Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation

Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.

Assessing the strength of evidence for genes implicated in fatty acid oxidation disorders using the ClinGen clinical validity framework

Newborn screening is an incredibly useful tool for the early identification of many metabolic disorders, including fatty acid oxidation (FAO) disorders. In many cases, molecular tests are necessary to reach a final diagnosis, highlighting the need for a thorough evaluation of genes implicated in FAO disorders. Using the ClinGen (Clinical Genome Resource) clinical validity framework, thirty genes were analyzed for the strength of evidence supporting their association with FAO disorders. Evidence was gathered from the literature by biocurators and presented to disease experts for review in order to assign a clinical validity classification of Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Reported Evidence. Of the gene-disease relationships evaluated, 22/30 were classified as Definitive, three as Moderate, one as Limited, three as No Reported Evidence and one as Disputed. Gene-disease relationships with a Limited, Disputed, and No Reported Evidence were found on two, six, and up to four panels out of 30 FAO disorder-specific panels, respectively, in the National Institute of Health Genetic Testing Registry, while over 70% of the genes on panels are definitively associated with an FAO disorder. These results highlight the need to systematically assess the clinical relevance of genes implicated in fatty acid oxidation disorders in order to improve the interpretation of genetic testing results and diagnosis of patients with these disorders.

Evidence-based assessments of clinical actionability in the context of secondary findings: Updates from ClinGen's Actionability Working Group

The use of genome-scale sequencing allows for identification of genetic findings beyond the original indication for testing (secondary findings). The ClinGen Actionability Working Group's (AWG) protocol for evidence synthesis and semi-quantitative metric scoring evaluates four domains of clinical actionability for potential secondary findings: severity and likelihood of the outcome, and effectiveness and nature of the intervention. As of February 2018, the AWG has scored 127 genes associated with 78 disorders (up-to-date topics/scores are available at www.clinicalgenome.org). Scores across these disorders were assessed to compare genes/disorders recommended for return as secondary findings by the American College of Medical Genetics and Genomics (ACMG) with those not currently recommended. Disorders recommended by the ACMG scored higher on outcome-related domains (severity and likelihood), but not on intervention-related domains (effectiveness and nature of the intervention). Current practices indicate that return of secondary findings will expand beyond those currently recommended by the ACMG. The ClinGen AWG evidence reports and summary scores are not intended as classifications of actionability, rather they provide a resource to aid decision makers as they determine best practices regarding secondary findings. The ClinGen AWG is working with the ACMG Secondary Findings Committee to update future iterations of their secondary findings list.

Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene

The ClinGen Inborn Errors of Metabolism Working Group was tasked with creating a comprehensive, standardized knowledge base of genes and variants for metabolic diseases. Phenylalanine hydroxylase (PAH) deficiency was chosen to pilot development of the Working Group's standards and guidelines. A PAH variant curation expert panel (VCEP) was created to facilitate this process. Following ACMG-AMP variant interpretation guidelines, we present the development of these standards in the context of PAH variant curation and interpretation. Existing ACMG-AMP rules were adjusted based on disease (6) or strength (5) or both (2). Disease adjustments include allele frequency thresholds, functional assay thresholds, and phenotype-specific guidelines. Our validation of PAH-specific variant interpretation guidelines is presented using 85 variants. The PAH VCEP interpretations were concordant with existing interpretations in ClinVar for 69 variants (81%). Development of biocurator tools and standards are also described. Using the PAH-specific ACMG-AMP guidelines, 714 PAH variants have been curated and will be submitted to ClinVar. We also discuss strategies and challenges in applying ACMG-AMP guidelines to autosomal recessive metabolic disease, and the curation of variants in these genes.

ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation

Genome-scale sequencing creates vast amounts of genomic data, increasing the challenge of clinical sequence variant interpretation. The demand for high-quality interpretation requires multiple specialties to join forces to accelerate the interpretation of sequence variant pathogenicity. With over 600 international members including clinicians, researchers, and laboratory diagnosticians, the Clinical Genome Resource (ClinGen), funded by the National Institutes of Health, is forming expert groups to systematically evaluate variants in clinically relevant genes. Here, we describe the first ClinGen variant curation expert panels (VCEPs), development of consistent and streamlined processes for establishing new VCEPs, and creation of standard operating procedures for VCEPs to define application of the ACMG/AMP guidelines for sequence variant interpretation in specific genes or diseases. Additionally, ClinGen has created user interfaces to enhance reliability of curation and a Sequence Variant Interpretation Working Group (SVI WG) to harmonize guideline specifications and ensure consistency between groups. The expansion of VCEPs represents the primary mechanism by which curation of a substantial fraction of genomic variants can be accelerated and ultimately undertaken systematically and comprehensively. We welcome groups to utilize our resources and become involved in our effort to create a publicly accessible, centralized resource for clinically relevant genes and variants.

