A comprehensive leukemia database: integration of cytogenetics, molecular genetics and microarray data with clinical information, cytomorphology and immunophenotyping.
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Cytogenetics↗
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Results for “clinical genetics database”
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Comparison between SLC3A1 and SLC7A9 cystinuria patients and carriers: a need for a new classification.
Recent developments in the genetics and physiology of cystinuria do not support the traditional classification, which is based on the excretion of cystine and dibasic amino acids in obligate heterozygotes. Mutations of only two genes (SLC3A1 and SLC7A9), identified by the International Cystinuria Consortium (ICC), have been found to be responsible for all three types of the disease. The ICC set up a multinational database and collected genetic and clinical data from 224 patients affected by cystinuria, 125 with full genotype definition. Amino acid urinary excretion patterns of 189 heterozygotes with genetic definition and of 83 healthy controls were also included. All SLC3A1 carriers and 14% of SLC7A9 carriers showed a normal amino acid urinary pattern (i.e., type I phenotype). The rest of the SLC7A9 carriers showed phenotype non-I (type III, 80.5%; type II, 5.5%). This makes the traditional classification imprecise. A new classification is needed: type A, due to two mutations of SLC3A1 (rBAT) on chromosome 2 (45.2% in our database); type B, due to two mutations of SLC7A9 on chromosome 19 (53.2% in this series); and a possible third type, AB (1.6%), with one mutation on each of the above-mentioned genes. Clinical data show that cystinuria is more severe in males than in females. The two types of cystinuria (A and B) had a similar outcome in this retrospective study, but the effect of the treatment could not be analyzed. Stone events do not correlate with amino acid urinary excretion. Renal function was clearly impaired in 17% of the patients.
Adolescent↗
Evaluation of referrals for genetic investigation of short stature in Hong Kong.
OBJECTIVE: To establish a profile of the causes of apparently unexplained SS in genetic referral center and evaluate the current referral system. METHODS: This was a retrospective database survey on patients who were referred our clinical genetic service from 1988 - 1998 primarily because of SS. We retrieved the study population from our computer database using "short stature"as a search handle and then studied the demographic, clinical and laboratory data from their medical records. RESULTS: Three hundred and fifty-three subjects were referred for genetic evaluation of SS in 1988 - 1998. The mean age of referred subjects was 11.5 years and the female to male ratio was 7.6. All referrals had undergone cytogenetic studies to exclude chromosomal abnormalities, 19% of girls with apparently unexplained short stature had Turner syndrome; at least 47.9% of the study population were normal variants and 25% of the referrals had inadequate information for classification. CONCLUSIONS: Genetic investigation is essential in the management of patients with SS, especially for girls suspected of having Turner syndrome, in which growth hormone treatment has shown to improve final height. We also highlight the inherited causes of short stature, which were often misdiagnosed as benign familial short stature, and discussed the drawbacks of the current referral system.
Child↗
Visual outcome in patients with isolated autosomal dominant congenital cataract.
OBJECTIVE: To determine the visual outcome and surgical complication rates of patients with isolated inherited congenital cataract. DESIGN: Retrospective noncomparative case series. PARTICIPANTS: Patients and their families were ascertained from the genetic eye clinic and outpatient databases of Moorfields Eye Hospital, London, and invited to participate in the study. Four hundred twenty-two individuals from 72 pedigrees with this form of autosomal dominant cataract underwent ophthalmologic assessment. MAIN OUTCOME MEASURES: Visual acuity and surgical complications (glaucoma, retinal detachment, amblyopia). RESULTS: In this study 49.4% of patients (46.8% of those operated) achieved a visual acuity (VA) of 20/40 or better, 35.9% (36.1% of those operated) a VA between 20/50 and 20/200, and 14.7% (17.1% of those operated) worse than 20/200. Opacities that were more diffuse or did not lie close to the visual axis were associated with a better prognosis for vision; 6.6% had glaucoma and 5.0% had retinal detachment develop. CONCLUSIONS: Patients with isolated inherited congenital cataract have a better visual and surgical outcome than those with coexisting ocular and systemic abnormalities. The improved prognosis is related in part to the lack of other developmental abnormalities of the eye, and, because inherited cataracts are often partial at birth, surgery may be delayed to later infancy and childhood when there is a lower incidence of surgical complications and refractive correction is easier. Certain inherited phenotypes (lamellar, pulverulent, polymorphic, coralliform, and cortical) also seem to have a better prognosis, and this should be borne in mind when counseling these families. A large number of the patients in this study underwent surgery many years previously, when surgical outcomes were less favorable, and thus the results of this study establish only a minimum acuity dataset for the purposes of counseling.
Adolescent↗
Prenatal diagnosis of mosaic trisomy 20 in New Zealand.
