Abstract P2-09-11: Consistency of pathogenicity determinations for hereditary cancer gene mutations

Background: As the number of laboratories offering genetic tests grows, the potential for inconsistent variant classifications increases. New resources can help address this: (a) ClinVar, a rapidly growing public database of clinical variants to which many (but not all) laboratories contribute; (b) the public release of thousands of BRCA1/2 reports from Myriad Genetics through the Sharing Clinical Reports Project (SCRP), the Free the Data (FTD) initiative, and recent publications; and (c) ExAC, a greatly improved database of population allele frequencies. These complement longstanding efforts, e.g. the ENIGMA consortium. In addition, the American College of Medical Genetics (ACMG) recently updated guidelines for the interpretation of sequence variants. Using these resources, we sought to investigate the consistency of variant classifications to help inform ongoing practice.

Methods: Pathogenicity assessments for variants in hereditary cancer genes were collected from multiple sources. Among these were 15,364 BRCA1/2 submissions to ClinVar, including 5416 submissions from SCRP and 1062 from our prior work [1]. When 3 or more submissions for a variant were available, we determined a consensus interpretation requiring 2 of 3 submitters to agree (or 3 of 4, etc.) to identify outliers. For our own classifications, we established a point-based system based on the 2015 ACMG guidelines, and independently applied it to publicly available evidence of pathogenicity without regard to other labs' classifications.

Results: Initially, discordance among ClinVar submissions appears high (20-30%). However, upon investigation much of this discordance is a result of (i) research submissions to ClinVar, (ii) differences in confidence (e.g. benign vs. likely benign), (iii) older data in ClinVar, (iv) single lab outliers, and (v) nuances in the detailed structure of the ClinVar database. A careful comparison using the consensus methodology of objectively filtered ClinVar data shows high concordance between our interpretations and consensus: 95% were identical and 99% were similar (e.g. benign and likely benign were considered similar). Where consensus was not achieved (8% of variants with 3 or more independent sources) or not possible (any variant with only 2 sources), pairwise comparisons showed that few of these remaining differences (5%) were clinically significant. Also, many variants with significant discordances appeared to be particularly rare in the human population, and thus would be present in few patients. The rate of discordances with SCRP/FTD data was similar with that of other ClinVar submitters.

Conclusions: Evaluations of inter-laboratory concordance need to be done carefully to avoid over-counting differences. Laboratories generally agree on the clinical significance of the vast majority of variants. Furthermore, the inter-laboratory consensus classification is often reached using a careful implementation of the ACMG guidelines and publicly available data. Thoroughly understanding the remaining differences is challenging when the evidence used by any laboratory is not available for peer review. Detailed data and methods from this study are available for review and alternate analyses.

[1] Lincoln et al. SABCS 2014; JMD 2015.

Citation Format: Lincoln S, Nykamp K, Kobayashi Y, Yang S, Powers M, Anderson M, Monzon F, Topper S. Consistency of pathogenicity determinations for hereditary cancer gene mutations. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-11.

Adverse effects of a 10-day course of ibuprofen in Holstein calves

Nonsteroidal anti-inflammatory drugs (NSAIDs) are recommended for various conditions in cattle. Ibuprofen is an inexpensive short-acting NSAID and is readily available in liquid formulation for administration to bottle-fed calves. We compared the adverse effects of a 10-day course of ibuprofen and placebo in 16 five- to six-week-old Holstein bull calves that were being treated for experimentally induced bovine respiratory syncytial virus infection. Ibuprofen was administered as a liquid in milk replacer at 30 mg/kg divided three times daily. We found an increased prevalence of abomasal ulceration 5 of 8 in the ibuprofen compared to placebo group 2 of 6 (P = NS). There was one (1 of 8) case of mild interstitial nephritis in the ibuprofen and none (0 of 8) in the placebo group (P = NS). Renal function as measured by serum BUN and creatinine levels was not different between groups; no animal demonstrated an increase in creatinine.