Development of Clinical Domain Working Groups for the Clinical Genome Resource (ClinGen): lessons learned and plans for the future

The Clinical Genome Resource (ClinGen) is supported by the National Institutes of Health (NIH) to develop expertly curated and freely accessible resources defining the clinical relevance of genes and variants for use in precision medicine and research. To facilitate expert input, ClinGen has formed Clinical Domain Working Groups (CDWGs) to leverage the collective knowledge of clinicians, laboratory diagnosticians, and researchers. In the initial phase of ClinGen, CDWGs were launched in the cardiovascular, hereditary cancer, and inborn errors of metabolism clinical fields. These early CDWGs established the infrastructure necessary to implement standardized processes developed or adopted by ClinGen working groups for the interpretation of gene-disease associations and variant pathogenicity, and provided a sustainable model for the formation of future disease-focused curation groups.

The establishment of CDWGs requires recruitment of international experts to broadly represent the interests of their field and ensure that assertions made are reliable and widely accepted. Building on the successes, challenges, and trade-offs made in establishing the original CDWGs, ClinGen has developed standard operating procedures for the development of CDWGs in new clinical domains, while maximizing efforts to scale up curation and facilitate involvement of external groups who wish to utilize ClinGen methods and infrastructure for expert curation.

Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup

The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded collaborative program that brings together a variety of projects designed to provide high-quality, curated information on clinically relevant genes and variants. ClinGen's EHR (Electronic Health Record) Workgroup aims to ensure that ClinGen is accessible to providers and patients through EHR and related systems. This article describes the current scope of these efforts and progress to date. The ClinGen public portal can be accessed at www.clinicalgenome.org.

Do peer educators make a difference? An evaluation of a youth-led HIV prevention model in Zambian Schools

Restless Development's youth-led model places trained Volunteer Peer Educators (VPEs), aged 18-25 years, in schools to teach HIV prevention and reproductive health (RH). VPEs also run youth centers, extracurricular and community-based activities. This evaluation assesses (i) program effects on students' HIV/RH knowledge, attitudes and behaviors using a non-randomized quasi-experimental design among 2133 eighth and ninth grade students in 13 intervention versus 13 matched comparison schools and (ii) program costs. Intervention students had significantly higher levels of knowledge related to HIV [odds ratio (OR) 1.61, 95% confidence interval (CI) 1.18-2.19; P < 0.01] and RH (OR 1.71; 95% CI 1.21-2.49; P < 0.01), more positive attitudes toward people living with HIV and greater self-efficacy to refuse unwanted sex and access condoms. No evidence of differences in ever having had sex was found (28% in the intervention; 29% in the comparison schools). However, intervention students were more likely not to have had sex in the previous year (OR 1.26, 95% CI 1.03-1.56; P < 0.05) and to have had only one sex partner ever (OR 1.43, 95% CI 1.00-2.03; P < 0.05). The average annual cost of the program was US$21 per beneficiary. In conclusion, the youth-led model is associated with increased HIV and RH knowledge and self-efficacy and lowered levels of stigma and sexual risk-taking behaviors.

Constructed wetlands as a component of the agricultural landscape: mitigation of herbicides in simulated runoff from upland drainage areas

Constructed wetlands are a recommended practice for buffering pollutant source areas and receiving waters. A wetland consisting of a sediment trap and two treatment cells was constructed in a Mississippi Delta lake watershed. A 3-h simulated runoff event was initiated (2003) to evaluate fate and transport of atrazine and fluometuron through the wetland. Water samples were collected during a runoff simulation and then afterward at selected intervals for 21d, and analyzed for the herbicides. Breakthrough patterns for herbicide concentrations in water samples during the first 20h after simulated runoff showed peak concentrations in the first 6h, with gradual tailing as the herbicide pulse was diluted in the second, excavated (deeper) cell. Atrazine and fluometuron concentrations in the first (shallower, non-excavated) cell averaged 12- and 20-fold greater, respectively, than those in the second cell following simulated runoff, indicating entrapment in the first cell. Atrazine and fluometuron concentrations in the shallower cell decreased 32% and 22%, respectively, 9d following simulated runoff, indicating either degradation or sorption to soil or wetland flora. In the excavated cell, concentrations were even lower, and atrazine declined more rapidly than fluometuron. Results indicate constructed wetlands can improve downstream water quality though sequestration or processing of pollutants.

