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At least 325 records · Page 18Linked to original sources
PubMed2000

A genome-wide autosomal screen for schizophrenia susceptibility loci in 71 families with affected siblings: support for loci on chromosome 10p and 6.

Evidence from epidemiological studies and segregation analysis suggests oligo- or polygenic inheritance in schizophrenia. Since model independent methods are thought to be most appropriate for linkage analysis in complex disorders, we performed a genome-wide autosomal screen in 71 families from Germany and Israel containing 86 independent affected sib-pairs with parental genotype information for statistical analysis strictly identity by descent. We genotyped 305 individuals with 463 markers at an average distance of approximately 10 cM genome-wide, and 1-2 cM in candidate regions (5q, 6p, q, 8p, 10p, 18p, 22q). The highest multipoint LOD scores (ASPEX) were obtained on 6p (D6S260, LOD = 2.0; D6S274, LOD = 2.2, MHC region, LOD = 2.15) and on 10p (D10S1714, LOD = 2.1), followed by 5q (D5S2066, LOD = 1.36), 6q (D6S271, LOD = 1.12; D6S1613, LOD = 1.11), 1q (D1S2675, LOD = 1.04), and 18p (broad disease model: D18S1116, LOD = 1.0). One hundred and thirty-three additional family members were available for some of the families (extended families) and were genotyped for these regions. GENEHUNTER produced a maximum NPL of 3.3 (P = 0.001) for the MHC region and NPL of 3.13 (P = 0.0015) for the region on 10p. There is support for these regions by independent groups. In genome-wide TDT analysis (sTDT, implemented in ASPEX), no marker passed the significance level of 0.0001 given by multiple testing, but nominal significance values for D10S211 (P = 0.03) and for GOLF (P = 0.0032) support further the linkage results on 10p and 18p. Our survey of 22 chromosomes identified candidate regions which should be useful to screen for schizophrenia susceptibility genes.

Chromosome Mapping↗
PubMed2001

Primate and feline lentivirus vector RNA packaging and propagation by heterologous lentivirus virions.

Development of safe and effective gene transfer systems is critical to the success of gene therapy protocols for human diseases. Currently, several primate lentivirus-based gene transfer systems, such as those based on human and simian immunodeficiency viruses (HIV/SIV), are being tested; however, their use in humans raises safety concerns, such as the generation of replication-competent viruses through recombination with related endogenous retroviruses or retrovirus-like elements. Due to the greater phylogenetic distance from primate lentiviruses, feline immunodeficiency virus (FIV) is becoming the lentivirus of choice for human gene transfer systems. However, the safety of FIV-based vector systems has not been tested experimentally. Since lentiviruses such as HIV-1 and SIV have been shown to cross-package their RNA genomes, we tested the ability of FIV RNA to get cross-packaged into primate lentivirus particles such as HIV-1 and SIV, as well as a nonlentiviral retrovirus such as Mason-Pfizer monkey virus (MPMV), and vice versa. Our results reveal that FIV RNA can be cross-packaged by primate lentivirus particles such as HIV-1 and SIV and vice versa; however, a nonlentivirus particle such as MPMV is unable to package FIV RNA. Interestingly, FIV particles can package MPMV RNA but cannot propagate the vector RNA further for other steps of the retrovirus life cycle. These findings reveal that diverse retroviruses are functionally more similar than originally thought and suggest that upon coinfection of the same host, cross- or copackaging may allow distinct retroviruses to generate chimeric variants with unknown pathogenic potential.

Animals↗
PubMed2004

Reverse methanogenesis: testing the hypothesis with environmental genomics.

Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.

Anaerobiosis↗
PubMed2003

Managed care in the genomics era: assessing the cost effectiveness of genetic tests.

BACKGROUND: Despite the fact that the Human Genome Project was completed only recently, genetic tests already have entered the marketplace, some with few or no long-term data to support their use. Managed care organizations will face reimbursement decisions for genetic tests on a growing scale, and they should have a framework in place to evaluate the clinical and economic outcomes of this new class of diagnostics. OBJECTIVE: To develop a set of criteria that could assist decision makers in evaluating the cost effectiveness of genetic testing. METHODS: A literature review was conducted of marketed genetic tests and criteria used to evaluate the clinical and economic benefits of genetic testing. Criteria were developed and pilot-tested on currently available genetic tests in colon cancer, periodontitis, acute lymphoblastic leukemia, and anticoagulation. RESULTS: A robust cost-effectiveness analysis requires data demonstrating (1) genotype-phenotype association; (2) genetic variant prevalence; (3) clinical outcome severity and incidence; (4) interventions for the variant group; and (5) sensitivity, specificity, and timing of the assay result. In addition, calculating the number of patients who need to be screened based on the above factors is useful for evaluating genetic tests. CONCLUSIONS: When evaluating a genetic test for reimbursement, these criteria can help to: (1) quantify the potential clinical benefit and economic savings; (2) assess the robustness of a cost-effectiveness analysis; and (3) clarify areas where data are deficient. These criteria should be used to inform the decision-making process in the context of ethical, legal, and social issues related to genetic testing.

