Search

Renal masses are commonly encountered on cross-sectional imaging examinations performed for nonrenal indications. Although most can be dismissed as benign cysts, a subset will be either indeterminate or suspicious; in many cases, imaging cannot be used to reliably differentiate between benign and malignant masses. On-going research in defining characteristics of common renal masses on advanced imaging shows promise in offering solutions to this issue. A recent update of the Bosniak classification (used to categorize cystic renal masses) was proposed with the goals of decreasing imaging follow-up in likely benign cystic masses, and therefore avoiding unnecessary surgical resection of such masses.

Objective To investigate the interpretation differences of germline-shared somatic variants. Methods A total of 123,302 COSMIC variants associated with hematologic malignant neoplasms were used. The pathogenicity and actionability of shared variants were analyzed based on the standardized guidelines. Results The overall frequency of variants shared in ClinVar/HGMD and COSMIC was 10%. The pathogenicity of 54 shared variants was pathogenic/likely pathogenic (P/LP; n = 30), variants of unknown significance (n = 3), and benign/likely benign (n = 21). In total, 30 P/LP variants were reclassified to tier I/tier II (83%) and tier III (17%) variants. Conclusions This is the first study about different clinical interpretations of shared variants based on the current standard guidelines. This study takes a meaningful step in bridging the interpretation gap between the somatic and germline variants.

BackgroundThis study aimed to identify and resolve discordant variant interpretations across clinical molecular genetic laboratories through the Canadian Open Genetics Repository (COGR), an online collaborative effort for variant sharing and interpretation.MethodsLaboratories uploaded variant data to the Franklin Genoox platform. Reports were issued to each laboratory, summarising variants where conflicting classifications with another laboratory were noted. Laboratories could then reassess variants to resolve discordances. Discordance was calculated using a five-tier model (pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), benign (B)), a three-tier model (LP/P are positive, VUS are inconclusive, LB/B are negative) and a two-tier model (LP/P are clinically actionable, VUS/LB/B are not). We compared the COGR classifications to automated classifications generated by Franklin.ResultsTwelve laboratories submitted classifications for 44 510 unique variants. 2419 variants (5.4%) were classified by two or more laboratories. From baseline to after reassessment, the number of discordant variants decreased from 833 (34.4% of variants reported by two or more laboratories) to 723 (29.9%) based on the five-tier model, 403 (16.7%) to 279 (11.5%) based on the three-tier model and 77 (3.2%) to 37 (1.5%) based on the two-tier model. Compared with the COGR classification, the automated Franklin classifications had 94.5% sensitivity and 96.6% specificity for identifying actionable (P or LP) variants.ConclusionsThe COGR provides a standardised mechanism for laboratories to identify discordant variant interpretations and reduce discordance in genetic test result delivery. Such quality assurance programmes are important as genetic testing is implemented more widely in clinical care.

To report BRCA1 and BRCA2 (BRCA1/2) variant reassessments and reclassifications between 2012 and 2017 at the Advanced Molecular Diagnostics Laboratory (AMDL) in Toronto, Canada, which provides BRCA1/2 testing for patients in Ontario, and to compare AMDL variant classifications with submissions in ClinVar. Variants were assessed using a standardized variant assessment tool based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology’s guidelines and tracked in an in-house database. Variants were shared through the Canadian Open Genetics Repository and submitted to ClinVar for comparison against other laboratories. AMDL identified 1209 BRCA1/2 variants between 2012 and 2017. During this period, 32.9% (398/1209) of variants were reassessed and 12.4% (150/1209) were reclassified. The majority of reclassified variants were downgraded (112/150, 74.7%). Of the reclassified variants, 63.3% (95/150) were reclassified to benign, 20.7% (31/150) to likely benign, 10.0% (15/150) to variant of uncertain significance, 2.0% (3/150) to likely pathogenic, and 4.0% (6/150) to pathogenic. Discordant ClinVar submissions were found for 40.4% (488/1209) of variants. BRCA1/2 variants may be reclassified over time. Reclassification presents ethical and practical challenges related to recontacting patients. Data sharing is essential to improve variant interpretation, to help patients receive appropriate care based on their genetic results.

PurposeThe Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel (VCEP) developed specifications for CDH1 variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations for effective medical care. In addition, the CDH1 VCEP continues to update these specifications in keeping with evolving clinical practice and variant interpretation guidelines.MethodsCDH1 variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen, and expert knowledge from ongoing CDH1 variant curations. Trained biocurators curated 273 variants using updated CDH1 interpretation guidelines and incorporated published and unpublished data provided by diagnostic laboratories. All variants were reviewed by the ClinGen VCEP and classifications submitted to ClinVar.ResultsUpdated CDH1-specific variant interpretation guidelines include eleven major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36/37) of variants with ClinVar conflicting interpretations were resolved into benign, likely benign, likely pathogenic, or pathogenic, and 35% (15/43) of VUS were resolved into benign or likely benign. Overall, 88% (239/273) of curated variants had non-VUS classifications.ConclusionThe development and evolution of CDH1-specific criteria by the expert panel results in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene.

