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PubMed2025

Genomic sequencing in diverse and underserved pediatric populations: Parent perspectives on understanding, uncertainty, psychosocial impact, and personal utility of results.

PURPOSE: Limited evidence evaluates parents' perceptions of their child's clinical genome-scale sequencing (GS) results, particularly among individuals from medically underserved groups. Five Clinical Sequencing Evidence-Generating Research consortium studies performed GS in children with suspected genetic conditions with high proportions of individuals from underserved groups to address this evidence gap. METHODS: Parents completed surveys of perceived understanding, personal utility, and test-related distress after GS result disclosure. We assessed outcomes' associations with child- and parent-related factors: child age; type of GS finding; and parent health literacy, numeracy, and education. RESULTS: A total of 1763 parents completed surveys; 83% met "underserved" criteria based on race, ethnicity, and risk factors for barriers to access. We observed high perceived understanding and personal utility and low test-related distress. Outcomes were associated with the type of GS finding; parents of children with a pathogenic or likely pathogenic finding endorsed higher personal utility and more test-related distress than those whose children had a variant of uncertain significance or normal finding. Personal utility was higher in parents who met the criteria for "underserved." CONCLUSION: Our findings shed light on correlates of parents' cognitive and emotional responses to their child's GS findings and emphasize the need for tailored support in disclosure discussions.

Humans↗
PubMed1998

Severity of color vision defects: electroretinographic (ERG), molecular and behavioral studies.

Earlier research on phenotype/genotype relationships in color vision has shown imperfect predictability of color matching from the photopigment spectral sensitivities inferred from molecular genetic analysis. We previously observed that not all of the genes of the X-chromosome linked photopigment gene locus are expressed in the retina. Since sequence analysis of DNA does not necessarily reveal which of the genes are expressed into photopigments, we used ERG spectral sensitivities and adaptation measurements to assess expressed photopigment complement. Many deuteranomalous subjects had L, M, and L-M hybrid genes. The ERG results showed that M pigment is not present in measurable quantities in deutan subjects. Using these results to determine gene expression improved the correlations between inferred pigment separation and color matching. Furthermore, we found a subject who had normal L and M genes and normal proximal promoter sequences, yet he had a single photopigment (M) by ERG and tested as a protanope. These results demonstrate the utility of ERG measurements in studies of molecular genetics of color vision deficiencies, and further support the conclusion that not all genes are expressed in color deficient subjects. In particular, deuteranomaly requires a presently unknown mechanism of selective expression which excludes normal M genes and allows expression of L-M hybrid genes in one cone type, and the normal L in another.

Adaptation, Ocular↗
PubMedDate not supplied

Technical standards and guidelines for Huntington disease testing.

One mission of the ACMG Laboratory Quality Assurance (QA) Committee is to develop standards and guidelines for clinical genetics laboratories, including cytogenetics, biochemical, and molecular genetics specialties. This document was developed under the auspices of the Molecular Subcommittee of the Laboratory QA Committee by the Huntington Disease (HD) Working Group. These guidelines are not to be interpreted as restrictive or the only approach but to provide a helpful guide. Certainly, appropriately trained and credentialed laboratory directors have flexibility to utilize various testing platforms and design testing strategies with considerable latitude. We felt that it was essential to include technique-specific guidelines of several current technologies commonly used in laboratories providing HD testing, because the technologies discussed are available commercially and are widely utilized. We take the view that these technologies may change, and thus this document may change with future review.

Credentialing↗
PubMed1997

The role of preoperative factor V Leiden screening in different geographic populations.

Patients harboring a specific mutation in the coagulation factor V gene have been identified as being at significantly increased risk for venous thrombosis. A simple genetic test that identifies carriers of this mutation (the factor V Leiden allele) is available and may have utility in various clinical settings, including preoperative risk assessment for thromboembolic complications. In this regard, it is generally agreed that prospective studies addressing the role of preoperative factor V Leiden mutational analysis are needed to clearly define the clinical prognostic/diagnostic significance of the presence of this mutation in surgical patients. This report questions the role that population dynamics (genetic and environmental backgrounds of individual populations) plays in the analysis of factor V genotypic data in relation to postsurgical thromboembolic complications. We have determined that the frequency of individuals carrying the factor V Leiden allele is 7.9 per cent for our South Central Pennsylvania population (395 wild type, 32 heterozygotes, 2 homozygotes) using a polymerase chain reaction-restriction fragment length polymorphism technique that specifically detects the factor V Leiden mutation. This baseline population information is useful from both a clinical and a basic science viewpoint. However, considering the various unknown genetic and environmental differences between geographically distinct populations, the significance of this result, in terms of clinical management of our surgical patients, is yet to be determined.