OBJECTIVE: Mosaic trisomy 20 is not an uncommon finding on amniocentesis or CVS. Unlike other mosaic aneuploidies it is a relatively benign abnormality which, along with a lack of long-term follow-up of cases, has led to uncertainty when counselling parents. We aimed to identify known mosaic trisomy 20 pregnancies in New Zealand in the last 10 years and document their outcome. DESIGN: Retrospective database review with prospective clinical follow-up. METHODS: Cases were identified from the databases of the two clinical genetic services, as well as the four regional cytogenetics laboratories. Medical records were reviewed and where patients were available they were offered follow-up. RESULTS: Fourteen cases were identified (13 on amniocentesis, one on CVS), all with low levels of mosaicism (8-50%). In 12 cases, the children were physically and developmentally normal, with the longest follow-up being 10 years. Minor anomalies were noted in two cases. There were no major malformations noted in any of the cases and where repeat karyotypes were performed on blood or urine cytology these were normal. CONCLUSIONS: This series confirms a much lower incidence of phenotypic abnormalities associated with mosaic trisomy 20 compared to other forms of mosaic aneuploidy. Attempts to predict which of these pregnancies will have poor outcomes have not proven to be reliable. We recommend that, if a detailed anatomy scan is normal, parents be counselled that the risk of abnormality is less than 10%. Further tests should be performed only on the basis of a clinical indication.
Adult↗
Biobanks. Private biobanks spark ethical concerns.
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Bioethical Issues↗
Locus-specific databases: from ethical principles to practice.
Locus-specific databases (LSDBs) play an essential role in clinical care and research. They differ from traditional genetic databases in that they propose to place the mutations of "anonymized" patients directly on the World Wide Web. The proliferation of ethical guidelines and legal requirements affects the rapid and free transmission of clinical data, which is vital for both the daily management of patients and research into better diagnostics and treatment. This paper proposes a review of ethical principles endorsed by international instruments that are of particular relevance to LSDBs. It aims to translate them into 12 proposed practical guidelines that LSDB curators can use in collecting data for clinical research. Perhaps these guideposts will serve as a first step toward translating principles into practice.
Databases, Nucleic Acid↗
Molecular diagnostics of genetic eye diseases.
Eye diseases can be simple or complex, and mostly of heterogeneous molecular genetics. Some eye diseases are caused by mutations in a single gene, but some diseases, such as primary open angle glaucoma, can be due to sequence variations in multiple genes. In some diseases, both genetic and epigenetic mechanisms are involved, as was recently revealed in the mechanism of retinoblastoma. Disease causative mutations and phenotypes may vary by ethnicity and geography. To date, more than a hundred candidate genes for eye diseases are known, although less than 20 have definite disease-causing mutations. The three common genetic eye diseases, primary open angle glaucoma, age-related macular degeneration, and retinitis pigmentosa, all have known gene mutations, but these account for only a portion of the patients. While the search for eye disease genes and mutations still goes on, known mutations have been utilized for diagnosis. Genetic markers for pre-symptomatic and pre-natal diagnosis are available for specific diseases such as primary open angle glaucoma and retinoblastoma. This paper reviews the molecular basis of common genetic eye diseases and the available genetic markers for clinical diagnosis. Difficulties and challenges in molecular investigation of some eye diseases are discussed. Establishment of ethnic-specific disease databases that contain both clinical and genetic information for identification of genetic markers with diagnostic, prognostic, or pharmacological value is strongly advocated.
Eye Diseases, Hereditary↗
[Human gene tests as laboratory medicine in the post-genome era].
Massive and systematic information on human genes and genome is accumulating with progress in the Human Genome Project. Information on the genome has a characteristic digital signal that is appropriate for high-throughput handling by computers. Therefore, the field of gene tests has a high affinity to the field of laboratory medicine. In addition, it is a important survival strategy for departments of laboratory medicine to remain at the cutting edge. We must establish an infrastructure for utilizing genome information in clinical medicine and must anticipate numerous issues. The following issues need to be addressed. 1. Online database of human gene tests (http://www.kuhp.kyoto-u.ac.jp/idennet/DB/index2.html) 2. Anonymous handling of patients' samples 3. Establishment of independent Department of Clinical Genetics 4. Education of clinical geneticists 5. Quality control of human gene tests (especially germline mutation tests) 6. Education of technicians handling human gene tests.
Clinical Laboratory Information Systems↗
Genetic analysis in the Asthma Clinical Research Network.
Because there is reason to believe that genetic variants could account for different treatment responses in subjects with asthma, it is important to collect blood for genetic-analysis purposes when conducting clinical trials in asthma. This article describes issues related to maintaining subject confidentiality, tracking and shipping blood samples, quality control procedures at the laboratory performing the genotyping, and necessary data verification checks when implementing the genetic-analysis database for the Asthma Clinical Research Network.
