The challenge of comprehensive and consistent sequence variant interpretation between clinical laboratories

PurposeGenetic testing has shifted from academic laboratories with expertise in specific genes to commercial laboratories that offer tests of a diverse array of genes. The purpose of this comparative study was to determine whether one academic laboratory’s model of variant interpretation is similar to that of several commercial laboratories.MethodsThe Collagen Diagnostic Laboratory (CDL) received, over a 14-month period, 38 requests to interpret variants originally identified by an outside laboratory (OL). The interpretations by the OL and CDL were compared and discrepancies were assessed.ResultsInterpretations from the OL and CDL were concordant in 11 inquiries (29%); discrepancies were moderate in 11 instances (29%) and significant in 16 (42%). Factors that caused discrepancies included the following: (i) private data were not shared in a public database (n = 9); (ii) publicly available allele frequency data were not referenced and used as evidence (n = 5); and (iii) important aspects of protein structure and function were not taken into account (n = 13).ConclusionComprehensive interpretation of sequence variants depends on good functional tests and well-curated variant databases. Provision of clinical information to the clinical laboratory, mandatory submission of identified variants with phenotype data to common resources, and collaboration between clinical laboratories and recognized experts is likely to improve consistency in variant interpretation among clinical laboratories.     

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar

PurposeData sharing through ClinVar offers a unique opportunity to identify interpretation differences between laboratories. As part of a ClinGen initiative, four clinical laboratories (Ambry, GeneDx, Partners Healthcare Laboratory for Molecular Medicine, and University of Chicago Genetic Services Laboratory) collaborated to identify the basis of interpretation differences and to investigate if data sharing and reassessment resolve interpretation differences by analyzing a subset of variants.MethodsClinVar variants with submissions from at least two of the four participating laboratories were compared. For a subset of identified differences, laboratories documented the basis for discordance, shared internal data, independently reassessed with the American College of Medical Genetics and Genomics–Association for Molecular Pathology (ACMG-AMP) guidelines, and then compared interpretations.ResultsAt least two of the participating laboratories interpreted 6,169 variants in ClinVar, of which 88.3% were initially concordant. Laboratories reassessed 242/724 initially discordant variants, of which 87.2% (211) were resolved by reassessment with current criteria and/or internal data sharing; 12.8% (31) of reassessed variants remained discordant owing to differences in the application of the ACMG-AMP guidelines.ConclusionParticipating laboratories increased their overall concordance from 88.3 to 91.7%, indicating that sharing variant interpretations in ClinVar—thereby allowing identification of differences and motivation to resolve those differences—is critical to moving toward more consistent variant interpretations.Genet Med advance online publication 09 March 2017     

Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data

Each year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next‐generation sequencing (NGS). This requires pathogenicity classification of millions of DNA variants on the standard 5‐tier scale. To reduce time spent on data interpretation and increase data quality and reliability, the nine Dutch labs decided to publicly share their classifications. Variant classifications of nearly 100,000 unique variants were catalogued and compared in a centralized MOLGENIS database. Variants classified by more than one center were labeled as “consensus” when classifications agreed, and shared internationally with LOVD and ClinVar. When classifications opposed (LB/B vs. LP/P), they were labeled “conflicting”, while other nonconsensus observations were labeled “no consensus”. We assessed our classifications using the InterVar software to compare to ACMG 2015 guidelines, showing 99.7% overall consistency with only 0.3% discrepancies. Differences in classifications between Dutch labs or between Dutch labs and ACMG were mainly present in genes with low penetrance or for late onset disorders and highlight limitations of the current 5‐tier classification system. The data sharing boosted the quality of DNA diagnostics in Dutch labs, an initiative we hope will be followed internationally. Recently, a positive match with a case from outside our consortium resulted in a more definite disease diagnosis.     

Long-term survival in multiple myeloma: a single-center experience

In patients with multiple myeloma the median overall survival is now approaching 5 years, following the introduction of autologous stem cell transplantation and targeted therapies. However, patients receiving conventional chemotherapy who have survived 10 years or longer have been repeatedly reported in the literature. From 723 patients with multiple myeloma seen in our department from January 1981 to June 2007, we selected 21 long-term (>/=10 years) survivors (2.9%) who had been treated with conventional chemotherapy. Potentially favourable prognostic factors, common to most patients, were: age 相似文献   

Challenges in genetic testing: clinician variant interpretation processes and the impact on clinical care