Cost-Benefit Analysis↗
PubMed1998

Ethnic cluster of HTLV-I infection in Israel among the Mashhadi Jewish population.

A high prevalence of human T-lymphotropic virus type I (HTLV-I) infection among Israeli Jews was previously reported. In the present study, screening for HTLV-I of Israeli Jews was expanded to 10 ethnic groups. HTLV-I antibodies were tested by the particle agglutination assay, ELISA, and by Western blot as a confirmatory method. The HTLV-I proviral genome was tested by nested PCR with tax primers (SK43/SK44 and Tr101/Tr102). The PCR tests were carried out in all seropositive subjects and the seronegative family members of the seropositives subjects in the Iranian population. Sixty-eight of the 1,679 subjects (4.1%) were found to be seropositive. The Jews originating from Mashhad had the highest infection rate of 60/306 (20%). Of the 479 Iranian non-Mashhadi Jews, 6 (1.3%) were seropositive. Of the 894 non-Iranian Israelis, only 2 (0.2%) were seropositive. HTLV-I proviral DNA was found in the peripheral blood lymphocytes of 66 out of 68 seropositive subjects and 6 out of 75 seronegative subjects. Sixty out of 123 (49%) Mashhadi Jews and 8 out of 14 (57%) non-Mashhadi Iranian Jews were PCR-positive. Three out of three seropositive non-Iranian Israelis were PCR positive. One non-Iranian Israeli (who originated from Ukraine) without family connections to the Iranian Jews was also PCR-positive. One hundred eighteen saliva samples (84 from subjects of Mashhadi origin, 31 from Iranian origin, and 4 of other origins) were also screened. Antibodies for HTLV-I were found in 23 out of 46 saliva samples from the individuals with particle agglutination (PA) and/or PCR-positive findings in blood. Twenty out of 23 PA-positive saliva samples also contained the proviral DNA. It is concluded that HTLV-I infection in Israel is mainly limited to Jews originating from Iran (most of them from Mashhad) and their family members.

Adolescent↗
PubMed1998

Phase I/IIa safety, immunogenicity, and efficacy trial of NYVAC-Pf7, a pox-vectored, multiantigen, multistage vaccine candidate for Plasmodium falciparum malaria.

Candidate malaria vaccines have failed to elicit consistently protective immune responses against challenge with Plasmodium falciparum. NYVAC-Pf7, a highly attenuated vaccinia virus with 7 P. falciparum genes inserted into its genome, was tested in a phase I/IIa safety, immunogenicity, and efficacy vaccine trial in human volunteers. Malaria genes inserted into the NYVAC genome encoded proteins from all stages of the parasite's life cycle. Volunteers received three immunizations of two different dosages of NYVAC-Pf7. The vaccine was safe and well tolerated but variably immunogenic. While antibody responses were generally poor, cellular immune responses were detected in >90% of the volunteers. Of the 35 volunteers challenged with the bite of 5 P. falciparum-infected Anopheles mosquitoes, 1 was completely protected, and there was a significant delay in time to parasite patency in the groups of volunteers who received either the low or high dose of vaccine compared with control volunteers.

Adolescent↗
PubMed1994

Endogenous viral complexes with long RNA cosediment with the agent of Creutzfeldt-Jakob disease.

