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PubMed2005

Mapping the new frontier: complex genetic disorders.

The remarkable achievements in human genetics over the years have been due to technological advances in gene mapping and in statistical methods that relate genetic variants to disease. Nearly every Mendelian genetic disorder has now been mapped to a specific gene or set of genes, but these discoveries have been limited to high-risk, variant alleles that segregate in rare families. With a working draft of the human genome now in hand, the availability of high-throughput genotyping, a plethora of genetic markers, and the development of new analytical methods, scientists are now turning their attention to common complex disorders such as diabetes, obesity, hypertension, and Alzheimer disease. In this issue, the JCI provides readers with a series dedicated to complex genetic disorders, offering a view of genetic medicine in the 21st century.

Alleles↗

PubMed2006

MultiSeq: unifying sequence and structure data for evolutionary analysis.

BACKGROUND: Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. RESULTS: Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. CONCLUSION: MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/

Algorithms↗

PubMed2002

Fish tale.

The draft sequence of the genome of the Japanese pufferfish has just been announced and the temptation to humor is great.

Animals↗

PubMed2004

Personalized psychiatry: a realistic goal.

It is becoming increasingly evident that the implementation of true personalized medicine will not come as rapidly and smoothly as initially hoped. In the aftermath of the drafting of the human genome in 2001, the popular and scientific media featured numerous commentaries heralding the approaching arrival of personalized medicine to the clinic, and describing its huge benefits for patients. Media coverage predicted a drastic transformation for the practice of medicine, second to the revolution brought about by the discovery of vaccines and antibiotics. From the perspective of another 3 years, during which substantial new insights were made into the enormous complexity of human genome variation, it seems that true personalized medicine may still be decades away for many aspects of medical treatment. Nonetheless, the prospects for implementation of at least certain elements of personalized medicine for one key discipline, psychiatry, might be relatively close and more realistic. With the correct focus, realization of some benefits of genetic patient profiling for psychiatric pharmacotherapy might be near, and in due course, lead the way for true personalized psychiatry.

Decision Making↗

PubMed2003

pp-Blast: a "pseudo-parallel" Blast.

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

Computing Methodologies↗

PubMed2000

The DNA Rx. Advances in genetics give physicians ability to tailor drugs to patients' unique makeup.

Thanks to the recently completed first draft of the human genome map, the potential for advances in medical science seems endless. That's especially true in pharmacogenomics, with futuristic-sounding drugs and screening tests already available. William Evans (left), chairman of pharmaceutical science at St. Jude Children's Research Hospital, Memphis, Tenn., developed one of only a few pharmacogenomic applications available so far.

Cost Savings↗

PubMed2000

Bioinformatics, target discovery and the pharmaceutical/biotechnology industry.

With the first draft of the human genome now available a directed genome-wide mining strategy is being implemented by many pharmaceutical and biotechnology companies in order to identify novel members of the most therapeutically relevant target families. At the same time there is an increasing amount of annotation relevant to the human genome sequence entering into the public domain. The ability to identify protein families on a genome-wide scale can only be done at speed by using high-throughput computational approaches. This review describes many of the latest algorithmic developments in this field and shows how they can be best put to use for target identification and prioritization.

Algorithms↗

PubMed2001

The genetic epidemiology of cancer: interpreting family and twin studies and their implications for molecular genetic approaches.

The recent completion of a rough draft of the human genome sequence has ushered in a new era of molecular genetics research into the inherited basis of a number of complex diseases such as cancer. At the same time, recent twin studies have suggested a limited role of genetic susceptibility to many neoplasms. A reappraisal of family and twin studies for many cancer sites suggests the following general conclusions: (a) all cancers are familial to approximately the same degree, with only a few exceptions (both high and low); (b) early age of diagnosis is generally associated with increased familiality; (c) familiality does not decrease with decreasing prevalence of the tumor-in fact, the trend is toward increasing familiality with decreasing prevalence; (d) a multifactorial (polygenic) threshold model fits the twin data for most cancers less well than single gene or genetic heterogeneity-type models; (e) recessive inheritance is less likely generally than dominant or additive models; (f) heritability decreases for rarer tumors only in the context of the polygenic model but not in the context of single-locus or heterogeneity models; (g) although the family and twin data do not account for gene-environment interactions or confounding, they are still consistent with genes contributing high attributable risks for most cancer sites. These results support continued search for genetic and environmental factors in cancer susceptibility for all tumor types. Suggestions are given for optimal study designs depending on the underlying architecture of genetic predisposition.

