Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies.

Harmonization of variant pathogenicity classification across laboratories is important for advancing clinical genomics. The two CLIA-accredited Electronic Medical Record and Genomics Network sequencing centers and the six CLIA-accredited laboratories and one research laboratory performing genome or exome sequencing in the Clinical Sequencing Evidence-Generating Research Consortium collaborated to explore current sources of discordance in classification. Eight laboratories each submitted 20 classified variants in the ACMG secondary finding v.2.0 genes. After removing duplicates, each of the 158 variants was annotated and independently classified by two additional laboratories using the ACMG-AMP guidelines. Overall concordance across three laboratories was assessed and discordant variants were reviewed via teleconference and email. The submitted variant set included 28 P/LP variants, 96 VUS, and 34 LB/B variants, mostly in cancer (40%) and cardiac (27%) risk genes. Eighty-six (54%) variants reached complete five-category (i.e., P, LP, VUS, LB, B) concordance, and 17 (11%) had a discordance that could affect clinical recommendations (P/LP versus VUS/LB/B). 21% and 63% of variants submitted as P and LP, respectively, were discordant with VUS. Of the 54 originally discordant variants that underwent further review, 32 reached agreement, for a post-review concordance rate of 84% (118/140 variants). This project provides an updated estimate of variant concordance, identifies considerations for LP classified variants, and highlights ongoing sources of discordance. Continued and increased sharing of variant classifications and evidence across laboratories, and the ongoing work of ClinGen to provide general as well as gene- and disease-specific guidance, will lead to continued increases in concordance.

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.

Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.

PURPOSE: Clinical sequencing emerging in health care may result in secondary findings (SFs). METHODS: Seventy-four of 6240 (1.2%) participants who underwent genome or exome sequencing through the Clinical Sequencing Exploratory Research (CSER) Consortium received one or more SFs from the original American College of Medical Genetics and Genomics (ACMG) recommended 56 gene-condition pair list; we assessed clinical and psychosocial actions. RESULTS: The overall adjusted prevalence of SFs in the ACMG 56 genes across the CSER consortium was 1.7%. Initially 32% of the family histories were positive, and post disclosure, this increased to 48%. The average cost of follow-up medical actions per finding up to a 1-year period was $128 (observed, range: $0-$678) and $421 (recommended, range: $141-$1114). Case reports revealed variability in the frequency of and follow-up on medical recommendations patients received associated with each SF gene-condition pair. Participants did not report adverse psychosocial impact associated with receiving SFs; this was corroborated by 18 participant (or parent) interviews. All interviewed participants shared findings with relatives and reported that relatives did not pursue additional testing or care. CONCLUSION: Our results suggest that disclosure of SFs shows little to no adverse impact on participants and adds only modestly to near-term health-care costs; additional studies are needed to confirm these findings.

Correction: Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study.

The originally published version of this Article contained errors in Fig. 2. The numbers below the black arrowheads were incorrect; please see incorrect Figure in associated Correction. These errors have now been corrected in the PDF and HTML versions of the Article.

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.

Eliciting preferences on secondary findings: the Preferences Instrument for Genomic Secondary Results.

PURPOSE: Eliciting and understanding patient and research participant preferences regarding return of secondary test results are key aspects of genomic medicine. A valid instrument should be easily understood without extensive pretest counseling while still faithfully eliciting patients' preferences. METHODS: We conducted focus groups with 110 adults to understand patient perspectives on secondary genomic findings and the role that preferences should play. We then developed and refined a draft instrument and used it to elicit preferences from parents participating in a genomic sequencing study in children with intellectual disabilities. RESULTS: Patients preferred filtering of secondary genomic results to avoid information overload and to avoid learning what the future holds, among other reasons. Patients preferred to make autonomous choices about which categories of results to receive and to have their choices applied automatically before results are returned to them and their clinicians. The Preferences Instrument for Genomic Secondary Results (PIGSR) is designed to be completed by patients or research participants without assistance and to guide bioinformatic analysis of genomic raw data. Most participants wanted to receive all secondary results, but a significant minority indicated other preferences. CONCLUSIONS: Our novel instrument-PIGSR-should be useful in a wide variety of clinical and research settings.Genet Med 19 3, 337-344.

