Evaluating the impact of in silico predictors on clinical variant classification

PURPOSE

According to the American College of Medical Genetics and Genomics/Association of Medical Pathology (ACMG/AMP) guidelines, in silico evidence is applied at the supporting strength level for pathogenic (PP3) and benign (BP4) evidence. Although PP3 is commonly used, less is known about the effect of these criteria on variant classification outcomes.

METHODS

A total of 727 missense variants curated by Clinical Genome Resource expert groups were analyzed to determine how often PP3 and BP4 were applied and their impact on variant classification. The ACMG/AMP categorical system of variant classification was compared with a quantitative point-based system. The pathogenicity likelihood ratios of REVEL, VEST, FATHMM, and MPC were calibrated using a gold standard set of 237 pathogenic and benign variants (classified independent of the PP3/BP4 criteria).

RESULTS

The PP3 and BP4 criteria were applied by Variant Curation Expert Panels to 55% of missense variants. Application of those criteria changed the classification of 15% of missense variants for which either criterion was applied. The point-based system resolved borderline classifications. REVEL and VEST performed best at a strength level consistent with moderate evidence.

CONCLUSION

We show that in silico criteria are commonly applied and often affect the final variant classifications. When appropriate thresholds for in silico predictors are established, our results show that PP3 and BP4 can be used at a moderate strength.

ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines

BACKGROUND

Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.

RESULTS

Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications.

CONCLUSIONS

The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures

Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.

LitGen: Genetic Literature Recommendation Guided by Human Explanations

As genetic sequencing costs decrease, the lack of clinical interpretation of variants has become the bottleneck in using genetics data. A major rate limiting step in clinical interpretation is the manual curation of evidence in the genetic literature by highly trained biocurators. What makes curation particularly time-consuming is that the curator needs to identify papers that study variant pathogenicity using different types of approaches and evidences-e.g. biochemical assays or case control analysis. In collaboration with the Clinical Genomic Resource (ClinGen)-the flagship NIH program for clinical curation-we propose the first machine learning system, LitGen, that can retrieve papers for a particular variant and filter them by specific evidence types used by curators to assess for pathogenicity. LitGen uses semi-supervised deep learning to predict the type of evi+dence provided by each paper. It is trained on papers annotated by ClinGen curators and systematically evaluated on new test data collected by ClinGen. LitGen further leverages rich human explanations and unlabeled data to gain 7.9%-12.6% relative performance improvement over models learned only on the annotated papers. It is a useful framework to improve clinical variant curation.

Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework

BACKGROUND

The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria for different types of evidence. This includes the strong evidence codes PS3 and BS3 for "well-established" functional assays demonstrating a variant has abnormal or normal gene/protein function, respectively. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes are a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation.

METHODS

The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated the odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development.

RESULTS

The SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are as follows: (1) define the disease mechanism, (2) evaluate the applicability of general classes of assays used in the field, (3) evaluate the validity of specific instances of assays, and (4) apply evidence to individual variant interpretation. We found that a minimum of 11 total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis.

CONCLUSIONS

The recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.

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 Allele Registry links information about genetic variants

Effective exchange of information about genetic variants is currently hampered by the lack of readily available globally unique variant identifiers that would enable aggregation of information from different sources. The ClinGen Allele Registry addresses this problem by providing (1) globally unique "canonical" variant identifiers (CAids) on demand, either individually or in large batches; (2) access to variant-identifying information in a searchable Registry; (3) links to allele-related records in many commonly used databases; and (4) services for adding links to information about registered variants in external sources. A core element of the Registry is a canonicalization service, implemented using in-memory sequence alignment-based index, which groups variant identifiers denoting the same nucleotide variant and assigns unique and dereferenceable CAids. More than 650 million distinct variants are currently registered, including those from gnomAD, ExAC, dbSNP, and ClinVar, including a small number of variants registered by Registry users. The Registry is accessible both via a web interface and programmatically via well-documented Hypertext Transfer Protocol (HTTP) Representational State Transfer Application Programming Interface (REST-APIs). For programmatic interoperability, the Registry content is accessible in the JavaScript Object Notation for Linked Data (JSON-LD) format. We present several use cases and demonstrate how the linked information may provide raw material for reasoning about variant's pathogenicity.

Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource

With advances in genomic sequencing technology, the number of reported gene-disease relationships has rapidly expanded. However, the evidence supporting these claims varies widely, confounding accurate evaluation of genomic variation in a clinical setting. Despite the critical need to differentiate clinically valid relationships from less well-substantiated relationships, standard guidelines for such evaluation do not currently exist. The NIH-funded Clinical Genome Resource (ClinGen) has developed a framework to define and evaluate the clinical validity of gene-disease pairs across a variety of Mendelian disorders. In this manuscript we describe a proposed framework to evaluate relevant genetic and experimental evidence supporting or contradicting a gene-disease relationship and the subsequent validation of this framework using a set of representative gene-disease pairs. The framework provides a semiquantitative measurement for the strength of evidence of a gene-disease relationship that correlates to a qualitative classification: "Definitive," "Strong," "Moderate," "Limited," "No Reported Evidence," or "Conflicting Evidence." Within the ClinGen structure, classifications derived with this framework are reviewed and confirmed or adjusted based on clinical expertise of appropriate disease experts. Detailed guidance for utilizing this framework and access to the curation interface is available on our website. This evidence-based, systematic method to assess the strength of gene-disease relationships will facilitate more knowledgeable utilization of genomic variants in clinical and research settings.

The DNA sequence and analysis of human chromosome 13

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Mechanisms of sunscreen failure

Sunscreen is used as a primary strategy to prevent sunburn and later skin cancer. However, sunscreen use has paradoxically been associated with the increasing incidence of skin cancer. One explanation for this puzzling observation is sunscreen failure (sunburn in the setting of sunscreen). Our purpose was to evaluate mechanisms of sunscreen failure in a sunscreen-using population. We carried out an epidemiologic comparison of sunburned and nonsunburned beachgoers who used sunscreen. We found that men were less likely to use sunscreen than women (chi(2) = 11.3, df = 1, P = .001), and when it was used, men were less likely to apply sunscreen to all sunlight-exposed skin (chi(2) = 18.4, df = 1, P = .0001). Swimmers who used sunscreen were significantly more likely to be sunburned compared with nonswimming sunscreen users (Fisher exact test, df = 1). Sunscreen may fail to prevent sunburn if it is washed off during swimming or if it is not applied to all exposed skin. Epidemiologic studies that link sunscreen use to skin cancer should evaluate whether sunburn occurred in this setting.

Basal cell carcinoma arising in a cleft lip repair scar

BACKGROUND

A case of basal cell carcinoma (BCC) developing in the repair scar of a cleft lip is presented.

OBJECTIVE

Primary BCCs arising in surgical scars are very rare and no known reported cases exist of a BCC developing in a surgically repaired cleft lip scar.

METHODS

A 69-year-old white man presented with a 5 mm primary BCC on his upper lip at the site of his cleft lip repair scar. The diagnosis was made by a tangential biopsy that showed an ulcerated BCC.

RESULTS

Review of the medical literature indicates that a scar may be an independent risk factor for developing BCC.

CONCLUSION

BCC may rarely arise in a cleft lip repair scar.

Retinal photoreceptors of paleognathous birds: the ostrich (Struthio camelus) and rhea (Rhea americana)

Microspectrophotometry was used to determine the absorbance spectra of both rod and cone visual pigments and oil droplets from the retinae of the ostrich (Struthio camelus) and rhea (Rhea americana). Light and fluorescence microscopy of whole fresh tissue mounts were used to determine the relative numbers and distribution of oil droplets in the retinae. Both species possessed rods, double cones and four classes of single cone identified by their oil droplets. The rods had lambda max at about 505 nm, whereas three cone pigments were recorded with lambda max at 570, 505 and 445 nm. The P570 pigment was located in both members of the double cones and in a class of single cone containing an R-type oil droplet (lambda cut at 555 nm). The P505 and P445 cone pigments were found in populations of single cones containing Y-type and C-type oil droplets (lambda cut of 500 and 420 nm, respectively). The fourth class of single cone contained a T-type droplet and in the ostrich contained a visual pigment with lambda max at about 405 nm. Double cones possessed a P-type droplet in the principal member and an A-type droplet in the accessory member. The complement of visual pigments and oil droplets, and the ratio of cone types in the ostrich and rhea, are remarkably similar to those found in many groups of neognathous birds.