Environment↗

PubMed2002

New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies.

Since public and private efforts announced the first draft of the human genome last year, researchers have reported great numbers of single nucleotide polymorphisms (SNPs). We believe that the availability of well-mapped, quality SNP markers constitutes the gateway to a revolution in genetics and personalized medicine that will lead to better diagnosis and treatment of common complex disorders. A new generation of tools and public SNP resources for pharmacogenomic and genetic studies--specifically for candidate-gene, candidate-region, and whole-genome association studies--will form part of the new scientific landscape. This will only be possible through the greater accessibility of SNP resources and superior high-throughput instrumentation-assay systems that enable affordable, highly productive large-scale genetic studies. We are contributing to this effort by developing a high-quality linkage disequilibrium SNP marker map and an accompanying set of ready-to-use, validated SNP assays across every gene in the human genome. This effort incorporates both the public sequence and SNP data sources, and Celera Genomics' human genome assembly and enormous resource ofphysically mapped SNPs (approximately 4,000,000 unique records). This article discusses our approach and methodology for designing the map, choosing quality SNPs, designing and validating these assays, and obtaining population frequency ofthe polymorphisms. We also discuss an advanced, high-performance SNP assay chemisty--a new generation of the TaqMan probe-based, 5' nuclease assay-and high-throughput instrumentation-software system for large-scale genotyping. We provide the new SNP map and validation information, validated SNP assays and reagents, and instrumentation systems as a novel resource for genetic discoveries.

Alleles↗

PubMed2003

Genetic mapping and characterization of the bleeding disorder in the fawn-hooded hypertensive rat.

Release of platelet dense granule contents occurs in response to vascular injury, playing an important role in platelet aggregation and primary hemostasis. Abnormalities of the platelet dense granules results in a bleeding disorder of variable severity termed "storage pool defect" (SPD). We have examined the fawn-hooded hypertensive (FHH) rat as a model of SPD in order to genetically map the locus (Bd) responsible for prolonged bleeding. Platelet function assays of the FHH rat confirmed the presence of a platelet dense granule SPD. However electron microscopy and lysosomal enzyme assays indicated differences between the FHH rat and other rodent models of SPD. Genetic mapping through the use of congenic FHH rats localized the Bd locus to an approximately 1 cM region on rat chromosome 1. Through the use of comparative mapping between species and analysis of the initial draft of the rat genome assembly, six known and thirty-four putative genes were identified in the Bd locus. None of these genes have been previously implicated in platelet function. Therefore positional cloning of the gene responsible for the bleeding disorder in the FHH rat will lead to new insights in platelet physiology, with implications for diagnosis and management of hemostatic and thrombotic disorders.

Animals↗

PubMed2004

Postmortem investigations of the pathophysiology of schizophrenia: the role of susceptibility genes.

Despite robust evidence for the heritability of schizophrenia, postmortem studies have not traditionally linked cellular and molecular neuropathology with underlying genetic mechanisms in this disorder. The completion of the first draft of the Human Genome Project and the use of novel strategies in studying complex genetic disorders including schizophrenia have led to the identification of a growing list of schizophrenia susceptibility genes. In this review, we describe the strategy used to incorporate 2 potential schizophrenia susceptibility genes in the postmortem investigation of the pathophysiology of schizophrenia driven by 2 well-established hypotheses, the dopamine hypothesis and the neurodevelopmental hypothesis. The first gene codes for catechol-O-methyltransferase, an enzyme involved in catecholamine degradation, and the second gene codes for brain-derived neurotrophic factor, a growth factor implicated in cell survival, synaptogenesis and the development of cortical pyramidal neurons.

Catechol O-Methyltransferase↗

PubMed2004

Structure and regulation of human troponin genes.

