Translational Bioinformatics: Challenges and Opportunities for Case-Based Reasoning and Decision Support.
ABSTRACT Translational bioinformatics is bioinformatics applied to human health. Although, up to now, its main focus has been to support
molecular medicine research, translational bioinformatics has now the opportunity to design clinical decision support systems
based on the combination of -omics data and internet-based knowledge resources. The paper describes the state-of-art of translational
bioinformatics highlighting challenges and opportunities for decision support tools and case-based reasoning. It finally reports
the design of a new system for supporting diagnosis in dilated cardiomyopathy. The system is able to combine text mining,
literature search and case-based retrieval.
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ABSTRACT: Although investigators using methodologies in bioinformatics have always been useful in genomic experimentation in analytic, engineering, and infrastructure support roles, only recently have bioinformaticians been able to have a primary scientific role in asking and answering questions on human health and disease. Here, I argue that this shift in role towards asking questions in medicine is now the next step needed for the field of bioinformatics. I outline four reasons why bioinformaticians are newly enabled to drive the questions in primary medical discovery: public availability of data, intersection of data across experiments, commoditization of methods, and streamlined validation. I also list four recommendations for bioinformaticians wishing to get more involved in translational research.Genome Medicine 07/2009; 1(6):64. DOI:10.1186/gm64 · 4.94 Impact Factor
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ABSTRACT: Tens of thousands of subjects may be required to obtain reliable evidence relating disease characteristics to the weak effects typically reported from common genetic variants. The costs of assembling, phenotyping, and studying these large populations are substantial, recently estimated at three billion dollars for 500,000 individuals. They are also decade-long efforts. We hypothesized that automation and analytic tools can repurpose the informational byproducts of routine clinical care, bringing sample acquisition and phenotyping to the same high-throughput pace and commodity price-point as is currently true of genome-wide genotyping. Described here is a demonstration of the capability to acquire samples and data from densely phenotyped and genotyped individuals in the tens of thousands for common diseases (e.g., in a 1-yr period: N = 15,798 for rheumatoid arthritis; N = 42,238 for asthma; N = 34,535 for major depressive disorder) in one academic health center at an order of magnitude lower cost. Even for rare diseases caused by rare, highly penetrant mutations such as Huntington disease (N = 102) and autism (N = 756), these capabilities are also of interest.Genome Research 09/2009; 19(9):1675-81. DOI:10.1101/gr.094615.109 · 13.85 Impact Factor
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ABSTRACT: We demonstrate the first successful application of exome sequencing to discover the gene for a rare mendelian disorder of unknown cause, Miller syndrome (MIM%263750). For four affected individuals in three independent kindreds, we captured and sequenced coding regions to a mean coverage of 40x and sufficient depth to call variants at approximately 97% of each targeted exome. Filtering against public SNP databases and eight HapMap exomes for genes with two previously unknown variants in each of the four individuals identified a single candidate gene, DHODH, which encodes a key enzyme in the pyrimidine de novo biosynthesis pathway. Sanger sequencing confirmed the presence of DHODH mutations in three additional families with Miller syndrome. Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.Nature Genetics 11/2009; 42(1):30-5. DOI:10.1038/ng.499 · 29.65 Impact Factor