Factor V↗
PubMed2025

Characterization of blaOXA-542-mediated carbapenem resistance in Acinetobacter baumannii.

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) causes multiple anatomical site infections, representing a significant public health threat. AIM: This study reports the isolation and characterization of a carbapenem-resistant A. baumannii harbouring blaOXA-542, followed by a comprehensive investigation of its antimicrobial resistance mechanisms and genomic characteristics. METHODS: Firstly, antimicrobial susceptibility testing was performed using the broth microdilution method. Subsequently, whole-genome sequencing was employed to identify and characterize the resistance and virulence determinants. The functional validation of resistance mechanisms was performed by gene knockdown and construction of expression vectors. The fitness cost of β-lactamase expression was identified by a bacterial growth kinetic test. Molecular docking was utilized to predict potential binding sites of β-lactamase and carbapenems. Finally, the genetic characteristics of the isolates were analysed through comparative genomics analyses and phylogenetic tree construction. RESULTS AND CONCLUSIONS: The results demonstrated that blaOXA-542 confers resistance to carbapenem and penicillin in A. baumannii and Escherichia coli while exhibiting no significant impact on cephalosporins. The ability of blaOXA-542 to hydrolyze meropenem was further confirmed by modified carbapenem inactivation assay (mCIM). Expression of blaOXA-542 in E. coli BL21 showed no significant growth rate alteration. Comparative analysis of the blaOXA-542 genetic environment revealed a close association with Acinetobacter pitti. This study reports the emergence of blaOXA-542-mediated carbapenem and penicillin resistance in a novel A. baumannii lineage (ST2795Pas/ST3464Oxf), highlighting the urgent need for rational antibiotic use against specific pathogens.

Acinetobacter baumannii↗
PubMed2002

Hepatobiliary nutrition: history and future.

The liver is a master metabolic gland; consequently, liver disease commonly results in significant malnutrition. Complex metabolic derangements always accompany liver failure, often reflect the magnitude of hepatic insufficiency, and are characterized by accentuated catabolism. Nutritional assessment is problematic in these patients, because many of the usual indicators of nutritional status are altered directly by the hepatic pathophysiology rather than, or in addition to, preexisting or subsequent secondary malnutrition. The objective of nutritional support in patients with liver failure is to provide adequate nutrients to ensure the availability of specific substrates for energy and protein synthesis and for normal hepatocyte survival and function, without inducing or accentuating encephalopathy or otherwise compounding hepatic insufficiency. In the near future, guidelines must be developed for the specific nutritional support of patients with fulminant hepatic failure, cholestatic liver disease, steatosis, and cirrhosis. Currently, work is underway to develop an artificial liver for patients awaiting transplantation; to use genetic engineering technology to provide an alternative source of hepatic tissue; and to test the utility of various intermediary metabolites for hepatobiliary nutrition support. No ideal regimen for nutritional support of all forms of liver failure exists, and this also represents a significant challenge for future basic and clinical investigations. However, it is mandatory to attempt to maintain optimal nutrition in patients with severe liver failure if morbidity and mortality are to be reduced and survival is to be maximized.

Chronic Disease↗
PubMed2006

Isolation of Wuchereria bancrofti microfilariae from archived stained blood slides for use in genetic studies and amplification of parasite and endosymbiont genes.

Information on change in genetic diversity of Wuchereria bancrofti is important in view of the launching of the Global Lymphatic Filariasis Elimination Programme, as it may have important consequences on the control operations and on the potential resurgence after their withdrawal. Since attention was not paid to generate such information when the programme was launched, use of archived parasite material will provide an opportunity to derive this information in a prospective manner. In this paper a simple and effective technique is reported for isolation of microfilariae of W. bancrofti from dried and stained slides archived for several years and their utility in analysis of genetic structure and amplification of certain genes of the parasite is tested. The method was found to be efficient in purifying mf from the dried smears and the DNA of the parasite found to be useful in studying the genetic structure of Wuchereria bancrofti populations using random amplified polymorphic DNA (RAPD)-PCR and for amplifying genes of the parasite and its endosymbiont, Wolbachia sp.