Adrenergic beta-Agonists↗
Genes and genetics in respiratory control.
The genetic approach to respiratory control is opening up new paths for research into developmental respiratory control disorders. Despite the identification of numerous genes involved in respiratory control, none of the genetically engineered mice developed to date fully replicate the human respiratory phenotype of human developmental respiratory disorders. However, combining studies in humans and studies in mouse models has proved useful in identifying candidate genes for human developmental respiratory control disorders and providing pathogenic information. In clinical practice, the development of databases that incorporate clinical phenotypes and genetic samples from patients would facilitate further genetic studies. International multicentre studies would advance the area of respiratory control research.
Animals↗
Creation of clinical research databases in the 21st century: a practical algorithm for HIPAA Compliance.
BACKGROUND: Enforcement of the Health Insurance Portability and Accountability Act (HIPAA) began in April, 2003. Designed as a law mandating health insurance availability when coverage was lost, HIPAA imposed sweeping and broad-reaching protections of patient privacy. These changes dramatically altered clinical research by placing sizeable regulatory burdens upon investigators with threat of severe and costly federal and civil penalties. This report describes development of an algorithmic approach to clinical research database design based upon a central key-shared data (CK-SD) model allowing researchers to easily analyze, distribute, and publish clinical research without disclosure of HIPAA Protected Health Information (PHI). METHODS: Three clinical database formats (small clinical trial, operating room performance, and genetic microchip array datasets) were modeled using standard structured query language (SQL)-compliant databases. The CK database was created to contain PHI data, whereas a shareable SD database was generated in real-time containing relevant clinical outcome information while protecting PHI items. Small (< 100 records), medium (< 50,000 records), and large (> 10(8) records) model databases were created, and the resultant data models were evaluated in consultation with an HIPAA compliance officer. RESULTS: The SD database models complied fully with HIPAA regulations, and resulting "shared" data could be distributed freely. Unique patient identifiers were not required for treatment or outcome analysis. Age data were resolved to single-integer years, grouping patients aged > 89 years. Admission, discharge, treatment, and follow-up dates were replaced with enrollment year, and follow-up/outcome intervals calculated eliminating original data. Two additional data fields identified as PHI (treating physician and facility) were replaced with integer values, and the original data corresponding to these values were stored in the CK database. Use of the algorithm at the time of database design did not increase cost or design effort. CONCLUSIONS: The CK-SD model for clinical database design provides an algorithm for investigators to create, maintain, and share clinical research data compliant with HIPAA regulations. This model is applicable to new projects and large institutional datasets, and should decrease regulatory efforts required for conduct of clinical research. Application of the design algorithm early in the clinical research enterprise does not increase cost or the effort of data collection.
Algorithms↗
Internet-based neuro-oncology patient recruitment.
THE PRIVACY RULE, as part of the Health Insurance Portability and Accountability Act, was implemented in 2003 as a response to public concern over potential abuses of private health information. Although the Privacy Rule was not intended to place limits on clinical research, its complexity has caused much confusion throughout the academic medicine and research communities. Many clinical and translational researchers have created clinical databases or human tissue banks to facilitate future research. Maintenance of such databases is considered a research activity under the Privacy Rule, and researchers are, therefore, subject to its regulations. We present a novel Internet-based method to generate and maintain a neurooncology patient registry and human tissue bank. Through our web site, we secure both Health Insurance Portability and Accountability Act research authorization and informed consent, enabling us to contact the treating physician for clinical data and pathological specimens. Considering the importance of continued use of clinical databases and tissue banks in the genetic era of medicine, our method offers one way for researchers to adapt to the changing world of clinical research.
Brain Neoplasms↗
Translating pharmacogenomics discoveries into clinical practice: the role of curated databases.
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Databases, Genetic↗
Familial Mediterranean fever (FMF) in Turkey: results of a nationwide multicenter study.
