PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “clinical genetics database”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed1997

Automated detection of hereditary syndromes using data mining.

Computer-based data mining methodology applied to family history clinical data can algorithmically create highly accurate, clinically oriented hereditary disease pattern recognizers. For the example of hereditary colon cancer, the data mining's selection of relevant factors to assess for hereditary colon cancer was statistically significant (P < 0.05). All final recognizer-formulated patterns of hereditary colon cancer were independently confirmed by a clinical expert. Applied to previously analyzed family histories, the recognizer identified the definitive hereditary histories, correctly responded negatively to the putative hereditary histories, and correctly responded negatively to empirically elevated colon cancer risk situations. This capability facilitates patient selection for DNA studies in search of gene mutations. When genetic mutations are included as parameters in a patient database for a genetic disease, the process yields an expert system which characterizes variations in clinical disease presentations in terms of genetic mutations. Such information can greatly improve the efficiency of gene testing.

Adult↗
PubMed2002

Developing a quality scoring system for epidemiological surveys of genetic disorders.

A prototype database of published articles containing data on the frequency of human inherited disorders has been developed for use in clinical contexts, in medical research, for epidemiological studies, and in the planning of genetic services. It can be accessed at http://www.uwcm.ac.uk/uwcm/mg/fidd/. The information available in the literature comes from a wide range of publications, not all can be described primarily as epidemiological surveys. A preliminary assessment indicated that the quality of published articles was highly variable. Very few published articles describe quality-scoring systems for epidemiological surveys in general. We have developed a new scoring system to assess the quality of published articles on genetic disease frequency based on five main criteria and nine component scores. We carried out a first pilot study, to test its feasibility, usefulness and reproducibility. Eleven assessors scored six papers on the epidemiology of Huntington disease. As a result of these findings, we modified the scoring system to define each component more clearly. This was then evaluated in a second pilot study, which utilized six assessors to score 20 papers. The consensus between assessors remained relatively poor. We feel that while it may be possible to improve the scoring system further, the degree of improvement attainable may be limited by the poor standards of content and presentation of published surveys, which led to confusion and uncertainty by assessors. This pilot exercise has shown the need to raise the awareness of researchers and clinicians about the basic quality standards to be required of epidemiological genetic surveys.

Epidemiologic Research Design↗
PubMed2005

Familial risk for non-Hodgkin lymphoma and other lymphoproliferative malignancies by histopathologic subtype: the Swedish Family-Cancer Database.

Non-Hodgkin lymphoma (NHL) consists of a heterogeneous group of tumors. Population-based data on the familial risk for specific histopathologic subtypes have not been established. Such data are useful for clinical counseling and for searching tumor subtypes sharing common genetic pathways. We used the Swedish Family-Cancer Database to calculate standardized incidence ratios (SIRs) for histopathology-specific subtypes of NHL in 4455 offspring with NHL whose parents or siblings were affected with different types of lymphoproliferative malignancies. A familial history of NHL significantly increased the risk for NHL (SIRparent = 1.8; SIRsibling = 1.9) and for diffuse large B-cell lymphoma (SIRparent = 2.3), follicular lymphoma (SIRsibling = 2.3), and B-cell lymphoma not otherwise specified (NOS) (SIRsibling = 3.4). For a parental history of histopathology-specific concordant cancer, the risks were significantly increased for diffuse large B-cell lymphoma (SIR = 11.8), follicular NHL (SIR = 6.1), plasma cell myeloma (SIR = 2.5), and chronic lymphocytic leukemia (SIR = 5.9). Familial clusters for NHL seemed stronger in females and in siblings. Our study provides the first quantification of the familial risks for NHL by histopathology. The present findings give evidence for a strong familial association of NHL, with little differences in the magnitude of risks for various histopathologic subtypes. The patterns of risks in parents and siblings support the hypothesis of an autosomal-dominant component for diffuse large B-cell NHL and a recessive one for follicular NHL.

Adult↗
PubMed2006

Personalized diagnosis by cached solutions with hypertension as a study model.