BackgroundIn silicoevidence is important to consider when interpreting genetic variants. According to the ACMG/AMP,in silicoevidence is applied at the supporting strength level using the PP3 and BP4 criteria, for pathogenic and benign evidence, respectively. While PP3 has been determined to be one of the most commonly applied criteria, less is known about the effect of these two criteria on variant classification outcomes.MethodsIn this study, a total of 727 missense variants curated by Clinical Genome Resource (ClinGen) Variant Curation Expert Panels (VCEPs) were analyzed to determine how often PP3 and BP4 were applied and how often they influenced final variant classifications. The current categorical system of variant classification was compared with a point-based system being developed by the ClinGen Sequence Variant Interpretation Working Group. In addition, the performance of fourin silicotools (REVEL, VEST, FATHMM, and MPC) was assessed by using a gold set of 237 variants (classified as benign or pathogenic independent of PP3 or BP4) to calculate pathogenicity likelihood ratios.ResultsCollectively, the PP3 and BP4 criteria were applied by ClinGen VCEPs to 55% of missense variants in this data set. Removingin silicocriteria from variants where they were originally applied caused variants to change classification from pathogenic to likely pathogenic (14%), likely pathogenic to variant of uncertain significance (VUS) (24%), or likely benign to VUS (64%). The proportion of downgrades with the categorical classification system was similar to that of the point-based system, though the latter resolved borderline classifications. REVEL and VEST performed at a level consistent with moderate strength towards either benign or pathogenic evidence, while FATHMM performed at the supporting level.ConclusionsOverall, this study demonstrates thatin silicocriteria PP3 and BP4 are commonly applied in variant classification and often affect the final classification. Our results suggest that when sufficient thresholds forin silicopredictors are established, PP3 and BP4 may be appropriate to use at a moderate strength. However, further calibration with larger datasets is needed to optimize the performance of currentin silicotools given the impact they have on clinical variant classification.

Up to 80% of BRCA1 and BRCA2 genetic variants remain of uncertain clinical significance (VUSs). Only variants classified as pathogenic or likely pathogenic can guide breast and ovarian cancer prevention measures and treatment by PARP inhibitors. We report the first results of the ongoing French national COVAR (cosegregation variant) study, the aim of which is to classify BRCA1/2 VUSs. The classification method was a multifactorial model combining different associations between VUSs and cancer, including cosegregation data. At this time, among the 653 variants selected, 101 (15%) distinct variants shared by 1,624 families were classified as pathogenic/likely pathogenic or benign/likely benign by the COVAR study. Sixty-six of the 101 (65%) variants classified by COVAR would have remained VUSs without cosegregation data. Of note, among the 34 variants classified as pathogenic by COVAR, 16 remained VUSs or likely pathogenic when following the ACMG/AMP variant classification guidelines. Although the initiation and organization of cosegregation analyses require a considerable effort, the growing number of available genetic tests results in an increasing number of families sharing a particular variant, and thereby increases the power of such analyses. Here we demonstrate that variant cosegregation analyses are a powerful tool for the classification of variants in the BRCA1/2 breast-ovarian cancer predisposition genes.

Background: Sequencing Mendelian arrhythmia genes in individuals without an indication for arrhythmia genetic testing can identify carriers of pathogenic or likely pathogenic (P/LP) variants. However, the extent to which these variants are associated with clinically meaningful phenotypes before or after return of variant results is unclear. In addition, the majority of discovered variants are currently classified as variants of uncertain significance, limiting clinical actionability. Methods: The eMERGE-III study (Electronic Medical Records and Genomics Phase III) is a multicenter prospective cohort that included 21 846 participants without previous indication for cardiac genetic testing. Participants were sequenced for 109 Mendelian disease genes, including 10 linked to arrhythmia syndromes. Variant carriers were assessed with electronic health record–derived phenotypes and follow-up clinical examination. Selected variants of uncertain significance (n=50) were characterized in vitro with automated electrophysiology experiments in HEK293 cells. Results: As previously reported, 3.0% of participants had P/LP variants in the 109 genes. Herein, we report 120 participants (0.6%) with P/LP arrhythmia variants. Compared with noncarriers, arrhythmia P/LP carriers had a significantly higher burden of arrhythmia phenotypes in their electronic health records. Fifty-four participants had variant results returned. Nineteen of these 54 participants had inherited arrhythmia syndrome diagnoses (primarily long-QT syndrome), and 12 of these 19 diagnoses were made only after variant results were returned (0.05%). After in vitro functional evaluation of 50 variants of uncertain significance, we reclassified 11 variants: 3 to likely benign and 8 to P/LP. Conclusions: Genome sequencing in a large population without indication for arrhythmia genetic testing identified phenotype-positive carriers of variants in congenital arrhythmia syndrome disease genes. As the genomes of large numbers of people are sequenced, the disease risk from rare variants in arrhythmia genes can be assessed by integrating genomic screening, electronic health record phenotypes, and in vitro functional studies. Registration: URL: https://www.clinicaltrials.gov ; Unique identifier; NCT03394859.

