Novel citation-based search method for scientific literature: application to meta-analyses.

BACKGROUND: Finding eligible studies for meta-analysis and systematic reviews relies on keyword-based searching as the gold standard, despite its inefficiency. Searching based on direct citations is not sufficiently comprehensive. We propose a novel strategy that ranks articles on their degree of co-citation with one or more "known" articles before reviewing their eligibility. METHOD: In two independent studies, we aimed to reproduce the results of literature searches for sets of published meta-analyses (n = 10 and n = 42). For each meta-analysis, we extracted co-citations for the randomly selected 'known' articles from the Web of Science database, counted their frequencies and screened all articles with a score above a selection threshold. In the second study, we extended the method by retrieving direct citations for all selected articles. RESULTS: In the first study, we retrieved 82% of the studies included in the meta-analyses while screening only 11% as many articles as were screened for the original publications. Articles that we missed were published in non-English languages, published before 1975, published very recently, or available only as conference abstracts. In the second study, we retrieved 79% of included studies while screening half the original number of articles. CONCLUSIONS: Citation searching appears to be an efficient and reasonably accurate method for finding articles similar to one or more articles of interest for meta-analysis and reviews.

Prioritizing genomic applications for action by level of evidence: a horizon-scanning method.

As evidence accumulates on the use of genomic tests and other health-related applications of genomic technologies, decision makers may increasingly seek support in identifying which applications have sufficiently robust evidence to suggest they might be considered for action. As an interim working process to provide such support, we developed a horizon-scanning method that assigns genomic applications to tiers defined by availability of synthesized evidence. We illustrate an application of the method to pharmacogenomics tests.

Viral hepatitis C gets personal--the value of human genomics to public health.

About 180 million people worldwide are chronically infected with hepatitis C virus (HCV), with 3-4 million newly infected each year. Only 15-25% of acute HCV infections clear spontaneously, and the remainder persists as chronic HCV infection. More than 350,000 people die every year from hepatitis C-related liver failure and cancer. There is currently no vaccine and the standard-of-care therapies--peg-interferon alpha (pegIFN) plus ribavirin (RBV)--are expensive and have serious side effects. Also, they may be effective in only 40-50% of patients infected with HCV genotype 1, the most common HCV genotype in the US. Interleukin 28B (IL28B) genotype was recently and convincingly associated with response to pegIFN and RBV therapy. It has emerged as a robust pretreatment predictor of sustained virological response (SVR, i.e. virologic clearance) to pegIFN and RBV as well as to new triple therapy regimens that include a direct-acting antiviral agent with pegIFN and RBV and increase SVR rates as much as 75% in patients infected with HCV genotype 1. Testing for IL28B genotype may contribute to clinical decision-making and could inform clinical guidelines and public health policies.

Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations.

SUMMARY: We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continuously updated from PubMed. These applications provide user-friendly interfaces for searching summarized information on human genetic associations, using either genes or diseases as the starting point. AVAILABILITY: Phenopedia and Genopedia can be freely accessed at http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do and http://www.hugenavigator.net/HuGENavigator/startPagePedia.do, respectively.

Trends in pharmacogenomic epidemiology: 2001-2007.

BACKGROUND: Pharmacogenomic epidemiology (PGxE) assesses the range of responses to pharmacologic agents in relation to genetic variation in population groups. We analyzed publication trends to describe the emerging field of PGxE. METHODS: We analyzed PGxE literature published from 2001 to 2007 by using the HuGE Navigator, a curated database of abstracts on human genome epidemiology extracted from PubMed. We summarized trends by gene and study design and, for the 4 most cited genes, by associated health outcomes and drugs. RESULTS: In all, 1,855 PGxE articles were indexed from 2001 through 2007, with annual publications increasing more than 15-fold during this period. Observational studies outnumbered clinical trials by a ratio of 10 to 1 (1,660 vs. 178). Just 4 genes together accounted for nearly one-fifth of all publications: ABCB1, CYP2C9, CYP2C19, and CYP2D6. For these 4 genes, the most frequently cited therapeutic category was antineoplastic agent, followed by anticoagulant, antiulcer, and antidepressant. Warfarin was the single most frequently cited drug. CONCLUSIONS: The field of PGxE is growing rapidly, encompassing a large spectrum of diseases and drugs important in clinical practice. Systematic tracking and synthesis of the published literature in PGxE can help identify promising applications and guide translation research.

A decade of public health genomics in the United States: centers for disease control and prevention 1997-2007.

Since 1997, the Centers for Disease Control and Prevention (CDC) has collaborated with numerous partners to develop and chart the course of the multidisciplinary field of public health genomics in the USA and globally. During this period, CDC has developed major initiatives for the appropriate integration of genomics into public health research, policy and programs. In this paper, we review briefly the progress in public health genomics made over the past decade in the USA, including population research, the human genome epidemiology network (HuGENet(TM)), the evaluation of genomic applications in practice and prevention (EGAPP), the family history public health initiative, and efforts in building the public health genomics capacity. We also outline a vision for public health genomics for the next decade.

The Gene Ontology (GO) database and informatics resource.

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.

Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

Informed consent for population-based research involving genetics.