Evaluation of bovine abortion cases and tissue suitability for identification of infectious agents in California diagnostic laboratory cases from 2007 to 2012

Establishing a definitive cause of bovine abortion is a challenging problem faced by veterinary practitioners and diagnosticians. Detection of an infectious or noninfectious source for abortion may facilitate interventions that mitigate future fetal loss in the herd. The purposes of this study were to identify the most common causes of bovine abortion in cases submitted to the California Animal Health and Food Safety Laboratory System, Davis (CAHFS) from 2007 to 2013 and to determine if detection of infectious pathogens differed with the fetal tissue evaluated. Records of 665 bovine abortion cases of 709 animals were reviewed for pathologic diagnoses, test methods used to identify causative conditions, and which tissues yielded successful identification of infectious agents associated with abortion. Over 58% of abortions were attributed to an infectious cause and 46.9% had an infectious agent identified. The most common infectious conditions were Epizootic Bovine Abortion (EBA) (16.2% of all fetuses), other fetal bacterial infections (14.7% of all fetuses), and Neospora caninum (9.3% of all fetuses.) The bacterium associated with EBA (currently named Pajaroellobacter abortibovis) was most commonly identified by immunohistochemistry (IHC) in lymphoid organs (thymus and spleen); N. caninum IHC was most frequently positive in brain, kidney, and placenta. In cases of pathogenic and opportunistic bacterial infections, abomasal samples yielded a significantly greater proportion of definitive aerobic culture results than lung or liver tissues. Direct fluorescent antibody test results for Bovine Viral Diarrhea Virus testing were identical between lung and kidney tissues and nearly identical (96.0%) for Bovine Herpesvirus I. Noninfectious abortive conditions included fetal stress (10.5%), dystocia (3.9%), congenital defects (3.3%), toxicological or mineral problems (1.8%), and death of the cow (1.1%). Just over 20% of the aborted fetuses had no gross or histopathological lesions to explain the abortion. This review highlights the need for submission of critical samples including abomasal contents, lymphoid tissues (thymus, spleen, and lymph nodes), and brain to maximize the diagnosticians' ability to identify causes of abortion.

Acute hepatitis C infection in HIV-negative men who have sex with men

Acute hepatitis C infection is recognized in HIV-infected men who have sex with men (MSM), but the risk in HIV-negative MSM remains unclear. We evaluated a population of MSM with acute hepatitis C. From January 2010 to May 2014, all cases of HCV antibody positive HIV-negative MSM were identified. European AIDS Network criteria were applied to determine acute infection, and 44 individuals fulfilled the criteria for acute hepatitis C. Ten were RNA negative at baseline and classed as prior spontaneous clearance. 15 (34.1%) had a previously negative HCV antibody within 1 year. 11 (25.0%) had significant elevation in ALT levels, and 18 (40.9%) were clinically diagnosed from risk exposure and history. Median age was 37 years (range 24-75). 41 (93.2%) individuals reported unprotected anal sex, 36 with (87.8%) both insertive and receptive intercourse, 4 (9.8%) with receptive intercourse, 1 (2.4%) with insertive intercourse, and no data were recorded for 3 (7.3%) patients. Individuals had an average of 7.3 reported (median 2, range 1-100) partners. 12 (27.3%) engaged in group sex, 11 (25.0%) practised fisting, 11 (25.0%) admitted using drugs during sexual activity, 16 (36.4%) reported nasal, and 9 (20.5%) reported injection drug use. 14 (31.8)% had unprotected sex whilst under the influence of recreational drugs. 29 individuals were aware of a partner's status. 2 (4.5%) individuals had sexual contact with a known HCV monoinfected partner, 13 (29.5%) with a HIV monoinfected partner and 6 (13.6%) with a HCV/HIV coinfected partner. 9 (20.5%) reported a partner/partners with no known infection. No data were available in 14 (31.8%) individuals. 13 (29.5%) individuals had a coexisting STI at the time of acute HCV diagnosis. 8 (18.2%) received HIV postexposure prophylaxis (PEP) within the 6 months prior to the HCV diagnosis (2 were participants in a HIV pre-exposure prophylaxis trial). 15 (34.1%) individuals achieved spontaneous clearance of HCV, and 11 patients received HCV treatment. Similar to the ongoing epidemic of acute HCV infection in HIV+ MSM, HIV-negative MSM remain at risk.

A procedural check list for pleural decompression and intercostal catheter insertion for adult major trauma

BACKGROUND

Intercostal catheter (ICC) insertion is the standard pleural decompression and drainage technique for blunt and penetrating traumatic injury. Potentially high complication rates are associated with the procedure, with the literature quoting over 20% in some cases (1-4). Empyema in particular is a serious complication. Risk adverse industries such as the airline industry and military services regularly employ checklists to standardise performance and decrease human errors. The use of checklists in medical practice is exemplified by introduction of the WHO Surgical Safety checklist.