The recent completion of a first draft of the human genome has allowed "in silico" genome browsing to become routine. Such computer-based research is now a useful adjunct to experiments based at the bench, and is accelerating gene discovery and the analysis and understanding of genes in their genomic contexts. This review summarises recent findings on genes encoding proteins of the troponin complex. We describe the organization of the three pairs of genes which encode isoforms of troponins I and T, and discuss how this relates to their evolution and regulation. Detailed analysis of the chromosomal context of the cardiac troponin I and slow skeletal troponin T genes reveals a region of densely packed differentially expressed genes, including new genes identified by automatic genome annotation. This information is discussed within the context of detailed analysis of the best-studied gene in this region, cardiac troponin I. In this way, we illustrate the uses to which a combination of conventional bench experiments and "in silico" analyses may be put in understanding the relationship between structure and function within the genome.

Animals↗

PubMed2002

[Predictive genetic testing - change in paradigms for prevention and health care?].

The post-genomic era promises to offer new insights into the nature of disease, its prevention, and treatment. But now that there is a draft code of the human genome, what does this knowledge mean and how might it be applied? How to use genetic information to promote health and prevent disease - the fundamental mission of public health - will be one of the most challenging tasks in future. Assessing the benefits and risks of predictive genetic testing and the efficacy of early interventions as well as exploring complex issues that have emerged (e. g., rapid commercialization of genetic tests, availability of and access to interventions, and potencial discrimination) call for public health leadership.

Forecasting↗

PubMed2001

A computational scan for U12-dependent introns in the human genome sequence.

U12-dependent introns are found in small numbers in most eukaryotic genomes, but their scarcity makes accurate characterisation of their properties challenging. A computational search for U12-dependent introns was performed using the draft version of the human genome sequence. Human expressed sequences confirmed 404 U12-dependent introns within the human genome, a 6-fold increase over the total number of non-redundant U12-dependent introns previously identified in all genomes. Although most of these introns had AT-AC or GT-AG terminal dinucleotides, small numbers of introns with a surprising diversity of termini were found, suggesting that many of the non-canonical introns found in the human genome may be variants of U12-dependent introns and, thus, spliced by the minor spliceosome. Comparisons with U2-dependent introns revealed that the U12-dependent intron set lacks the 'short intron' peak characteristic of U2-dependent introns. Analysis of this U12-dependent intron set confirmed reports of a biased distribution of U12-dependent introns in the genome and allowed the identification of several alternative splicing events as well as a surprising number of apparent splicing errors. This new larger reference set of U12-dependent introns will serve as a resource for future studies of both the properties and evolution of the U12 spliceosome.

Alternative Splicing↗

PubMed2002

Initial sequencing and comparative analysis of the mouse genome.

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Animals↗

PubMed2001

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.

We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.

Alu Elements↗

PubMed2001

The role of oncology nurses in gene therapy.

In February 2001, the Human Genome Project international consortium announced the publication of a draft sequence and initial analysis of the human genome. Although a definitive count of human genes must await further experimental and computational analysis, scientists now estimate that the human genome contains 30000-35000 genes--a much smaller number than initially estimated. The advances in treatment which will result from this research and our improved understanding of cancer at a molecular level will rapidly change the management of cancer. Gene therapy represents one new approach to treatment, but is currently still experimental. This article reviews the important role of the oncology nurse as a member of the multidisciplinary team caring for patients who receive gene therapy as part of a clinical trial.

Genetic Therapy↗

PubMed2026

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

SUMMARY: Next Generation Sequencing is widely deployed in cholera-endemic regions, yet an end-to-end reproducible pipeline that unifies read QC, filtering, reference mapping, variant calling/annotation, recombination screening, and extraction of parsimony informative sites/variant codons, phylogenetic inference for downstream phylodynamic and epidemiological analyses have been lacking, slowing outbreak investigation and public health response. CholeraSeq is a high-throughput genomics pipeline for cholera genomic surveillance. It ingests consensus genomes, short read sequence data, draft assemblies, and scales seamlessly from local to cloud environments. To accelerate epidemiological context placement of new outbreak strains, we provide a curated ready-to-use core genome alignment compiled from public data, enabling flexible, fast, integration of new samples for outbreak investigations. AVAILABILITY AND IMPLEMENTATION: CholeraSeq is freely available on the GitHub platform https://github.com/CERI-KRISP/CholeraSeq. CholeraSeq is implemented in Nextflow with a modular design building upon the nf-core community standards.

Cholera↗