Familial Mediterranean fever (FMF) is an autosomal recessive disease that is prevalent among eastern Mediterranean populations, mainly non-Ashkenazi Jews, Armenians, Turks, and Arabs. Since a large proportion of all the FMF patients in the world live in Turkey, the Turkish FMF Study Group (FMF-TR) was founded to develop a patient registry database and analyze demographic, clinical, and genetic features. The cohort was composed of 2838 patients (mean age, 23.0 +/- 13.33 yr; range, 2-87 yr), with a male:female ratio of 1.2:1. There was a mean period of 6.9 +/- 7.65 years from disease onset to diagnosis; the period was about 2 years shorter for each decade since 1981. Ninety-four percent of patients were living in the central-western parts of the country; however, their familial origins (70% from the central-eastern and Black Sea regions) reflected not only the ongoing east to west migration, but also the historical roots of FMF in Turkey. Patients' clinical features included peritonitis (93.7%), fever (92.5%), arthritis (47.4%), pleuritis (31.2%), myalgia (39.6%), and erysipelas-like erythema (20.9%). Arthritis, arthralgia, myalgia, and erysipelas-like erythema were significantly more frequent (p < 0.001) among patients with disease onset before the age of 18 years. Genetic analysis of 1090 patients revealed that M694V was the most frequent mutation (51.4%), followed by M680I (14.4%) and V726A (8.6%). Patients with the M694V/M694V genotype were found to have an earlier age of onset and higher frequencies of arthritis and arthralgia compared with the other groups (both p < 0.001). In contrast to other reported studies, there was no correlation between amyloidosis and M694V homozygosity in this cohort. However, amyloidosis was still remarkably frequent in our patients (12.9%), and it was prevalent (27.8%) even among the 18 patients with a disease onset after age 40 years. Twenty-two patients (0.8%) had nonamyloid glomerular diseases. The high prevalence of vasculitides (0.9% for polyarteritis nodosa and 2.7% for Henoch-Schonlein purpura) and high frequency of pericarditis (1.4%) were striking findings in the cohort. Phenotype II cases (those patients with amyloidosis as the presenting or only manifestation of disease) were rare (0.3% or less). There was a high rate of a past diagnosis of acute rheumatic fever, which suggested a possible misdiagnosis in children with FMF presenting with recurrent arthritis. To our knowledge, this is the largest series of patients with FMF reported from 1 country. We describe the features of the disease in the Turkish population and show that amyloidosis is still a substantial problem.
Adolescent↗
Oculoauriculovertebral abnormalities in children of diabetic mothers.
Maternal diabetes is known to have teratogenic effects. Malformations including neural tube defects, caudal dysgenesis, vertebral defects, congenital heart defects, femoral hypoplasia, and renal anomalies are described in infants of diabetic mothers. However, craniofacial anomalies have rarely been reported in such infants. Here we document craniofacial anomalies of patients born to diabetic mothers. We describe two patient populations: individuals evaluated through our genetics services for multiple malformations and individuals identified through a database search in our craniofacial clinic. The first group consists of 14 individuals evaluated in our genetics clinics who were born to diabetic mothers and had craniofacial anomalies. The second group consists of seven individuals who were identified from a craniofacial database search of patients with hemifacial microsomia and who were born to diabetic mothers. Thus, both groups were born to diabetic mothers and had hemifacial microsomia (67%), microtia (52%), hearing loss (43%), epibulbar dermoids (24%), and fused cervical vertebrae (24%). Therefore, the teratogenic effects of maternal diabetes probably include such craniofacial malformations as the oculoauriculovertebral/Goldenhar complex. Infants of diabetic mothers should be evaluated for craniofacial anomalies. Conversely, mothers of infants with craniofacial anomalies should be evaluated for diabetes to aid in counseling concerning cause and recurrence risks.
Abnormalities, Multiple↗
Family data in Rett syndrome: association with other genetic disorders.
BACKGROUND: Rett syndrome is a neurological disorder, almost exclusively affecting girls. METHODOLOGY: Between 1993 and 1995 pedigree data were obtained from families of girls registered with the Australian Rett syndrome database. RESULTS: Although 21 individual disorders were reported to be present in family members of affected girls, there was no apparent clustering of the same disorder in different families. However it was certain that a geneticist had been involved in only 10.9% of cases. CONCLUSIONS: Mutations in the MECP2 gene have now been reported in a proportion of sporadic cases. Thus, it will be important to examine this phenotype-genotype correlation in the Australian cohort. Where a mutation is found, prenatal diagnosis in a subsequent pregnancy will be a possibility. Using the Australian population database and in conjunction with the clinical genetic services in each state it is planned to contact families with an affected girl to offer testing and counselling.
Child↗
ReCAP: the Registry of Cytogenetic Abnormalities and Phenylketonuria.
The Registry of Cytogenetic Abnormalities and Phenylketonuria (ReCAP) is a multicenter collaborative registry of information on patients with constitutional cytogenetic abnormalities or hyperphenylalaninemia (HPA). Data are entered by microcomputer at four contributing centers. Records are then electronically transmitted to the coordinating center, where the composite cytogenetic and hyperphenylalaninemia databases are maintained on a mainframe computer. A set of programs, known as the ReCAP ISCN Translator, is used to create additional database records describing in detail the chromosome abnormalities present in each patient. The ReCAP computer system permits rapid and flexible retrieval of cases on the basis of any combination of laboratory, clinical, psychometric, or genetic characteristics contained within the databases. Special procedures protect patient confidentiality and assure that ReCAP data are of consistently high quality. Qualified investigators may use ReCAP as a resource for a variety of scientific studies.
Chromosome Aberrations↗