A class of viruslike agents that induces Creutzfeldt-Jakob Disease (CJD) and scrapie remains undefined at the molecular level. Several investigators believe this infectious agent is constituted by a single host protein or 'prion', and have emphasized data that would seem to exclude the presence of any viral nucleic acids. However, more rigorous evaluations in scrapie have shown reasonably abundant nucleic acids. Additionally, in highly purified 120S CJD preparations that have been treated with nucleases, RNAs as long as 6,000 bases have been detected. Few nucleic acids have been characterized in either scrapie or CJD, but previous cloning experiments delineated relatively short LTR regions of the endogenous IAP retrovirus in 120S CJD preparations. We therefore used specific primers encompassing the entire IAP genome to test for the presence of long viral RNAs, and here show approximately 5,000 contiguous bases of the IAP RNA genome can be recovered from reasonable amounts of starting brain. The 3' env region of IAP is comparably truncated in CJD and normal preparations, and we find no evidence for IAP transduction of CJD-specific sequences. Because IAP cores can coencapsidate unrelated sequences, and are unusually resistant to physical and chemical treatments, it was relevant to find if cosedimenting cognate proteins of the IAP core, such as gag, could be detected. The predicted approximately 65 kd acidic gag protein, showing appropriate antigenic and nucleic acid binding features, was apparent in both one and 2-D Western blots. This data strongly indicates specific viral complexes cofractionate with the CJD agent. Interestingly, these nuclease resistant IAPs do not appear to be in morphologically recognizable 'R' particles. This cosedimenting viral assembly therefore provides a paradigm for non-particulate CJD complexes in infectious preparations. In developing strategies to identify a CJD specific sequence, cosedimenting IAPs can be used to assess the quality, length and recovery of RNAs extracted from highly resistant viral complexes.

Animals↗
PubMed1992

RNA sequence variants in live poliovirus vaccine and their relation to neurovirulence.

Mutant analysis by polymerase chain reaction and restriction enzyme cleavage (MAPREC) was used to study sequence heterogeneity and stability in attenuated poliovirus type 3 at positions in which the vaccine virus differs from its wild-type progenitor. Of seven genomic positions tested, only two (positions 472 and 2493) show nucleotide heterogeneity. Propagation of the vaccine virus in cell cultures leads to rapid selection of virus with reversions at these two positions of the genome. The relative abundance of reversions at position 472 correlates with the results of monkey neurovirulence tests, while the mutation at position 2493 is not directly associated with neurovirulence of the virus in monkeys. Instead, the abundance of mutations at the latter position correlates with the source of the seed virus and its passage level. These results further indicate that MAPREC at position 472 can be used to assess the quality of poliovirus type 3 vaccine.

Animals↗
PubMed2026

Genomic Medicine Sweden: Advancing precision medicine at the national level.

High-throughput sequencing has transformed clinical diagnostics of rare diseases (RD), cancer and infectious diseases by enabling the identification of disease-causing genetic alterations and facilitating individualised treatment and care. In response to these advances, Genomic Medicine Sweden (GMS) was established in 2017 as a national collaborative effort to accelerate implementation of genomics-based precision medicine within Sweden's regionally organized, publicly funded healthcare system. GMS brings together the seven university healthcare regions and their associated medical faculties, in collaboration with healthcare regions across Sweden, Science for Life Laboratory, patient organizations, industry and governmental agencies. Activities are coordinated through national disease-specific expert groups, supported by cross-cutting functions in bioinformatics, health economics, ethics, education and patient engagement. At the operational level, seven Genomic Medicine Centres, embedded at university hospitals, develop and deliver harmonised genomic diagnostics nationwide. The National Genomics Platform provides secure infrastructure for large-scale data storage, analysis, and national and international data sharing. Following initial project-based funding, GMS now receives long-term governmental support. This review describes the national implementation of genomic-based precision diagnostics, discusses challenges and lessons learnt, and highlights key milestones across disease areas, including whole-genome sequencing in RD and paediatric cancer, comprehensive genomic profiling of haematological malignancies and solid tumours, pathogen genomics in microbiology, pharmacogenomic testing and emerging applications of polygenic risk scores in complex diseases. Collectively, these efforts have contributed to more than 500,000 genomic tests being performed within Swedish healthcare between 2017 and 2025. Finally, we outline future diagnostic needs and priority areas to ensure sustainable, scalable and equitable access to precision medicine.

Precision Medicine↗
PubMed2005

Genomic medicine and thrombotic risk: who, when, how and why?

Major advances in Human Genome research could significantly change the clinical medical practice, providing new possibilities for both diagnosing and treating common pathologies. Many genetic tests are now commercially available for predicting future risk of common disorders. However, genetic testing has potential benefits but also limitations for the patients, and it should not be used to 'screen' the general population. Diagnostic assays for a predisposition of both venous and arterial thrombosis are among the most requested genetic tests in molecular diagnostics laboratories. However, there is considerable uncertainty as to how this information should be utilized in patient management. Both the medical community and the patients need to obtain accurate information concerning the appropriate use of genetic testing. The purpose of this article is to discuss the usefulness and the practical applications of thrombotic genetic testing in order to define which patients should be tested for both venous and arterial thrombotic risk as well as to have an acceptable cost/benefit ratio and to prevent patients' anxiety.