PurposeEfforts have been made to standardize laboratory variant interpretation, but clinicians are ultimately tasked with clinical correlation and application of genetic test results in patient care. This study aimed to explore processes clinicians utilize when reviewing and returning genetic test results, and how they impact patient care.MethodsMedical geneticists, genetic counselors, and nongenetics clinicians from two Midwestern states completed surveys (n = 98) and in-depth interviews (n = 29) on practices of reviewing and returning genetic test results. Retrospective chart review (n = 130) examined discordant interpretations and the impact on care.ResultsParticipants reported variable behaviors in both reviewing and returning results based on factors such as confidence, view of role, practice setting, and relationship with the lab. Providers did not report requesting changes to variant classifications from laboratories, but indicated relaying conflicting classifications to patients in some cases. Chart reviews revealed medically impactful differences in interpretation between laboratories and clinicians in 18 (13.8%) records.ConclusionClinician practices for reviewing and integrating genetic test results into patient care vary within and between specialties and impact patient care. Strategies to better incorporate both laboratory and clinician expertise into interpretation of genetic results could result in improved care across providers and settings.     

Allergic diseases in the elderly population: a single-center experience

Background/aim Although allergic diseases are generally considered to be diseases of childhood and youth, the first symptoms of allergic diseases can be seen in old age sometimes. The aim of this study was to determine the prevalence and characteristics of allergic diseases in the elderly population admitted to the allergy unit on an outpatient basis.Materials and methods The files of the patients who applied to our clinic’s allergy unit during the 8-year period were retrospectively analyzed. The data of patients aged ≥ 65 years were obtained from the files of our allergy unit archive.ResultsA total of 1272 patients aged ≥ 65 years old were included in the study. The mean age was 70 years (range: 65–97 years). Most of the patients were female (n = 704, 55.3%). Of the patients, 887 (69.8%) presented with cutaneous symptoms, and urticaria was identified in 500 of them (56.3%). Drug hypersensitivity reactions were detected in 175 (13.7%) patients. A total of 71 (5.6%) patients had asthma, 65 (5.1%) had anaphylaxis, 48 (3.8%) had allergic rhinitis, 24 (1.9%) had hymenoptera venom allergy, and 18 (1.4%) had food allergies.Atopy history (OR = 2.323, 95% CI = 1.590–3.393, p < 0.001) and comorbidity (OR = 1.631, 95% CI = 1.050–2.533, p = 0.029) were found to be risk factors for drug hypersensitivity reactions. Male sex (OR = 3.462, 95% CI = 1.097–10.933, p = 0.034) and atopy history (OR = 14.877, 95% CI = 6.081–36.393, p < 0.001) were found to be risk factors for hymenoptera venom allergy.ConclusionDiagnosis becomes difficult due to the perception that allergic diseases mainly affect young people. Clinical symptoms are not evident in the elderly and age-related difficulties are encountered in diagnostic tests. There is a need to develop specific guidelines for the diagnosis of allergic diseases in the elderly.     

Endoscopic interventional treatment for gastric schwannoma: a single-center experience

Background and aims: Endoscopic Interventional Treatment is of little trauma and less complications in the treatment of gastric schwannoma and leads to faster recovery and fewer days of hospitalization. This study was aimed to investigate the safety and efficacy of endoscopic interventional therapy for gastric schwannoma, including endoscopic submucosal excavation, non-laparoscopic-assisted endoscopic full-thickness resection, endoscopic tunneling submucosal resection, and so on. Methods: Six patients of gastric schwannoma diagnosed by pathology examination were retrospectively analyzed ranging from Oct 2011 to Feb 2014 at Shandong Provincial Hospital affiliated to Shandong University. Five of the six patients accepted endoscopic interventional therapy. Results: Among the five patients, there were four males and one female, aged from 48 to 65 years old (the average age was 58 ± 6.4). The lesions located at the fundus, the fundus-cardia, gastric body or gastric antrum, respectively, with the diameters ranged from 8 to 25 millimeter (the average was 17.1 ± 7.8 mm). All the patients were performed endoscopic interventional therapy successfully. Among five patients, one patient was treated by endoscopic tunneling submucosal resection, two by endoscopic submucosal excavation, and the other two were given endoscopic full-thickness resection. Operation duration was about 43 to 83 minutes (the average was 57.6 ± 16.1 minutes). The mass were completely removed, with limited bleeding. During the operation, perforation and pneumoperitoneum occurred in two patients, who finally recovered by endoscopic and conservative treatment. No bleeding, inflammation or infection occurred in these patients. The average follow-up time was (7.4 ± 4.4) months. Neither recurrence nor metastasis was found during follow-up. Conclusion: Endoscopic interventional therapy is a safe and effective treatment for gastric schwannoma.     