Clinical factors associated with fatigue over time in paediatric oncology patients receiving chemotherapy

The purpose of this study was to investigate the relationships between clinical factors (including haemoglobin value, chemotherapeutic agents, and corticosteroid use) and changing patterns of fatigue before and for the next 10 days following the start of a new round of chemotherapy in children with cancer. A prospective longitudinal design was used to collect data from 48 paediatric oncology patients who were about to begin a new round of chemotherapy and their parents. Fatigue levels were assessed using multidomain questionnaires with three categories of patient self-report (including 'General Fatigue', 'Sleep/Rest Fatigue', and 'Cognitive Fatigue') and four categories of parent proxy-report (including 'Lack of Energy', 'Unable to Function', 'Altered Sleep', and 'Altered Mood'). The findings suggest that fatigue from both patient self-report and parent proxy-report changed significantly over time. The major findings from this study are that patients have more problems with fatigue in the first few days after the start of a cycle of chemotherapy. Corticosteroid use and haemoglobin value were associated with significant increases in fatigue that were sustained for several days and reached the highest level of fatigue at day 5 for those receiving concurrent steroids. The association of chemotherapeutic agents with fatigue varied between patient self-report and parent report, but the type of chemotherapeutic agents used was not associated with most changes in fatigue.

Laboratory assessment of atrazine and fluometuron degradation in soils from a constructed wetland

Constructed wetlands offer promise for removal of nonpoint source contaminants such as herbicides from agricultural runoff. Laboratory studies assessed the potential of soils to degrade and sorb atrazine and fluometuron within a recently constructed wetland. The surface 3 cm of soil was sampled from two cells of a Mississippi Delta constructed wetland; one shallow area disturbed only hydrologically, and the second excavated to provide greater water-holding capacity. The excavated area was more acidic on average (pH 4.85 versus 5.21), but otherwise the physical properties and general microbial enzyme activities in the two areas were similar. Soils were treated with 84 and 68 microg kg(-1) soil (14)C-ring labeled atrazine and fluometuron, respectively, and incubated under either saturated (88% moisture, w:w) or flooded (1cm standing water) conditions. Soils were sampled over 32 days and extracted for herbicide and metabolite analysis. Under saturated conditions, fluometuron metabolized to desmethylfluometuron (DMF) with a half-life equal 25-27 days. However, under flooded conditions, the half-life of fluometuron was more than 175 days. Atrazine dissipated rapidly in saturated and flooded soil with a half-life of approximately 23 days, but only 10% of atrazine was mineralized to CO(2). The overall atrazine and fluometuron dissipation rates were similar between the two cells, but each area had a different pattern of metabolite accumulation. The major route of atrazine dissipation was incorporation of atrazine residues into methanol-nonextractable (soil-bound) components, with minimal extractable metabolite accumulation. A mixed-mode extractant (potassium phosphate:acetonitrile) recovered greater amounts of (14)C-residues from atrazine-treated soils, suggesting that hydrolysis of atrazine to hydroxylated metabolites was a major component of the bound residues. These studies indicate the potential for herbicide dissipation in wetland soils and a differential effect of flooding on the fate of these herbicides.

Comparison of cultural and analytical methods for determination of aflatoxin production by Mississippi DeltaAspergillusisolates

This study compared cultural and analytical methods for detecting aflatoxin production by Aspergillus species. Aspergillus isolates were obtained from various Mississippi Delta crops (corn, peanut, rice, cotton) and soils. Most of the isolates (99%) were A. flavus and the remainder comprised A. parasiticus and A. nomius. The following three cultural methods were evaluated on potato dextrose agar: fluorescence (FL) on β-cyclodextrin-containing media (CD), yellow pigment (YP) formation in mycelium and medium, and color change after ammonium hydroxide vapor exposure (AV). Aflatoxins in culture extracts were confirmed by thin-layer chromatography (TLC) and quantified by enzyme-linked immunosorbent assay (ELISA). Of the 517 isolates, 314 produced greater than 20 ng/g of total aflatoxin based on ELISA, and 180 produced greater than 10 000 ng/g of aflatoxin in the medium. Almost all the toxigenic isolates (97%) were confirmed by TLC as producers. Of the toxigenic isolates, as determined by ELISA, 93%, 73%, and 70% gave positive FL, YP, and AV responses, respectively. Of the 203 isolates producing less than 20 ng/g of aflatoxin, 20%, 6%, and 0% of respective FL, YP, and AV methods gave false-positive responses. The 9% false-positive results from TLC fall within this range. This study showed good agreement among all tested cultural methods. However, these cultural techniques did not detect aflatoxin in all cultures that were found to produce aflatoxins by ELISA, LC/MS, and TLC. The best results were obtained when the AV color change and CD fluorescence methods were used together, yielding an overall success rate comparable to TLC but without the need for chemical extraction and the time and expense of TLC.Key words: aflatoxins, analytical methods, Aspergillus flavus, Aspergillus parasiticus, cultural methods, β-cyclodextrin, fluorescence enhancers, mycotoxins, yellow pigment.