Animals↗
PubMed1987

Isolation of polymorphic DNA fragments from human chromosome 4.

We have identified and characterized 40 DNA probes detecting restriction fragment length polymorphism (RFLP) on human chromosome 4. Single copy human clones were isolated from a bacteriophage library enriched for chromosome 4 sequences. Each clone was hybridized to somatic cell hybrid DNAs for verification of its species and chromosomal origin and for regional localization. Sequences specific for chromosome 4 were tested for their ability to detect RFLPs in human DNA and their potential utility as genetic markers was assessed. Approximately 263,000 base pairs or 0.13% of the chromosome was screened for sequence variation. The estimate of heterozygosity calculated from this large body of data, H = 0.0021, indicates that the degree of sequence variation on chromosome 4 is comparable to other autosomes. The characterization of these 40 markers has tripled the number of polymorphic loci available for linkage studies on chromosome 4, making it feasible to begin construction of a detailed linkage map that will span the entire chromosome.

Animals↗
PubMed2003

The activation of the retinoic acid response element is inhibited in an animal model of congenital diaphragmatic hernia.

Defects very similar to those seen in infants born with congenital diaphragmatic hernias can be induced in rodents by the administration of the teratogen nitrofen. There is an interest in understanding the biochemical mechanisms of nitrofen's actions in hopes of gaining insights into the etiology of congenital diaphragmatic hernia. In this study, we test the hypothesis that nitrofen is acting to perturb the retinoid signaling pathway by utilizing genetically engineered mice that have the lacZ reporter gene linked to a retinoic acid response element (RARE). We demonstrate a pronounced suppression of RARE-lacZ expression by nitrofen in vitro (by approximately 64%) and in vivo (by approximately 43%).

Animals↗
PubMed2003

Diagnosis of periodontal diseases.

At the present time, the diagnosis and classification of periodontal diseases are almost entirely based on traditional clinical assessments. Supplemental quantitative and qualitative assessments of the gingival crevicular fluid and subgingival microflora can potentially provide useful information about the patient's periodontal disease. In certain situations, these supplemental risk-assessment tests may be particularly valuable in establishing the endpoint of therapy prior to placing patients on a periodontal maintenance program. Although the clinical utility of none of these tests has been validated, their further development is warranted. A genetic test for susceptibility to periodontitis has become commercially available. How best to use this and future host-based tests in clinical practice remains to be determined. Probing depth and clinical attachment loss measurements obtained with periodontal probes are practical and valid methods for assessing periodontal status. Computer-linked, controlled-force electronic periodontal probes are commercially available and are currently in use by some practitioners. Many of the logistical problems associated with subtraction radiography are being overcome and this powerful diagnostic tool may soon come into widespread use. Future developments in this and other imaging techniques are likely to have a profound effect on our approach to the diagnosis of periodontal diseases.

Clinical Enzyme Tests↗
PubMed2026

Are we Prepared? Genetic Counseling for Stillbirth in the Sequencing Era.