Ethics, Medical↗
PubMed2006

Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana.

Duplication of chromatin following DNA replication requires spatial reorganization of chromatin domains assisted by chromatin assembly factor CAF-1. Here, we tested the genomic consequences of CAF-1 loss and the function of chromatin assembly factor CAF-1 in heterochromatin formation. Genes located in heterochromatic regions are usually silent, and we found that this transcriptional repression persists in the absence of CAF-1 in Arabidopsis. However, using microarrays we observed that genes that are active during late S-phase, when heterochromatin is duplicated, were up-regulated in CAF-1 mutants. Arabidopsis CAF-1 mutants also have reduced cytological heterochromatin content; however, DNA methylation of pericentromeric repeats was normal, demonstrating that CAF-1 is not required for maintenance of DNA methylation. Instead, hypomethylation of the genome, which has only mild effects on the development of wild-type plants, completely arrested development of CAF-1 mutants. These results suggest that CAF-1 functions in heterochromatin formation. CAF-1 and DNA methylation, which is also needed for heterochromatin formation, have partially redundant functions that are essential for cell proliferation. Interestingly, transcriptional repression and heterochromatin compaction can be genetically separated, and CAF-1 is required only for the complete compaction of heterochromatin but not to maintain transcriptional repression of heterochromatic genes.

Arabidopsis↗
PubMed1998

Genome search in celiac disease.

Celiac disease (CD), a malabsorption disorder of the small intestine, results from ingestion of gluten. The HLA risk factors involved in CD are well known but do not explain the entire genetic susceptibility. To determine the localization of other genetic risk factors, a systematic screening of the genome has been undertaken. The typing information of 281 markers on 110 affected sib pairs and their parents was used to test linkage. Systematic linkage analysis was first performed on 39 pairs in which both sibs had a symptomatic form of CD. Replication of the regions of interest was then carried out on 71 pairs in which one sib had a symptomatic form and the other a silent form of CD. In addition to the HLA loci, our study suggests that a risk factor in 5qter is involved in both forms of CD (symptomatic and silent). Furthermore, a factor on 11qter possibly differentiates the two forms. In contrast, none of the regions recently published was confirmed by the present screening.

Celiac Disease↗
PubMed2003

HPV 16 detection in cervical lesions, physical state of viral DNA and changes in p53 gene.

CONTEXT: Persistent infection with high risk human papillomavirus (HPV) has been linked to cervical carcinoma. Integration of viral DNA into host cell DNA is essential for this cancer development, promoting disruption of the HPV E2 gene, thus leading to unregulated increases in E6 and E7 proteins and inactivating the products of p53 and Rb tumor suppressor genes. OBJECTIVE: To investigate HPV 16 infection in cervical lesions, physical state of viral DNA and p53 gene alterations in a group of women attending a public health service. DESIGN: Prospective, non-controlled, transversal study. SETTING: Gynecological clinic of the School of Medicine, Universidade Federal Fluminense. SAMPLE: 43 consecutive patients with cervical lesions referred to our service. MAIN MEASUREMENTS: Cases were classified via cytology/histology as normal, HPV infection, condyloma, low-grade squamous intraepithelial lesion (LSIL), high-grade squamous intraepithelial lesion (HSIL) and carcinoma. HPV infection was studied via polymerase chain reaction (PCR) using two PCR primer sets, to determine DNA integration. p53 gene changes were investigated by single-strand conformation polymorphism (SSCP) analysis. RESULTS: One normal case, 7 HPV infections, 6 condylomas, 7 LSIL, 14 HSIL and 8 cancers were found, with 95% positive for HPV genome when tested using both L1 and E6 primers. HPV 16 was most prevalent (73.1%). HPV 16 DNA was integrated within the host genome in 3 LSIL. One LSIL progressed to HSIL by 13 months after first diagnosis. Among HPV 16-positive HSIL cases, 50% contained integrated viral DNA. HPV 16 E2 gene disruption was seen in 7 cancers (87.5%). Only smal-cell carcinoma showed intact HPV 16 E2 gene. Abnormal p53 bands detected by PCR/SSCP were observed in 4 cases: 2 squamous carcinoma with parametrium (exon 8) and two cervical intraepithelial neoplasia (CIN) III (exons 5 and 7). All cases presented HPV 16 E2 gene loss. CONCLUSIONS: The sample had a high rate of high-risk HPV detected in benign and malignant lesions; high cervical cancer burden; HPV 16 DNA integration in all except one case of cancer; p53 gene changes in CIN III and in invasive cancer cases associated with DNA integration.

Adolescent↗