Effects of patents and licenses on the provision of clinical genetic testing services

The growth of patents that include genetic sequences has been accompanied by concern about their impact on the ability of physicians to provide clinical genetic testing services and to perform research. Therefore, we conducted a survey of clinical laboratory directors that perform DNA-based genetic tests to examine potential effects. We performed a telephone survey between July and September in 2001 of all laboratory directors in the United States who were members of the Association for Molecular Pathology or who were listed on the GENETESTS:org website. One hundred thirty-two of 211 (63%) laboratory directors were interviewed. Ten of these were excluded because they did not conduct DNA-based genetic tests. Almost all performed genetic tests for clinical purposes. Half performed tests for research purposes as well. Twenty-five percent of respondents reported that they had stopped performing a clinical genetic test because of a patent or license. Fifty-three percent of respondents reported deciding not to develop a new clinical genetic test because of a patent or license. In total, respondents were prevented from performing 12 genetic tests, and all of these tests were among those performed by a large number of laboratories. We found 22 patents that were relevant to the performance of these 12 tests. Fifteen of the 22 patents (68%) are held by universities or research institutes, and 13 of the 22 patents (59%) were based on research funded by the United States Government. Overall, respondents reported that their perceptions of the effects of patents on the cost, access, and development of genetic tests, or data sharing among researchers, were negative. In contrast, most respondents felt that patents did not have an effect on the quality of testing. We conclude that patents and licenses have had a significant effect on the ability of clinical laboratories to develop and provide genetic tests. Furthermore, our findings suggest that clinical geneticists feel that their research is inhibited by patents. The effects of patents and licenses on patients' access to tests, and the costs and quality thereof, remains to be determined.

A pilot survey on the licensing of DNA inventions

Intellectual property in biotechnology invention provides important incentives for research and development leading to advances in genetic tests and treatments. However, there have been numerous concerns raised regarding the negative effect patents on gene sequences and their practical applications may have on clinical research and the availability of new medical tests and procedures. One concern is that licensing policies attempting to capture for the benefit of the licensor valuable rights to downstream research results and products may increase the financial risks and cliniinish potential payoffs of — and therefore motivation for — performing downstream research and development. In addition, very broad patent claims allowed by the U.S. Patent and Trademark Office, the sheer growth in patents claiming genetic sequences, and threats of overlapping patents create a veritable minefield for researchers in both academia and industry. The concern is that research may be stifled because of the high cost and hassle of negotiating access.

A semiparametric empirical likelihood method for data from an outcome-dependent sampling scheme with a continuous outcome

Outcome-dependent sampling (ODS) schemes can be a cost effective way to enhance study efficiency. The case-control design has been widely used in epidemiologic studies. However, when the outcome is measured on a continuous scale, dichotomizing the outcome could lead to a loss of efficiency. Recent epidemiologic studies have used ODS sampling schemes where, in addition to an overall random sample, there are also a number of supplemental samples that are collected based on a continuous outcome variable. We consider a semiparametric empirical likelihood inference procedure in which the underlying distribution of covariates is treated as a nuisance parameter and is left unspecified. The proposed estimator has asymptotic normality properties. The likelihood ratio statistic using the semiparametric empirical likelihood function has Wilks-type properties in that, under the null, it follows a chi-square distribution asymptotically and is independent of the nuisance parameters. Our simulation results indicate that, for data obtained using an ODS design, the semiparametric empirical likelihood estimator is more efficient than conditional likelihood and probability weighted pseudolikelihood estimators and that ODS designs (along with the proposed estimator) can produce more efficient estimates than simple random sample designs of the same size. We apply the proposed method to analyze a data set from the Collaborative Perinatal Project (CPP), an ongoing environmental epidemiologic study, to assess the relationship between maternal polychlorinated biphenyl (PCB) level and children's IQ test performance.