Stillbirth affects approximately 1 in 175 pregnancies annually in the United States. Although the American College of Obstetricians and Gynecologists recommends genetic testing as part of the stillbirth evaluation, families often face barriers to obtaining a complete evaluation. Expansion of the diagnostic evaluation of stillbirth is expected to include exome/genome sequencing, with preliminary studies demonstrating its diagnostic utility. Consequently, genetic counselors (GCs) are expected to play an expanding role in post-stillbirth care. This study explored current genetic counseling practices for stillbirth and GCs' preparedness to support patients in this setting. A cross-sectional survey was distributed across four channels. Eligible participants included GCs in the United States and Canada with at least 1 year of prenatal experience. The survey assessed GC frequency and timing in stillbirth counseling, genetic testing practices, comfort addressing psychosocial needs, and perceived barriers to care. Responses were analyzed using descriptive statistics. Group comparisons were performed using Chi-square and Fisher's exact tests. Open-ended responses were coded for themes. Seventy-one responses were analyzed. Approximately half of respondents (49.3%, n = 36) reported "never/very rarely/rarely" counseling patients postpartum, despite this being the optimal time to offer genetic testing. Delivering providers (46.5%, n = 33) were often responsible for informing patients about testing and obtaining consent, compared to GCs (11.3%, n = 8). Although chromosomal microarray (CMA) is recommended as the standard of care (SOC), 12.7% (n = 9) of GCs reported not offering CMA for anomalous and non-anomalous stillbirths. Perceived barriers to SOC testing included reported lack of obstetrician awareness (91.5%, n = 65) and challenges coordinating specimen collection (90.1%, n = 64). These findings highlight barriers to SOC genetic evaluation and underscore the need to strengthen institutional protocols, enhance provider education, and develop stillbirth-specific genetic counseling guidelines. GC involvement in these efforts will be essential to promoting equitable access to comprehensive post-stillbirth care as sequencing becomes integrated into practice.

Humans↗
PubMed1991

Amniocentesis or chorionic villus sampling for prenatal genetic testing: a decision analysis.

We used decision analysis to examine the strategies of amniocentesis, chorionic villus sampling, and no prenatal testing for a pregnant woman who would be 35 years of age at the expected date of delivery. Probabilities were obtained from the obstetric and genetic literature, and utilities from previously published standard reference gambles and from responses of obstetric residents and students recorded on a linear rating scale. The expected utility of amniocentesis exceeded that of chorionic villus sampling by 0.1 utility units, and of no prenatal testing by 0.12 utility units. The decision was insensitive to clinically plausible values for the probabilities of spontaneous abortion after amniocentesis and chorionic villus sampling, the probabilities of abnormal and indeterminate chorionic villus sampling results, the probability of an abnormal amniocentesis result after an indeterminate chorionic villus sampling, the sensitivities and specificities of amniocentesis and chorionic villus sampling, and the probabilities of significant maternal morbidity after first- and second-trimester therapeutic abortion. Chorionic villus sampling was preferred to amniocentesis when the utility of a first-trimester therapeutic abortion exceeded that of a second-trimester abortion by 23.2 utility units, or when the anxiety "cost" of awaiting second-trimester amniocentesis results exceeded 0.1 utility unit. We conclude that over a range of assumptions concerning the probabilities involved in the prenatal testing decision, amniocentesis was preferred to chorionic villus sampling. However, for a decision maker for whom a second-trimester therapeutic abortion would be significantly less acceptable than a first-trimester procedure, or for whom the anxiety of awaiting second-trimester chromosomal diagnosis might be an important consideration, chorionic villus sampling could become the procedure of choice.

Adult↗
PubMed1995

Metabolic screening.

The time-honored concept of utilization of the laboratory for screening for metabolic diseases has taken on new meaning in the face of the extensive heterogeneity of genetic diseases that has been revealed by DNA research. Some of the conditions for which screening was used in the past are now known to produce physically identifiable features so more definitive tests may be utilized for them. There remains a set of diseases that are difficult to characterize physically and it is for these that screening tests are most needed. Initial screening procedures for most of them are available in most general hospitals but comprehensive screening is usually done in biochemical genetics laboratories. Numerous and somewhat arcane bedside screening tests have been replaced by a short list of more modern procedures which are much more accurate and reliable.

Epilepsy↗
PubMed2006

Utility of molecular testing for related retinal dystrophies.

BACKGROUND: The purpose of this study was to describe our experience with the clinical effects of molecular genetic testing for retinitis pigmentosa (RP) and related retinal dystrophies. METHODS: Chart review of 303 consecutive patients with retinal dystrophies was done when blood was sent for molecular genetic testing between 1993 and 2001. Phenotype information was retrieved for patients with identified mutations. The yield of positive and clinically useful results was assessed. RESULTS: Participants comprised 35 patients with Leber congenital amaurosis, 18 with Usher syndrome, and 250 with isolated RP or other retinal dystrophies. Of these 303 participants, 203 (67%) received positive or negative results of molecular testing for an average of 2.7 genes. Positive results were available in 19 patients after an average time interval of 38+/-22 months (median 33 months, range 1-89 months). No results were received for 84 (28%) patients. In 16 (5%) cases, patients received partial results. Only 19 (6%) patients were found to have sequence changes in RHO, RDS, CRB1, or USH2A, 2 of which were thought to be disease-causing. Only 2 sequence changes were previously documented mutations, but several other novel changes were suspected to be disease-causing mutations also. INTERPRETATION: Molecular testing was helpful only in the minority of cases, largely because of a lack of availability, as well as the complexity of the molecular genetics of RP. Improvements in funding, infrastructure, and molecular knowledge will be necessary to improve the transformation of molecular genetic testing into a clinically relevant bedside tool.