Bone morphogenetic protein 2­mediated mandible reconstruction successfully heals bony defects but inhibits concurrent inferior alveolar nerve grafting: a rabbit experimental model.

BACKGROUND: Bone morphogenetic protein 2 (BMP-2) has been used to reconstruct mandibular defects. An elegant addition to this reconstruction method would be incorporation of a nerve graft wrapped in a BMP-2 carrier to reconstitute the inferior alveolar nerve (IAN) and restore sensation to the lower face. We developed a rabbit model to determine the effect BMP-2 has on nerve regeneration following neurorrhaphy. METHODS: An inferior border mandibulectomy was created in 16 adult New Zealand white rabbits. The IAN was protected, divided, and repaired with either primary neurorrhaphy or reverse autografts. Bone defects were treated with no treatment controls (n = 2), absorbable collagen sponge (ACS) (vehicle controls) (n = 7), and ACS soaked in BMP-2 (treatment group) (n = 7). Animals underwent computed tomography (CT) 2 days and 6 weeks postoperatively. The percent bone defect healing was calculated using Amira 3D imaging software. At 6 weeks, IANs were harvested mesial to the reconstruction and were evaluated with toluidine blue histology to identify myelinated axons. Reconstructed mandible segments were evaluated with micro-CT and hematoxylin-eosin histology. RESULTS: Bone morphogenetic protein 2-treated animals demonstrated significantly more bone healing than did the ACS and empty defect groups (82%, 38%, 44%, respectively; P < 0.01). One hundred percent of ACS-treated nerves (n = 4) demonstrated axon regrowth, whereas only 25% of BMP-2-treated nerves (n = 4) did. Micro-CT and histology showed BMP-2 caused bone growth around the IAN, but regenerated bone infiltrated the repair site and created a physical barrier to axon growth. CONCLUSIONS: Bone morphogenetic protein 2 can successfully heal bone defects in the rabbit mandible, but ectopic bone growth can inhibit IAN recovery after repair. Level of Evidence: Not gradable.

Diversity supplements: An underutilized opportunity to improve the diversity of the health sciences research workforce.

Purpose: This paper describes the process developed at the University of Pittsburgh to increase the number of NIH-funded Diversity Supplements. Method: The authors formed a Diversity in Academia Workgroup where we created the infrastructure and process to increase the number of Diversity Supplements. Each year, the Office of Sponsored Programs provided a list of grants that would be eligible to submit a Diversity Supplement. We surveyed the Principal Investigators inquiring about their interest in working with a trainee on a Diversity Supplement. If yes, we included their information in a database we built so that trainees could search for eligible research studies. The Diversity Deans then identified underrepresented faculty and postdoctoral researchers. We invited Program Officers from NIH to participate in a panel presentation for trainees, which was well attended. Results: The number of Diversity Supplements awarded to Pitt researchers has significantly increased from 7 in 2020 to 10 in 2021 and to 15 in 2022. Six more have been awarded in the first half of 2023. Conclusions: We created the Diversity in Academia Workgroup with the goal to increase the number of Diversity Supplements at the University of Pittsburgh and in so doing, increase the diversity in the biomedical research workforce. While challenging, we know the critical importance and benefits of increased diversity at the University, and we have made significant strides toward this goal.

Moving to the Middle Ground: Redefining Genomic Utility to Expand Understanding of Familial Benefit.

Translational research has tended to ignore the question of whether receiving a genomic diagnosis provides utility in community care contexts outside of doctors' offices and hospitals. However, empirical research with parents has highlighted numerous ways that a genomic diagnosis might be of practical value in the care provided by teachers, physical or occupational therapists, speech-language pathologists, behavior analysts, and nonphysician mental health providers. In this essay, we propose a new conceptual model of genomic utility that offers the opportunity to better capture a broad range of potential implications of genomic technologies for families in various social and organizational systems. We explore crucial research directions to better understand how redefined utility might affect families and nonphysician professionals.