The choice of weapons in firearm suicides

We report on the firearms used in 235 suicides in Sacramento County, California, during 1983-85. Handguns were used in 69 per cent of firearm suicides--65 per cent for males, 88 per cent for females--and in all such deaths among women ages 35 and older. We tested the hypothesis that the choice of firearms by persons committing suicide at home would passively reflect the reported prevalence of firearms by type in households in the region. Handguns were used more frequently (rate ratio 2.00; 95% CI = 1.68, 2.39), and rifles and shotguns less frequently than expected.

The use of lipid emulsion as an intravesical medium to disperse light in the potential treatment of bladder tumors

An obstacle to satisfactory treatment of early bladder cancer with hematoporphyrin derivative-photoradiation therapy is nonuniform illumination of the bladder mucosa. This study was done to determine the characteristics and attenuation of laser light passing through the dispersion medium. Bladder simulation was achieved with the use of 5 different sizes of round-bottom flasks. Intralipid was the dispersion medium. For each flask, 6 different concentrations of the dispersion medium were used. An Argon ion laser was used to stimulate a dye laser at 630 nm. The laser was directed toward the center of the flasks via a fiberoptic cable and energy concentration at 7 different angles was measured. We concluded that the optimal medium was a 1:100 dilution of Intralipid with water, which produced an almost uniform dispersion of light on the walls of the flask. There is a linear correlation between power as measured at the fiber tip and the amount of radiation detected on the walls of the flasks. After determining optimal concentration of medium, we calculated the amount of time needed for a desired energy (Joules/cm.2) to treat a tumor. This calculation was based on the size of the bladder and the power as measured at the fiber tip. The results indicate it is possible to treat the entire mucosa of the bladder with a uniform dose of photoradiation energy.

Synthesis of some derivatives of 2,5-Anhydro-D-mannitol

The synthesis of 2,5:3,4-dianhydro-D-allitol and of a variety of derivatives (sulfonyloxy, deoxy, azido, iodo, etc.) of 2,5-anhydro-D-mannitol is described.

Behavioural and social characteristics of the patient with repeated venereal disease and his effect on statistics on venereal diseases

The current study investigated personality characteristics and social circumstances in patients repeatedly infected with venereal diseases. An effort was made to identify characteristics that would differentiate a repeat patient (RP) from a non-repeat patient (NRP). Two studies were carried out. In the first, a group of patients from a venereal disease clinic in a large general hospital was first interviewed and then the patients were asked to complete a questionnaire. In the second study, an attempt was made to validate the findings from the first study by comparing data from RP and NRP venereal disease patients drawn from medical and social case histories from a second hospital. Results of both studies support the hypothesis that repeat patients are different from non-repeat venereal disease patients in terms of social and psychological characteristics. The significance of these findings is discussed.

The effects of drugs on psychiatric patients' performance on the Halstead-Reitan neuropsychological test battery

The relationship between the type and amount of psychotropic drug ingestion was evaluated for 184 psychiatric patients using a complex battery of cognitive-sensory-motor tests (Halstead-Reitan). The total patients' group included 68 psychotic patients who were being treated with either phenothiazines or "another drug," and 80 neurotically depressed patients who were taking either no drugs, phenothiazines, minor tranquilizers, tricyclic antidepressants, or sedatives. Little, if any, effect was noted in terms of psychological test performance when individual drug types were combined and considered in terms of dosage. However, upon a more specific analysis of the data, several suggestive trends occurred, demonstrating that individual drugs have variable effects and that some age groupings are more sensitive to drug effects than other groupings. As these trends were a result of a secondary analysis, further investigation was recommended in order to delineate the variables involved. For the present, this investigation has demonstrated the important influence of age and drug type variables upon patient neuropsychological test performance.