SG-ADVISER CNV: copy-number variant annotation and interpretation

PurposeCopy-number variants have been associated with a variety of diseases, especially cancer, autism, schizophrenia, and developmental delay. The majority of clinically relevant events occur de novo, necessitating the interpretation of novel events. In this light, we present the Scripps Genome ADVISER CNV annotation pipeline and Web server, which aims to fill the gap between copy number variant detection and interpretation by performing in-depth annotations and functional predictions for copy number variants.MethodsThe Scripps Genome ADVISER CNV suite includes a Web server interface to a high-performance computing environment for calculations of annotations and a table-based user interface that allows for the execution of numerous annotation-based variant filtration strategies and statistics.ResultsThe annotation results include details regarding location, impact on the coding portion of genes, allele frequency information (including allele frequencies from the Scripps Wellderly cohort), and overlap information with other reference data sets (including ClinVar, DGV, DECIPHER). A summary variant classification is produced (ADVISER score) based on the American College of Medical Genetics and Genomics scoring guidelines. We demonstrate >90% sensitivity/specificity for detection of pathogenic events.ConclusionScripps Genome ADVISER CNV is designed to allow users with no prior bioinformatics expertise to manipulate large volumes of copy-number variant data. Scripps Genome ADVISER CNV is available at http://genomics.scripps.edu/ADVISER/.Genet Med17 9, 714–718.     

Mycobacterial testing in hospital laboratories: results from a questionnaire survey in Italy

Between 1999 and 2001, 355 hospital laboratories in Italy were asked to complete a questionnaire addressing mycobacterial test methods, 1-year workloads and laboratory safety features. Analysis of the data showed that rapid methods for mycobacterial testing were being used by most larger laboratories; however, sub-optimal methods were still in use in small and medium-size laboratories. In a country such as Italy, which has a low prevalence of tuberculosis cases, implementation of rapid technologies, combined with regionalisation of mycobacterial diagnostic services, seems to be the most reasonable and cost-effective strategy.     

Pancreatic MR imaging and endocrine complications in patients with beta-thalassemia: a single-center experience

Iron deposition in various organs can cause endocrine complications in patients with transfusion-dependent beta-thalassemia. The aim was to investigate the relationship between endocrine complications and pancreatic iron overload using magnetic resonance imaging (MRI). Forty patients with transfusion-dependent thalassemia (TDT) were enrolled in the study. The magnetic resonance imagings of the patients were performed using a 1.5 Tesla Philips MRI scanner. Two out of three patients had at least one clinical endocrine complication. The rate of iron deposition was 62.5% in liver, and 45% in pancreas tissue, and was 12.5% in heart tissue. Pancreatic T2* and hepatic T2* values were significantly positively correlated (p?=?0.006). Pancreatic T2* and ferritin were significantly negatively correlated (p?=?0.03). Cardiac T2* values were negatively correlated with fasting blood glucose (p?=?0.03). Patients with short stature had significantly higher cardiac iron burden (22.3 vs. 36.6 T2*ms; p 0.01), and patients with hypothyroidism had higher liver iron concentrations (9.9 vs. 6.4 LIC mg/g; p?=?0.05). The ferritin level of 841 ng/mL and liver iron concentration (LIC) value of 8.7 mg/g were detected as the threshold level for severe pancreatic iron burden (AUC 70%, p:0.04, AUC 80%, p?=?0.002, respectively). Moreover, males were found to have decreased pancreas T2* values compared with the values in females (T2* 19.3 vs. 29.9, p?=?0.05). Patients with higher ferritin levels over than 840 ng/mL should be closely monitored for pancreatic iron deposition, and patients with endocrine complications should be assessed in terms of cardiac iron burden.

     

Quality assurance practices in Europe: a survey of molecular genetic testing laboratories

In the 2000s, a number of initiatives were taken internationally to improve quality in genetic testing services. To contribute to and update the limited literature available related to this topic, we surveyed 910 human molecular genetic testing laboratories, of which 291 (32%) from 29 European countries responded. The majority of laboratories were in the public sector (81%), affiliated with a university hospital (60%). Only a minority of laboratories was accredited (23%), and 26% was certified. A total of 22% of laboratories did not participate in external quality assessment (EQA) and 28% did not use reference materials (RMs). The main motivations given for accreditation were to improve laboratory profile (85%) and national recognition (84%). Nearly all respondents (95%) would prefer working in an accredited laboratory. In accredited laboratories, participation in EQA (P<0.0001), use of RMs (P=0.0014) and availability of continuous education (CE) on medical/scientific subjects (P=0.023), specific tasks (P=0.0018), and quality assurance (P<0.0001) were significantly higher than in non-accredited laboratories. Non-accredited laboratories expect higher restriction of development of new techniques (P=0.023) and improvement of work satisfaction (P=0.0002) than accredited laboratories. By using a quality implementation score (QIS), we showed that accredited laboratories (average score 92) comply better than certified laboratories (average score 69, P<0.001), and certified laboratories better than other laboratories (average score 44, P<0.001), with regard to the implementation of quality indicators. We conclude that quality practices vary widely in European genetic testing laboratories. This leads to a potentially dangerous situation in which the quality of genetic testing is not consistently assured.     