Statistical modeling of links between genetic profiles with environmental and clinical data to aid in medical diagnosis is a challenge. Here, we present a computational approach for rapidly selecting important clinical data to assist in medical decisions based on personalized genetic profiles. What could take hours or days of computing is available on-the-fly, making this strategy feasible to implement as a routine without demanding great computing power. The key to rapidly obtaining an optimal/nearly optimal mathematical function that can evaluate the "disease stage" by combining information of genetic profiles with personal clinical data is done by querying a precomputed solution database. The database is previously generated by a new hybrid feature selection method that makes use of support vector machines, recursive feature elimination and random sub-space search. Here, to evaluate the method, data from polymorphisms in the renin-angiotensin-aldosterone system genes together with clinical data were obtained from patients with hypertension and control subjects. The disease "risk" was determined by classifying the patients' data with a support vector machine model based on the optimized feature; then measuring the Euclidean distance to the hyperplane decision function. Our results showed the association of renin-angiotensin-aldosterone system gene haplotypes with hypertension. The association of polymorphism patterns with different ethnic groups was also tracked by the feature selection process. A demonstration of this method is also available online on the project's web site.

Algorithms↗
PubMedDate not supplied

The Diamond Blackfan Anemia Registry: tool for investigating the epidemiology and biology of Diamond-Blackfan anemia.

Diamond-Blackfan anemia (DBA) is a heterogeneous genetic disorder characterized by red cell aplasia and congenital anomalies. One of what appears to be multiple DBA genes has been cloned. Affected individuals in the same family may vary dramatically as to the degree of anemia, response to corticosteroids, and the presence of congenital anomalies. The epidemiology of DBA has been gleaned largely from literature reviews. This approach is limited because of the two-fold disadvantage of the reporting bias inherent in the literature and the lack of an active patient database. The Diamond Blackfan Anemia Registry of North America (DBAR) is designed to overcome these disadvantages to study the epidemiology and biology of DBA. The DBAR is a comprehensive database of patients with DBA who are enrolled after informed consent is obtained. Identification of patients is made through outreach to pediatric and adult hematologists and the Diamond Blackfan Anemia Foundation. The patients and/or their families complete a detailed questionnaire. A review of medical records and telephone interviews are performed to complete and clarify the information provided. To date, 354 patients have been enrolled in the DBAR. Using this database, important epidemiologic, clinical, and laboratory observations have been made with regard to the clinical presentation, the inheritance of DBA, the genetics of congenital malformations, the therapeutic outcome, including the efficacy of hematopoietic stem cell transplantation, and the recognition of DBA as a cancer predisposition syndrome. In particular, the database is an essential substrate for DBA gene discovery.

Child↗
PubMed2026

A Case Report of a Pedigree with Distal Hereditary Motor Neuropathy Caused by a Homozygous c.1124G>A Variant an the /*9Vaccinia-Related Kinase 1 Gene.

This study aimed to analyze the clinical phenotypes, neurophysiological characteristics, and pathogenicity of gene variants in a pedigree with distal hereditary motor neuropathy (dHMN) caused by VRK1 variants, and to provide evidence to support clinical diagnosis and genetic counseling for this disease. We report a Chinese consanguineous family with dHMN caused by a homozygous c.1124G>A variant in the VRK1 gene. Clinical and electrophysiological data of the proband were collected. Whole-exome sequencing (WES) and validation by Sanger sequencing were performed to identify the variant site, and pathogenicity interpretation was conducted in accordance with American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines. The proband was a 24-year-old male who presented with 2 years of progressive weakness and atrophy of the distal lower limbs, accompanied by slender upper limbs and no sensory disturbance. Electrophysiological examination showed decreased compound muscle action potential (CMAP) amplitude in motor nerves of both upper and lower limbs, indicating peripheral neurogenic damage, while sensory nerve conduction was normal. Genetic testing detected a homozygous c.1124G>A (p.Trp375Ter) variant in the VRK1 gene. His parents and elder sisters were heterozygous carriers, and the pedigree conformed to autosomal recessive inheritance. According to ACMG guidelines, this variant was classified as pathogenic (evidence: PVS1, PM2, PP1). The homozygous VRK1 c.1124G>A variant causes adult-onset dHMN, rather than pontocerebellar hypoplasia type 1A (PCH1A) as annotated in some genetic databases. This pedigree presents distinctive phenotypes, including slender upper limbs and diffusely decreased CMAP amplitudes in both upper and lower limbs, thereby expanding the clinical and genetic spectrum of VRK1-related dHMN in the Chinese population.