Sociodemographic and clinical factors associated with receipt of biomarker testing in patients with metastatic colorectal cancer.

BACKGROUND: Standard clinical practice and national guidelines dictate somatic testing of metastatic colorectal cancer (mCRC) tumors to guide appropriate therapy; however, previous studies suggest that not all patients are tested. The objective of this study was to investigate potential differences in testing for mCRC by demographic and clinical factors. METHODS: We performed a retrospective review of de-identified patient data derived from electronic health records (EHRs) of 25,469 patients diagnosed with mCRC between the years 2013 and 2020. Our outcome was a receipt of the following tests: (a) biomarker testing (BRAF, KRAS, NRAS, MMR/MSI) and (b) next-generation sequencing (NGS). We interrogated our data using the machine-learning algorithm Classification and Regression Tree (CART), a unique approach to identifying combinations of, rather than individual demographic and clinical characteristics associated with receipt of testing. RESULTS: A total of 25,469 patients were identified with mCRC. Of these, 21,133 (83%) received either biomarker testing only (n = 12,485) or any testing (biomarker + NGS) (n = 8648). The proportion of patients who received any testing increased over calendar time for all age, race, and sex categories. Receipt of any testing was highest (90%) among younger and patients with better performance status, and there was no difference in receipt of any testing by race. The highest percentage of NGS testing was among those with better performance status, <70 years old, commercial or other governmental program payers, and low comorbidity burden; however, those who were Black or Hispanic had a lower prevalence of NGS testing than those who were White. CONCLUSIONS AND RELEVANCE: Considerable variations exist in somatic biomarker testing across subgroups of the population. Identification of genomic alterations can aid in determining targeted treatment and improving clinical outcomes; therefore, equitable use of these testing strategies, particularly NGS, is necessary.

Variation in KRAS/NRAS/BRAF-Mutation Status by Age, Sex, and Race/Ethnicity Among a Large Cohort of Patients with Metastatic Colorectal Cancer (mCRC).

BACKGROUND: Racial/ethnic disparities in metastatic colorectal cancer (mCRC) survival are well documented as is the impact that tumor mutation of KRAS and BRAF has on prognosis. It has been suggested that frequency differences of KRAS- and BRAF-mutated tumors may partially explain this disparity. Demographic differences in mutation frequency are not well established nor whether mutation and microsatellite instability (MSI) differentially impact survival among groups. METHODS: Using data for 11,117 patients diagnosed with de-novo mCRC from an electronic health record-derived database we estimated adjusted odds ratios (aOR) to characterize the association between demographics and MSI and KRAS/NRAS/BRAF-mutation status. Stratified Cox models were used to identify differences in overall survival (OS), adjusting for treatment and demographics. RESULTS: Being female, compared to male, (aORKRAS:1.33 (1.23-1.44); aORBRAF:1.84 (1.56-2.16)), and non-Hispanic Black race (NHB), compared to non-Hispanic White (NHW) (aORKRAS:1.62 (1.42-1.85); aORBRAF: 0.55 (0.38-0.77)) were associated with KRAS- or BRAF-mutant tumors. MSI prevalence was similar across race/ethnicity but higher in women. BRAF-mutant tumors were associated with poorer prognosis overall, especially among non-white patients. Among patients who had KRAS/NRAS/BRAF-WT tumors we observed no difference in OS by race or MSI. Among patients with KRAS-mutant tumors, Hispanic patients had more favorable prognosis adjusted hazards ratio (aHR) = 0.76 (0.65-0.89)) than their NHW counterparts. Among those with BRAF-mutant tumors, NHB patients had poorer prognosis than NHW patients (aHR:1.78 (1.08-2.93)). CONCLUSION: MSI and frequency of KRAS and BRAF mutations differed by demographics. Racial/ethnic disparities in OS differed by mutation. Future studies should explore biological and/or social determinants underlying these differences.