The diagnosis of MODY as a subtype of gestational diabetes mellitus (GDM) is important for an adequate management during pregnancy and the postnatal period. The present report describes a case of GDM caused by a synonymous с.666C>G р.V222V substitution in the GCK gene. The variant, which was initially ranked as ‘likely benign’, was later proven to be pathogenic by in vitro studies. The с.666C>G substitution led to the use of a new donor splice site and synthesis of the aberrant mRNA with deletion of 16 base pairs. The case illustrates that additional clinical and experimental data may be required for the correct interpretation of sequence variants pathogenicity.

OBJECTIVE We evaluated the effects of platforms, size filter cutoffs, and targeted regions of cytogenomic microarray (CMA) on the detection of copy number variants (CNVs) and uniparental disomy (UPD) in prenatal diagnosis. METHODS Five thousand twenty-six consecutive prenatal specimens (>98% high-risk pregnancy) were studied by high-resolution CMA, with cutoffs of 50 kb for losses and 200 kb for gains in nontargeted regions and 20 kb for losses and 100 kb for gains in targeted regions. We assessed actual detection rates using the current assay as well as hypothetical detection rates using platforms with the same or lower resolution and smaller or larger cutoffs. RESULTS The detection rate of our current assay was 11.2% (562 of 5026), including abnormal findings in 543 cases and likely pathogenic variants in 19. The hypothetical decrease in the overall detection of variants (excluding likely benign) and UPD ranged from 3.8% to 23.0%. For the subgroup of pathogenic and likely pathogenic CNVs

The ClinGen PTEN Expert Panel was organized by the ClinGen Hereditary Cancer Clinical Domain Working Group to assemble clinicians, researchers, and molecular diagnosticians with PTEN expertise to develop specifications to the 2015 ACMG/AMP Sequence Variant Interpretation Guidelines for PTEN variant interpretation. We describe finalized PTEN-specific variant classification criteria and outcomes from pilot testing of 42 variants with benign/likely benign (BEN/LBEN), pathogenic/likely pathogenic (PATH/LPATH), uncertain significance (VUS), and conflicting (CONF) ClinVar assertions. Utilizing these rules, classifications concordant with ClinVar assertions were achieved for 14/15 (93.3%) BEN/LBEN and 16/16 (100%) PATH/LPATH ClinVar consensus variants for an overall concordance of 96.8% (30/31). The variant where agreement was not reached was a synonymous variant near a splice donor with non-canonical sequence for which in silico models cannot predict the native site. Applying these rules to six VUS and five CONF variants, adding shared internal laboratory data enabled one VUS to be classified as LBEN and two CONF variants to be as classified as PATH and LPATH. This study highlights the benefit of gene-specific criteria and the value of sharing internal laboratory data for variant interpretation. Our PTEN-specific criteria and expertly reviewed assertions should prove helpful for laboratories and others curating PTEN variants.

PurposeThe ClinGen Variant Curation Expert Panels (VCEPS) provide disease-specific rules for accurate variant interpretation. Using hearing loss-specific American College of Medical Genetics/Association for Molecular Pathology (HL-specific ACMG/AMP) guidelines, the ClinGen Hearing Loss VCEP (HL VCEP) illustrates the utility of expert specifications in resolving conflicting variant interpretations.MethodsA total of 157 variants across nine hearing loss genes were curated and submitted to ClinVar by the HL VCEP. The curation process consisted of collecting published and unpublished data for each variant by biocurators, followed by bi-monthly meetings of an expert curation subgroup that reviewed all evidence and applied the HL-specific ACMG/AMP guidelines to reach a final classification.ResultsBefore expert curation, 75% (117/157) of variants had single or multiple VUS submissions (17/157) or had conflicting interpretations in ClinVar (100/157). After applying the HL-specific ACMG/AMP guidelines, 24% (4/17) of VUS variants and 69% (69/100) of discordant variants were resolved into Benign (B), Likely Benign (LB), Likely Pathogenic (LP), or Pathogenic (P). Overall, 70% (109/157) variants had unambiguous classifications (B, LB, LP, P). We quantify the contribution of the HL-specified ACMG/AMP codes to variant interpretation.ConclusionExpert specification and application of the HL-specific ACMG/AMP guidelines effectively resolved discordant interpretations in ClinVar. This study supports the utility of ClinGen VCEPs in helping the community move towards more consistent variant interpretations, which will improve the care of patients with genetic disorders.