Simultaneous assessment of occupational exposures from multiple worker groups

The methods developed by Rappaport et al. [Ann. Occup. Hyg. 39 (1995) 469] and Lyles et al. [J. Agri. Bio. Environ. Stat. 2 (1997a) 64; Ann. Occup. Hyg. 41 (1997b) 63]) for assessing workplace exposures on a group-by-group basis are extended to allow for the simultaneous assessment of data from multiple worker groups within the same industry. These extended methods allow models to be fit simultaneously to data on all groups in a study, even when some of the groups might not contribute adequate information to be modeled separately. We assume that the exposures are log-normally distributed, and that they can be adequately modeled by a mixed effects regression model with parameters for exposure levels and for between- and within-worker variance components. Simultaneously analyzing data from multiple groups is only advantageous when at least one of these variance components can be assumed to be homogeneous across the groups. Here, we advocate testing an assumption of homogeneous within-worker variance components, sigma(2)(w,h), using a likelihood ratio test to choose between a full model (distinct sigma(2)(w,h) for each group) and a reduced model (common sigma(2)(w) across groups). We then develop a procedure, which is conditional on the results of the likelihood ratio test, for testing whether or not each group of workers is overexposed to the contaminant of interest. This modeling and testing procedure was applied to 39 different data sets, each containing data for multiple groups, from a wide variety of industries. For these data, the testing procedure generally resulted in the same conclusion regarding overexposure under both models, even in those data sets where the within-worker variance components appeared to be quite heterogeneous. We also conducted a small simulation study to estimate the significance level of the proposed testing procedure, and found that the significance levels tended to be adequately close to the specified nominal level when a likelihood ratio test with significance level of at least 0.01 was used as a preliminary test. Additionally, we make specific recommendations for designing studies and suggest a method for determining whether engineering and administrative controls or individual-level interventions would be of most benefit to an overexposed group of workers.

Acute and chronic pain management in palliative care

Every palliative care patient should have the expectation that acute and chronic pain management will be an integral part of their overall care. However, in all too many instances, the pain of cancer is often grossly under-treated. This issue is of concern because more than 80% of patients with cancer pain can find adequate relief through the use of simple pharmacological methods. It is even more troubling to note that women and minority groups have their cancer pain under-treated more frequently. Physicians with the basic skills of assessment and treatment will be able to control the symptoms in the majority of cancer pain patients. However, there are still some patients who may require other modalities to control their moderate to severe pain. A thorough understanding of all pain management options will help the gynaecological oncologist to maintain an acceptable quality of life for their patients throughout the therapeutic and palliative phases of care.

Psychological testing variables as predictors of return to work by chronic pain patients

After multidisciplinary pain treatment, pretreatment psychological testing variables were compared for 20 chronic pain patients who were working and 42 who were not working. Symptom Checklist-90-R scores for Depression, Anxiety, Phobic Anxiety, Psychoticism, Global Severity, and Positive Symptom Distress were lower for working subjects as were those on the Beck Depression Inventory. In contrast, workers scored higher on self-efficacy to manage pain, self-efficacy to function, self-efficacy to manage other symptoms, and over all self-efficacy.

A beta-glucuronidase reporter gene construct for monitoring aflatoxin biosynthesis in Aspergillus flavus

Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and A. parasiticus. Current research is directed at the elimination of these compounds in important food sources. The objective of this research was to develop a method to study the induction and regulation of aflatoxin biosynthesis by examining the expression of one aflatoxin pathway gene, ver1. The promoter region of ver1 was fused to the beta-glucuronidase (GUS) gene (uidA) from Escherichia coli to form the reporter construct, GAP13. A. flavus 656-2 was transformed with this construct. Aflatoxin production, GUS activity, and transcript accumulation were determined in transformants after shifting the cultures from a nonconducive medium to a medium conducive to aflatoxin biosynthesis. Transformants harboring GAP13 displayed GUS expression only when aflatoxin was detected in culture. Further, the transcription of the uidA gene driven by the ver1 promoter followed the same profile as for the ver1 genes. The results show that the GAP13 construct may be useful as a genetic tool to study the induction of aflatoxin in situ and to identify substances that affect the expression of genes involved in aflatoxin biosynthesis. The utility of this construct to detect inducers of aflatoxin biosynthesis in maize kernels was tested in a bioassay. A heat-stable inducer of aflatoxin with a molecular size of less than 10 kDa was detected in extracts from maize kernels colonized by A. flavus.