Use of a novel anticoagulation strategy during ECMO in a pediatric population: single-center experience

We describe a novel anticoagulation strategy with continuous intravenous antithrombin infusion and intermittent heparin infusion in pediatric population during extracorporeal membrane oxygenation (ECMO). From November 2004 through February 2006, 11 patients required ECMO for postcardiotomy cardiorespiratory failure. The mean duration of support time was 112 hours (range 68-192 hours). Since April 2005, we modified our anticoagulation protocol in the last six patients. Continuous antithrombin infusion was started immediately after surgery based on the lab result. The antithrombin level was maintained >100% using the following formula: 100 (target value) - (Antithrombin value on lab test) x weight in 4 hours. Antithrombin value was checked at 4-hour intervals. Heparin infusion was started when the antithrombin value was > 100% and remained stable for more than 12 hours and the amount of bleeding was < 2 ml/kg for more than 3 consecutive hours; then heparin infusion was started at 2 UI/kg/h via the oxygenator (target ACT was not < 150 seconds). Three patients in the first group died. Eight patients were weaned and discharged; the third, fourth, and fifth required surgical revision for bleeding. One experienced minor neurologic sequelae. Neither surgical revision nor thromboembolic complications occurred in the new anticoagulation group. A novel anticoagulation strategy utilizing continuous intravenous antithrombin and intermittent heparin infusion reduced significantly surgical revision for bleeding in the first 48 hours. This has translated into excellent overall outcomes.     

Poly-autoimmunity in patients with myasthenia gravis: A single-center experience

Abstract

We evaluated the co-occurrence of autoimmune diseases (ADs) in a large population of myasthenia gravis (MG) patients from a single center. Our survey included 984 patients, 904 with anti-acetylcholine receptor antibodies and 80 with anti-muscle specific kinase antibodies. The anti-acetylcholine receptor positive population included patients with early-onset (age at onset ≤50 years), late-onset and thymoma-associated disease. Follow-up ranged 2–40 years. Two-hundred and fourteen ADs were diagnosed in 185 patients; 26 of them had two or more ADs in association with MG. Thyroid disorders were the most common and, together with vitiligo and thrombocytopenia, occurred in all disease subsets. Otherwise, there was a broad variability with partial overlap among patient groups. The highest rate of ADs was observed in early-onset patients, while clusters, i.e. 2 or more ADs other than MG in the same individual, were more common among thymoma cases. Thirty-four diseases were diagnosed at the same time, 88 occurred before and 92 after the onset of MG. On multivariate analysis, immunosuppressive treatment was the only independent variable which negatively influenced the risk of developing other ADs in our cohort.     

Maternal behavior: differences between mother and virgin mice as a function of the testing procedure

Retrieval by lactating and virgin mice was compared in a straight alley and a T-maze. In both test situations the retrieval performance of the lactating mouse was superior to that of the virgin animal. No discrimination was seen between a live pup and a dead pup; a rubber toy, however, was retrieved least by both the lactating and virgin mice. Contrary to previous results, these experiments demonstrate a significant difference in maternal behavior between lactating and virgin mice.     

Clinicopathologic comparisons of IgA nephropathy and IgA vasculitis nephropathy in children: a ten-year single-center experience

Background/aim To investigate the similarities and differences of renal clinical and renal pathology between IgA nephropathy (IgAN) and IgA vasculitis nephritis (IgAVN) in children. Materials and methodsA total of 237 children with IgAN and 190 children with IgAVN were included. The general conditions, clinical characteristics, final diagnosis, clinical and pathological classification of the children were intercepted at the time of admission, and the retrospective comparative analysis was carried out. ResultsThe results showed that the median course of disease in IgAN group was longer than that in IgAVN group (p = 0.02). Patients with IgAN had a significantly higher duration of infection than the patients with IgAVN (p = 0.03). The white blood cell count (WBC), hemoglobin (HGB) in IgAN group were significantly lower than that in IgAVN group (p = 0.02). The serum creatinine in IgAN group was higher than that in IgAVN group (p = 0.02). Patients with IgAN and IgAVN had statistically significant differences in pathological typing between clinical types: hematuria and proteinuria, nephrotic syndrome and chronic nephritis (p = 0.004). ConclusionThe clinical manifestations of IgAN and IgAVN were similar, but the onset of IgAN was hidden and the clinical manifestations were relatively serious. Renal pathology was mainly glomerulosclerosis and renal tubular atrophy. IgAVN was characterized by acute onset and good renal function. Renal pathology was dominated by endothelial hyperplasia and crescent formation. These differences did not support the hypothesis that the two diseases are the same.