Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium

Evaluating the pathogenicity of a variant is challenging given the plethora of types of genetic evidence that laboratories consider. Deciding how to weigh each type of evidence is difficult, and standards have been needed. In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for the assessment of variants in genes associated with Mendelian diseases. Nine molecular diagnostic laboratories involved in the Clinical Sequencing Exploratory Research (CSER) consortium piloted these guidelines on 99 variants spanning all categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign). Nine variants were distributed to all laboratories, and the remaining 90 were evaluated by three laboratories. The laboratories classified each variant by using both the laboratory's own method and the ACMG-AMP criteria. The agreement between the two methods used within laboratories was high (K-alpha = 0.91) with 79% concordance. However, there was only 34% concordance for either classification system across laboratories. After consensus discussions and detailed review of the ACMG-AMP criteria, concordance increased to 71%. Causes of initial discordance in ACMG-AMP classifications were identified, and recommendations on clarification and increased specification of the ACMG-AMP criteria were made. In summary, although an initial pilot of the ACMG-AMP guidelines did not lead to increased concordance in variant interpretation, comparing variant interpretations to identify differences and having a common framework to facilitate resolution of those differences were beneficial for improving agreement, allowing iterative movement toward increased reporting consistency for variants in genes associated with monogenic disease

Actionable exomic incidental findings in 6503 participants: challenges of variant classification

Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

The Effect of Gene-Obesity and Gene-Care Setting Interactions on Risk of Major Bleeding Events in Warfarin Users

Thesis (Master's)--University of Washington, 2014A commonly prescribed anticoagulant, Warfarin (Coumadin®), reduces thromboembolic (blood clotting) event rates in patients with atrial fibrillation, stroke, joint replacement, and other conditions that present increased clotting risk. Unfortunately, pharmacogenetic-guided dosing algorithms have not yielded the predicted effect clinicians and researchers anticipated compared to using the clinically guided dosing methods. Further explanations for effects modifying the genetic effects present on bleeding risk in warfarin patients are warranted. We analyzed a case-control study to investigate gene-environment interaction effects on risk of serious bleeding in warfarin users in a community setting. No interaction was found between CYP2C9/VKORC1 and obesity. A statistically significant interaction was found between CYP4F2 x obesity, however, the p-value of 0.049 would not hold its statistical significance to Bonferroni correction for multiple comparisons. No statistically significant interaction was found between CYP2C9/VKORC1 x care setting or between CYP4F2 x care setting. These findings need to be validated in a larger population to inform future clinical guidelines in order for warfarin users to receive the optimal benefit

Exploring Strategies to Optimize the Value of Pharmacogenomic Testing

Thesis (Ph.D.)--University of Washington, 2018The emergence and continual advancement of genomic technologies offer numerous areas that warrant a critical appraisal for integrating new health care services to increase access and improve outcomes for patients. This dissertation examines two strategies in the context of pharmacogenomics (PGx) testing. In the Overall Introduction, we initially focus on identifying clinical utility and economic evidence gaps necessary to inform appropriate clinical adoption of PGx testing across diverse healthcare settings. In Chapter 1, we report our findings from an analysis of real-world evidence from a commercial PGx knowledge resource, which is comprised of data from patients who have undergone PGx testing. Additionally, we characterize gene-drug pair level of evidence as developed by expert groups, and present associated predictive factors that may inform clinical actionability. Following this, in Chapter 2, we focus on a hypothetical clinical cohort of acute coronary syndrome patients undergoing percutaneous coronary intervention. We use decision modeling methods to estimate the projected cost-effectiveness of a multi-gene panel to guide two treatment decisions for this clinical cohort from the payer perspective. We describe influential parameters in the model, discuss limitations of this work, and denote implications to health policy decision making. In the Overall Conclusions, we summarize and describe future considerations. To increase appropriate clinical PGx testing adoption, we provide evidence that healthcare entities may wish to consider the use of a commercially-developed PGx knowledge resource solution in lieu of delaying implementation awaiting publicly available PGx knowledge resource solutions. Additionally, for the aforementioned patient cohort, we provide evidence that the multi-gene panel estimates are projected to be cost-effective at a $100,000 willingness-to-pay threshold when compared to either a single-gene panel or to no gene testing. These findings build upon the available economic evidence for multi-gene panels that payer decision makers may consider during their health technology assessment evaluations to determine inclusion of covered services within their medical policies. Finally, the contents of this dissertation contribute to the broader discourse regarding value assessments in the interplay between precision medicine and clinical genomics