METHODS

The Alfred Hospital in Melbourne, Australia is an Adult Level 1 Trauma Centre. In August 2009 The Alfred Trauma Service introduced an evidence-based checklist system for the insertion of ICCs, combined with standardised formal training for resident medical staff, in an attempt to minimise the incidence of ICC related empyema.

RESULTS

Between January 2003 and July 2009 the incidence of empyema was 1.44% (29 in 2009 insertions). This decreased to 0.57% between August 2009 and December 2011 (6 in 1060 insertions) when the measures described above were introduced [p=0.038 Fisher's exact test, 2-tailed].

CONCLUSION

Quality control checklists - such as the ICC checklist described - are a sensible and functional means to standardise practice, to decrease procedural error and to reduce complication rates during trauma resuscitation.

Aleutian Disease: An Emerging Disease in Free-Ranging Striped Skunks (Mephitis mephitis) From California

Aleutian disease virus (ADV, Amdovirus, Parvoviridae) primarily infects farmed mustelids (mink and ferrets) but also other fur-bearing animals and humans. Three Aleutian disease (AD) cases have been described in captive striped skunks; however, little is known about the relevance of AD in free-ranging carnivores. This work describes the pathological findings and temporospatial distribution in 7 cases of AD in free-ranging striped skunks. All cases showed neurologic disease and were found in a 46-month period (2010-2013) within a localized geographical region in California. Lesions included multisystemic plasmacytic and lymphocytic inflammation (ie, interstitial nephritis, myocarditis, hepatitis, meningoencephalitis, pneumonia, and splenitis), glomerulonephritis, arteritis with or without fibrinoid necrosis in several organs (ie, kidney, heart, brain, and spleen), splenomegaly, ascites/hydrothorax, and/or encephalomalacia with cerebral microangiopathy. ADV infection was confirmed in all cases by specific polymerase chain reaction and/or in situ hybridization. The results suggest that AD is an emerging disease in free-ranging striped skunks in California.

Organic cleanliness of the Mars Science Laboratory sample transfer chain

One of the primary science goals of the Mars Science Laboratory (MSL) Rover, Curiosity, is the detection of organics in Mars rock and regolith. To achieve this, the Curiosity rover includes a robotic sampling system that acquires rock and regolith samples and delivers it to the Sample Analysis at Mars (SAM) instrument on board the rover. In order to provide confidence that any significant organics detection result was Martian and not terrestrial in origin, a requirement was levied on the flight system (i.e., all sources minus the SAM instrument) to impart no more than 36 parts per billion (ppb by weight) of total reduced carbon terrestrial contamination to any sample transferred to the SAM instrument. This very clean level was achieved by a combination of a rigorous contamination control program on the project, and then using the first collected samples for a "dilution cleaning" campaign of the sample chain prior to delivering a sample to the SAM instrument. Direct cleanliness assays of the sample-contacting and other Flight System surfaces during pre-launch processing were used as inputs to determine the number of dilution cleaning samples needed once on Mars, to enable delivery of suitably clean samples to the SAM experiment. Taking into account contaminant redistribution during launch thorough landing of the MSL on Mars, the amount of residue present on the sampling hardware prior to the time of first dilution cleaning sample acquisition was estimated to be 60 ng/cm(2) on exposed outer surfaces of the sampling hardware and 20 ng/cm(2) on internal sample contacting surfaces; residues consisting mainly of aliphatic hydrocarbons and esters. After three dilution cleaning samples, estimated in-sample contamination level for the first regolith sample delivered to the SAM instrument at the Gale Crater "Rocknest" site was bounded at ≤10 ppb total organic carbon. A Project decision to forego ejecting the dilution cleaning sample and instead transfer the first drill-acquired sample at the "John Klein" site to SAM resulted in an estimated level of terrestrial contamination of ≤430 ppb. The estimated terrestrial contamination for portions from the second drill-acquired sample, at Cumberland, was ≤69 ppb; the estimate for a future, third, drilled sample is ≤38 ppb. These levels are comparable in magnitude to the SAM instrument blanks at the nanomole level (as chlorohydrocarbon).