only beginning to support simple genetic tests and need significant extension. In addition, our understanding of the clinical implications of genomic data is evolving and translation of new discovery into clinical care remains a challenge. Therefore, priority areas include CDS, educational resources, and knowledgebases for the EHR, clinical and research data warehouses, messaging frameworks, and continued review of healthcare policies and regulations supporting personalized medicine. Where core infrastructure remains to be developed and implemented, funding is needed for pilot projects, data standards, policy, and stakeholder collaboration.

show abstract

“…caBIG has been the foundation for other projects, including The Cancer Genome Atlas, the Repository of Molecular Brain Neoplasia Data, and the National Health Information Network. Many other information-system projects are under way to build the infrastructure required to support personalized medicine (27). One example is the development of a database for CER based on a prospective study being conducted at 19 sites throughout the United States and based at the Moffitt Cancer Center (28).…”

Section: Design Of a Health Information Systemmentioning

confidence: 99%

The 2010 Health Care Reform Act: A Potential Opportunity to Advance Cancer Research by Taking Cancer Personally

Dalton

Sullivan²,

Yeatman³

et al. 2010

Clinical Cancer Research

View full text Add to dashboard Cite

The Patient Protection and Affordable Care Act of 2010 will have a profound influence on health care in the United States, including how we conduct cancer research and cancer care delivery. For this reason, oncologists and researchers must be intimately involved in the implementation and interpretation of this important legislation. A major goal of the Act is to improve access to affordable, quality health care. An important element in achieving this goal will be to learn from patients' experiences and build the foundation for evidence-based personalized medicine. This will require a partnership among researchers, clinicians, policy makers and regulators, and patients to design an integrated information network system that will be the basis for providing the right treatment for the right patient in the right place at the right time.In this review, we will discuss the salient points of the Act that specifically affect cancer research and care, as well as highlight opportunities for oncologists and researchers to play a primary role in developing a health care system that includes personalized medicine approaches that will in turn enhance the likelihood of achieving the goals and objectives of the health care reform act.

show abstract

Genotype–phenotype databases: challenges and solutions for the post-genomic era

Cited by 88 publications

References 48 publications

Evaluating Human Resource Capacity for Crop Breeding in National Programs in Africa and South and Southeast Asia

Evaluating Human Resource Capacity for Crop Breeding in National Programs in Africa and South and Southeast Asia

Emerging landscape of genomics in the electronic health record for personalized medicine

The 2010 Health Care Reform Act: A Potential Opportunity to Advance Cancer Research by Taking Cancer Personally

Contact Info

Product

Resources

About