DNA Mutational Analysis↗
PubMed2002

Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium.

Pooling DNA samples can yield efficient estimates of the prevalence of genetic variants. We extend methods of analyzing pooled DNA samples to estimate the joint prevalence of variants at two or more loci. If one has a sample from the general population, one can adapt the method for joint prevalence estimation to estimate allele frequencies and D, the measure of linkage disequilibrium. The parameter D is fundamental in population genetics and in determining the power of association studies. In addition, joint allelic prevalences can be used in case-control studies to estimate the relative risks of disease from joint exposures to the genetic variants. Our methods allow for imperfect assay sensitivity and specificity. The expected savings in numbers of assays required when pooling is utilized compared to individual testing are quantified.

Alleles↗
PubMed2006

Pharmacogenetics of irinotecan: clinical perspectives on the utility of genotyping.

Depending upon the UDP glucuronosyltransferase 1A1 (UGT1A1) genotype, patients are more or less susceptible to the risk of severe toxicity of irinotecan. As the US FDA-approved label of irinotecan (CPT-11, Camptosar) has been recently revised to include UGT1A1 genotype among potential risk factors for toxicity, it is expected that UGT1A1 genotyping will be increasingly used in patients undergoing irinotecan treatment. At present, the label states that *28/*28 (7/7) genotype patients are at higher risk of neutropenia and should be treated at a lower dose of irinotecan. Although effective alternative drugs (i.e., oxaliplatin) exist for metastatic colorectal cancer (the main indication of irinotecan), recent studies have confirmed that irinotecan has an important place in the management of this disease. We feel that now is the time for addressing questions around the UGT1A1*28 testing that many oncologists might have had but remained unanswered. For example, does the test have adequate sensitivity/specificity? Can the test results be effectively utilized to guide therapy of metastatic colorectal cancer patients? Is it possible that the *1/*1 (6/6) patients are underdosed? How can the genetic prediction of irinotecan toxicity be improved? Is the UGT1A1*28 test fully predictive of the UGT1A1 deficiency in patients who are not of Caucasian origin? Clinicians and investigators interested in a discussion of each of these points could find this article a useful source.

Antineoplastic Agents, Phytogenic↗
PubMed2005

Randomized comparison of group versus individual genetic education and counseling for familial breast and/or ovarian cancer.

PURPOSE: An efficient approach to education and counseling before BRCA1 and BRCA2 mutation testing is necessary for effective utilization of testing in the community. Education and counseling, when delivered individually, are limited by a shortage of trained health care providers as well as by financial and time constraints. The purpose of this study was to determine whether pretest education and counseling for breast cancer genetics in a group setting is equivalent to that provided on an individual basis. PATIENTS AND METHODS: One hundred forty-two patients at high risk for harboring a BRCA mutation were randomly assigned to group or individual education and counseling sessions. Group education was followed by brief individual counseling. Knowledge and Impact of Events Scales (IES) were administered at baseline and after education and counseling and at 1 week and 3, 6, and 12 months. Satisfaction with education and counseling was measured at completion of the session. Preferred method of education and counseling was solicited at 3 months. RESULTS: There was no difference in knowledge or IES scores between groups. When stratified by genetic test results, knowledge scores showed no difference. Regardless of group, post-test IES scores in patients with positive results were higher than patients with negative or uninformative results but returned to baseline by 12 months. Participants were equally satisfied with either method they were assigned. Significantly more time was spent per patient in individual sessions (1.25 hours) than in group education (0.74 hours). CONCLUSION: Our data suggest that group education and counseling may confer similar benefits compared with traditional individual sessions. Additional investigation of this approach in larger numbers of patients is warranted.

Adult↗