Humans↗
PubMed2001

Genomics and large scale phenotypic databases.

Progress in the development of molecular genetic tools and in sequencing the human genome will accelerate the understanding of complex genetic diseases. However, phenotypic clinical data needs to be obtained and recorded to a similar degree of precision in order to match the wealth of molecular genetic data. To achieve this goal, large scale phenotypic databases of complex genetic diseases are under construction. LURIC (the LUwigshafen Risk and Cardiovascular Health Study) is such a project, aiming to identify new genetic and environmental risk factors or markers for cardiovascular disease in order to better understand the pathophysiology of complex genetic disease. It should also allow the determination of the prognostic role of new markers by studying functional genomics, (the association between a gene variant and phenotype), and pharmacogenomics (the influence of genetic variation on the response to therapeutic agents).

Cardiovascular Diseases↗
PubMed2002

Status and potential of gene therapy in clinical medicine. Assessment of an emerging health technology through systematic survey of clinical gene therapy protocols and published results.

OBJECTIVE: Somatic gene therapy is a new method in the rapidly expanding field of molecular medicine. Due to recent encouraging results and the promising prospect for some disease groups, Norwegian health authorities wanted to assess somatic therapy with evidence-based standards for strategic use. This article presents the results of this assessment, discussed in the context of the policy-making process in Norway, including ethical and legislational considerations. METHODS: Clinical gene therapy protocols, ongoing or completed with published results, where available, were identified through a systematic survey of descriptive protocols and publications. Preclinical literature was also reviewed. RESULTS: Gene therapy is dominated by preclinical and clinical research. Most of the gene therapy protocols identified are in early phases (phases I and II) with only a few patients in each study. Of the protocols included in the assessment, only three phase III studies are represented. Except for the use of soluble antisense oligonucleotides against cytomegalovirus eye infection, gene therapy is presently not an established treatment modality. Promising results have been observed in treatment of cancer and cardiovascular diseases and, most recently, in inherited severe combined immunodeficiency and hemophilia. Several interesting principles addressing a large panel of conditions are currently being developed and tested. CONCLUSIONS: Gene therapy is developing into an important medical concept that needs to be included within the Norwegian healthcare system. It is recommended that the Norwegian Ministry of Health and Social Affairs fund a national program to boost infrastructure in selected scientific groups both in preclinical and clinical research. The national procedures regulating approval of gene therapy trials should be made more efficient while at the same time allowing for proper control and ethical considerations. It is emphasized that gene therapy trials should be carefully monitored for side effects.

Clinical Protocols↗
PubMed2026

Mapping the development pipeline of genomic point-of-care tests: a horizon scan.

INTRODUCTION: As precision medicine increasingly relies on genetic information, the development of reliable genomic point-of-care tests (POCTs) is essential. However, the number of technologies that have reached true clinical usability is limited. There is a growing need for POCTs that enable rapid, accurate analysis of human genetic variation, particularly across diverse clinical settings without requiring specialist expertise. AREAS COVERED: This horizon scan aimed to provide an overview of the development pipeline of POCTs to identify variation(s) in the genome and epigenome that enable the use of genetic information to inform diagnosis, prognosis, and treatment decisions in any clinical area. Database (Embase and MEDLINE) and clinical trial registry (ClinicalTrials.gov) searches were conducted from 2019 to 19 December 2024; 346 unique technologies were identified. EXPERT OPINION AND COMMENTARY: A range of purposes and conditions were identified; the most common being diagnosis (n&#x2009;=&#x2009;263) and cancer (n&#x2009;=&#x2009;237) respectively. We defined 'true POCTs' as those that were highly automated, capable of analyzing complex samples, and operable by non-specialists. Only 36&#x2009;met these criteria; six are already on the market, one is in clinical trials, and the remaining 29 are at various stages of development. Overall, most technologies were in early stages of development, highlighting the need for further innovation and validation.