Bridging the gap between gene discovery and our ability to use genetic information to benefit health requires population-based knowledge about the contribution of common gene variants and gene-environment interactions to the risk of disease. The risks and benefits associated with population-based research involving genetics, especially lower-penetrance gene variants, can differ in nature from those associated with family-based research. In response to the urgent need for appropriate guidelines, the Centers for Disease Control and Prevention formed a multidisciplinary group to develop an informed consent approach for integrating genetic variation into population-based research. The group used expert opinion and federal regulations, the National Bioethics Advisory Commission's report on research involving human biological materials, existing consent forms, and literature on informed consent to create suggested language for informed consent documents and a supplemental brochure. This language reflects the premise that the probability and magnitude of harm, as well as possible personal benefits, are directly related to the meaning of the results for the health of the participant and that appropriate disclosures and processes for obtaining consent should be based on an assessment at the outset of the likelihood that the results will generate information that could lead directly to an evidence-based intervention. This informed consent approach is proposed to promote discussion about how best to enable potential participants to make informed decisions about population-based research involving genetics and to suggest issues for consideration by research sponsors, institutional review boards, and investigators.

Public health impact of genetic tests at the end of the 20th century.

PURPOSE: To evaluate genetics tests available for clinical, research, and public health purposes in terms of their public health impact as measured by the number of people who could potentially be tested. METHODS: Genetic tests for the 751 inherited diseases or conditions listed in the GeneTests database as of November 2000, were classified on the basis of their use for population-based testing and the prevalence of the disease or condition being tested. The GeneTests database divides the tests into two groups: those offered for clinical use and those available for research only. RESULTS: Of the 423 clinical tests, 51 had potentially greater impact on public health because of their use in statewide newborn screening programs, other population screening programs, or testing for common diseases with a prevalence over 1 in 2,000 people. Among the 328 tests performed for research purposes only, 18 met the criteria for potentially greater public health impact. CONCLUSIONS: Our classification scheme indicated that fewer than 10% of the genetic tests listed in the GeneTests database at the end of 2000 are highly relevant to public health. The majority of genetic tests are used in diagnosis and/or genetic counseling for rare, single-gene disorders in a limited number of people. However, as more tests are being considered for newborn screening, and associations between genes and common diseases are being discovered, the impact of genetic testing on public health is likely to increase.

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.

The 2,160,837-base pair genome sequence of an isolate of Streptococcus pneumoniae, a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; of these, 1440 (64%) were assigned a biological role. Approximately 5% of the genome is composed of insertion sequences that may contribute to genome rearrangements through uptake of foreign DNA. Extracellular enzyme systems for the metabolism of polysaccharides and hexosamines provide a substantial source of carbon and nitrogen for S. pneumoniae and also damage host tissues and facilitate colonization. A motif identified within the signal peptide of proteins is potentially involved in targeting these proteins to the cell surface of low-guanine/cytosine (GC) Gram-positive species. Several surface-exposed proteins that may serve as potential vaccine candidates were identified. Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity.

Incidence of HIV among injection drug users entering drug treatment programs in four US cities.

We estimated seroincidence of human immunodeficiency virus (HIV) and prevalence of risk behaviors among injection drug users (IDUs) who accepted voluntary HIV testing on entry to drug treatment. Record-based incidence studies were conducted in 12 drug treatment programs in New York City (n = 890); Newark, New Jersey (n = 521); Seattle, Washington (n = 1,256); and Los Angeles, California (n = 733). Records of confidential HIV tests were abstracted for information on demographics, drug use, and HIV test results. More detailed data on risk behaviors were obtained by a standardized questionnaire. Although overall incidence rates were relatively low in this population (<1/100 person-years), there was a high prevalence of risk behaviors. Needle sharing was reported by more than one-third of the participants in each of the cities. HIV seroincidence rates were up to three-fold higher among younger ID Us. We found that HIV continued to be transmitted among ID Us who had received both drug treatment and HIV counseling and testing. HIV/AIDS (acquired immunodeficiency syndrome) prevention education should continue to be an important component of drug treatment.

Hemochromatosis-associated morbidity in the United States: an analysis of the National Hospital Discharge Survey, 1979-1997.

PURPOSE: The recent discovery of the HFE gene and its association with hereditary hemochromatosis has renewed the attention directed to iron-overload diseases. Population screening for hereditary hemochromatosis is under debate, and population-based estimates of morbidity associated with hereditary hemochromatosis are needed. The purpose of this study is to estimate the number of hemochromatosis-associated hospitalizations in the United States using a population-based dataset. METHODS: National Hospital Discharge Survey and census data were used to estimate hemochromatosis-associated hospitalization rates for persons 18 years of age and over. RESULTS: From 1979 through 1997, the rate of hemochromatosis-associated hospitalizations was 2.3 per 100,000 persons in the United States. The rate among persons 60 years of age and over increased more than 60% during this time period. CONCLUSION: The increase in the rate of hereditary hemochromatosis-associated hospitalizations among older persons is consistent with recent trends in mortality data and may reflect the rising awareness of iron-overload disorders in the United States.

Complete genome sequence of Caulobacter crescentus.

The complete genome sequence of Caulobacter crescentus was determined to be 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. This organism, which grows in a dilute aquatic environment, coordinates the cell division cycle and multiple cell differentiation events. With the annotated genome sequence, a full description of the genetic network that controls bacterial differentiation, cell growth, and cell cycle progression is within reach. Two-component signal transduction proteins are known to play a significant role in cell cycle progression. Genome analysis revealed that the C. crescentus genome encodes a significantly higher number of these signaling proteins (105) than any bacterial genome sequenced thus far. Another regulatory mechanism involved in cell cycle progression is DNA methylation. The occurrence of the recognition sequence for an essential DNA methylating enzyme that is required for cell cycle regulation is severely limited and shows a bias to intergenic regions. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing the organism with the ability to respond to a wide range of environmental fluctuations. C. crescentus is, to our knowledge, the first free-living alpha-class proteobacterium to be sequenced and will serve as a foundation for exploring the biology of this group of bacteria, which includes the obligate endosymbiont and human pathogen Rickettsia prowazekii, the plant pathogen Agrobacterium tumefaciens, and the bovine and human pathogen Brucella abortus.