Collective opinion paper on findings of the 2011 convocation of experts on laboratory quality.

In April of 2011, Bio-Rad Laboratories Quality System Division (Irvine, CA, USA) hosted its third annual convocation of experts on laboratory quality in the city of Salzburg, Austria. As in the past 2 years, over 60 experts from across Europe, Israel, USA and South Africa convened to discuss contemporary issues and topics of importance to the clinical laboratory. This year's conference had EN/ISO 15189 and accreditation as the common thread for most discussions, with topics ranging from how to meet requirements like uncertainty to knowledge gained from those already accredited. The participants were divided into five discussion working groups (WG) with assigned topics. The outcome of these discussions is the subject of this summary.

Education and Training of Non-Genetics Providers on the Return of Genome Sequencing Results in a NICU Setting.

To meet current and expected future demand for genome sequencing in the neonatal intensive care unit (NICU), adjustments to traditional service delivery models are necessary. Effective programs for the training of non-genetics providers (NGPs) may address the known barriers to providing genetic services including limited genetics knowledge and lack of confidence. The SouthSeq project aims to use genome sequencing to make genomic diagnoses in the neonatal period and evaluate a scalable approach to delivering genome sequencing results to populations with limited access to genetics professionals. Thirty-three SouthSeq NGPs participated in a live, interactive training intervention and completed surveys before and after participation. Here, we describe the protocol for the provider training intervention utilized in the SouthSeq study and the associated impact on NGP knowledge and confidence in reviewing, interpreting, and using genome sequencing results. Participation in the live training intervention led to an increased level of confidence in critical skills needed for real-world implementation of genome sequencing. Providers reported a significant increase in confidence level in their ability to review, understand, and use genome sequencing result reports to guide patient care. Reported barriers to implementation of genome sequencing in a NICU setting included test cost, lack of insurance coverage, and turn around time. As implementation of genome sequencing in this setting progresses, effective education of NGPs is critical to provide access to high-quality and timely genomic medicine care.

Collective opinion paper on findings of the 2010 convocation of experts on laboratory quality.

As a part of a series of yearly meeting, in May 2010 over 40 medical laboratory opinion leaders, pathologists, clinical biochemists and physicians from Europe, Israel and South Africa gathered together in Bardolino, Italy to discuss issues and current challenges for laboratory medicine, including a) the use of biological variation 10 years after the Stockholm Conference; b) achieving quality in point-of-care testing; c) assessing risk and controlling sources of error in the laboratory; d) determining the appropriate frequency of quality control; and f) putting laboratory medicine at the core of patient care. The intended goal of the convocation was to give laboratory professionals from different countries and backgrounds the opportunity to share ideas, concerns and experiences in previously mentioned areas of interest. This paper provide a synopsis of the reports from each working group.

The Therapeutic Odyssey: Positioning Genomic Sequencing in the Search for a Child's Best Possible Life.

Background: The desire of parents to obtain a genetic diagnosis for their child with intellectual disability and associated symptoms has long been framed as a diagnostic odyssey, an arduous and sometimes perilous journey focused on the goal of identifying a cause for the child's condition.Methods: Semi-structured interviews (N = 60) were conducted with parents of children (N = 59, aged 2-24 years) with intellectual disability and/or developmental delay (IDD) who underwent genome sequencing at a single pediatric multispecialty clinic. Interviews were conducted after parents received their child's sequencing result (positive findings, negative findings, or variants of unknown significance). Thematic analysis was performed on all interviews.Results: Parents reported that obtaining a genetic diagnosis was one important step in their overall goal of helping their child live their best life possible life. They intended to use the result as a tool to help their child by seeking the correct school placement and obtaining benefits and therapeutic services.Conclusions: For the parents of children with IDD, the search for a genetic diagnosis is best conceptualized as a part of parents' ongoing efforts to leverage various diagnoses to obtain educational and therapeutic services for their children. Cleaving parents' search for a genetic diagnosis from these broader efforts obscures the value that some parents place on a sequencing result in finding and tailoring therapies and services beyond the clinic. Interviews with parents reveal, therefore, that genomic sequencing is best understood as one important stage of an ongoing therapeutic odyssey that largely takes place outside the clinic. Findings suggest the need to expand translational research efforts to contextualize a genetic diagnosis within parents' broader efforts to obtain educational and therapeutic services outside clinical contexts.