Point-of-care↗
PubMed1990

The phakomatoses as paracrine growth disorders (paracinopathies).

A microcomputer database management system retrieved all 170 probands with phakomatoses evaluated through the genetic clinics at the University of South Florida between January 2, 1982 and December 31, 1987. Neurofibromatosis (NF) was the diagnosis of 118 of them; 42 had other phakomatoses and 10 had transitional phenotypes difficult to classify. The analysis of the hamartomas of all probands indicated disorganized differentiation and overgrowth of cell species characteristic for the involved tissue and location. Abundance of extracellular fibrillary components was also evident in most hamartomas. Adequate blood supply was a conditio sine qua non. This was seen in monogenic, sporadic, transitional and combined phakomatoses alike and implied a common pathogenesis. The paracrine growth factors and their regulation emerged as the most plausible common denominator for the pathogenesis. A unitary pathogenetic hypothesis is proposed that the phakomatoses represent paracrine growth regulation disorders (paracrinopathies). Conditions such as fibromatoses, lipomatoses, lipodystrophies, hemihyper/hypotrophies, including Russell-Silver and Beckwith-Wiedemann syndromes may be proven to be paracrinopathies as well.

Dysplastic Nevus Syndrome↗
PubMed2006

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies.

BACKGROUND: Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. RESULTS: Using two publicly available datasets, i.e., gene-expression data of 285 patients with Acute Myeloid Leukemia (AML, Affymetrix HG-U133A GeneChip) and 42 samples of tumor tissue of the embryonal central nervous system (CNS, Affymetrix HuGeneFL GeneChip), we tested the effect of the four pre-processing strategies mentioned above, on (1) expression level measurements, (2) detection of differential expression, (3) cluster analysis and (4) classification of samples. In most cases, the effect of pre-processing is relatively small compared to other choices made in an analysis for the AML dataset, but has a more profound effect on the outcome of the CNS dataset. Analyses on individual probe sets, such as testing for differential expression, are affected most; supervised, multivariate analyses such as classification are far less sensitive to pre-processing. CONCLUSION: Using two experimental datasets, we show that the choice of pre-processing method is of relatively minor influence on the final analysis outcome of large microarray studies whereas it can have important effects on the results of a smaller study. The data source (platform, tissue homogeneity, RNA quality) is potentially of bigger importance than the choice of pre-processing method.

Algorithms↗
PubMed2006

Epidemiological studies in the information and genomics era: experience of the Clinical Genome of Cancer Project in São Paulo, Brazil.

Genomics is expanding the horizons of epidemiology, providing a new dimension for classical epidemiological studies and inspiring the development of large-scale multicenter studies with the statistical power necessary for the assessment of gene-gene and gene-environment interactions in cancer etiology and prognosis. This paper describes the methodology of the Clinical Genome of Cancer Project in São Paulo, Brazil (CGCP), which includes patients with nine types of tumors and controls. Three major epidemiological designs were used to reach specific objectives: cross-sectional studies to examine gene expression, case-control studies to evaluate etiological factors, and follow-up studies to analyze genetic profiles in prognosis. The clinical groups included patients' data in the electronic database through the Internet. Two approaches were used for data quality control: continuous data evaluation and data entry consistency. A total of 1749 cases and 1509 controls were entered into the CGCP database from the first trimester of 2002 to the end of 2004. Continuous evaluation showed that, for all tumors taken together, only 0.5% of the general form fields still included potential inconsistencies by the end of 2004. Regarding data entry consistency, the highest percentage of errors (11.8%) was observed for the follow-up form, followed by 6.7% for the clinical form, 4.0% for the general form, and only 1.1% for the pathology form. Good data quality is required for their transformation into useful information for clinical application and for preventive measures. The use of the Internet for communication among researchers and for data entry is perhaps the most innovative feature of the CGCP. The monitoring of patients' data guaranteed their quality.

Adult↗