Comparison of recruitment efforts targeted at primary care physicians versus the community at large for participation in Alzheimer disease clinical trials.

Inefficient and delayed recruitment into clinical trials in Alzheimer disease are major obstacles impeding progress in the discovery of more effective therapeutic strategies to combat this disease. Despite widespread recognition of this problem, limited empirical data demonstrating the effectiveness of specific recruitment strategies are available to guide recruitment endeavors. This study was designed to evaluate the effectiveness of recruitment efforts targeting either the primary care health professionals (PCPs) or patients and families with a community grass-roots outreach event. The primary outcome measure was actual study recruitment and participation in the 4 months postintervention. No research subjects were recruited from the PCP intervention, whereas 69 subjects were recruited into clinical studies from the community grass-roots outreach event activity (0% vs. 28%, P<0.0001, Fisher exact test). Barriers to recruitment success in the PCP arm included a perception of perceived harm to subjects from research participation and fear of losing patients through clinical research participation. Our results suggest that outreach efforts directed at the potential study subject/caregiver are not only cost-effective but are able to easily accomplish the desired result of direct recruitment into clinical research studies.

Collective opinion paper on findings of the 2009 convocation of experts on quality control.

On May 28-29, 2009, a number of medical laboratory opinion leaders, pathologists and biochemists met in Sitges, Spain to discuss issues of interest to medical laboratory professionals. The meeting was sponsored by Bio-Rad Laboratories Inc. (Hercules, CA). Over 40 persons representing Austria, Belgium, Czech Republic, Finland, Germany, Great Britain, Israel, Italy, Netherlands, Portugal, South Africa, Spain, Sweden and the US participated in the 1.5 days meeting. The intended purpose of the convocation was to give medical laboratory professionals from different countries and backgrounds an opportunity to share ideas, concerns and experiences in five areas of interest of the sponsor. These areas of interest included: * a requirement for medical laboratory accreditation across Europe * uncertainty of measurement in a clinical laboratory setting * application of Six Sigma values to characterize laboratory quality * effects of analytical errors on patient care and outcomes * harmonization of allowable total error (TEa) specifications The convocation began with a keynote speech by Dr. James Westgard on "Managing quality vs. measuring uncertainty in the medical laboratory". Dr. Westgard's presentation was thought provoking and called into question the utility and practicality of using uncertainty in a medical laboratory setting. This journal contains a companion article written by Dr. Westgard on this topic. After the keynote speech, the meeting adjourned into five discussion groups and reconvened the next day to hear the outcomes of the discussions by each of the working groups. This article provides a synopsis of the reports from each working group.

Acetylcholinesterase inhibitor treatment is associated with relatively slow cognitive decline in patients with Alzheimer's disease and AD + DLB.

Dementia can be caused by different diseases including Alzheimer's disease (AD), dementia with Lewy bodies (DLB), or both (AD + DLB). University of Kentucky AD Center pathologically-diagnosed AD and AD + DLB cases were evaluated who had three or more longitudinal antemortem mental status examinations (n = 156). Patients with important concomitant pathology (n = 5) or patients that were profoundly demented at recruitment (intake MMSE < 20; n = 86) were excluded to strengthen our ability to test the association of specific clinical and pathological indices. Patients with pathologically-diagnosed AD + DLB (n = 25) lost cognitive capacity faster than patients with AD alone (n = 40). In both diseases, treatment with acetylcholinesterase inhibitors was associated with a slower rate of cognitive decline.