A 2-month-old male harboring a duplication of DMD exons 1-7 classified as pathogenic by an outside institution presented with mildly elevated CK levels; molecular breakpoint analysis by our laboratory reclassified the duplication as likely benign. To date, proband continues to develop normally with decreased CK levels, further supporting our reclassification.

We read with interest the recent publication by Weiss and colleagues, which addressed the pitfalls of using next-generation sequencing (NGS) to diagnose PRSS1 variants in chronic pancreatitis (CP).1 Specifically, having failed to authenticate an NGS-identified ‘ PRSS1 c.47C>T (p.Ala16Val) variant’ by Sanger sequencing the PRSS1 gene in the supposed carrier, they postulated that this artefact could have arisen from sequence reads emanating from one of PRSS1 ’ highly homologous and closely linked (7q34) pseudogenes, PRSS3P2 . Herein, we address another NGS-related pitfall that contributes to confusion in relation to the clinical interpretation of PRSS1 p.Ala16Val. p.Ala16Val is the third most commonly detected rare PRSS1 variant in CP; its putative pathological involvement is supported by its ability to increase trypsinogen autoactivation.2 ClinVar, however, ascribes to it conflicting interpretations of pathogenicity (ie, likely benign (1); pathogenic (3) and uncertain significance (2)).3 The main reason for this appears to be its relatively high allele frequency (ie, 0.006607) in all gnomAD V.2.1.1 …

Ataxia with oculomotor apraxia type 2 (AOA2) is a slowly progressive, autosomal recessive disease characterized by the triad of ataxia, oculomotor apraxia, and sensorimotor neuropathy. The genetic basis of AOA2 is biallelic mutation of the SETX gene, resulting in reduced or absent senataxin, a DNA/RNA repair protein essential for genomic stability.In this case report, we described a case of AOA2 with two clear pathogenic SETX mutations, one of which is novel. We then discussed two further likely “in cis” SETX sequence changes (previously reported in the literature as pathogenic), and presented the case that they are likely benign polymorphisms.

Objective We investigated the proportions of and reclassified BRCA1/2 variants of unknown significance (VUS) in Korean patients with epithelial ovarian, tubal, and primary peritoneal cancers. Methods Data from 805 patients who underwent genetic testing for BRCA1/2 from January 1, 2006 to August 31, 2018 were included. The VUS in BRCA1/2 were reclassified using the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology standards and guidelines. Results A BRCA1 pathogenic variant was found in 17.0% (137/805) of the patients, and BRCA1 VUS were found in 15.9% (128/805) of the patients. Further, 8.7% (69/805) of the patients possessed a BRCA2 pathogenic variant and 18.4% (148/805) of the patients possessed BRCA2 VUS. Fifty-three specific BRCA1 VUS were found and 20 were further reclassified as benign (n=11), likely benign (n=5), likely pathogenic (n=3), and pathogenic (n=1). The remaining 33 remained classified as VUS. For BRCA2, 55 specific VUS were detected; among these, 14 were reclassified as benign or likely benign, and 2 were reclassified as likely pathogenic. Among the 805 patients, 195 were found to have only VUS and no pathogenic variants (PV), and 41.5% (81/195) were reclassified as benign or likely benign, and 10.3% (20/195) as pathogenic or likely pathogenic variants. Conclusions Approximately 33.3% (36/108) of the specific BRCA1/2 variants analyzed in this study that were initially classified as VUS over a 13-year period were reclassified. Among these, 5.6% (6/108) were reclassified as pathogenic or likely pathogenic variants.

We have identified six patients harbouring distinct germline BAP1 mutations. In this study, we functionally characterise known BAP1 pathogenic and likely benign germline variants out of these six patients to aid in the evaluation and classification of unknown BAP1 germline variants. We found that pathogenic germline variants tend to encode truncated proteins, show diminished expression of epithelial-mesenchymal transition (EMT) markers, are localised in the cytosol and have reduced deubiquitinase capabilities. We show that these functional assays are useful for BAP1 variant curation and may be added in the American College of Medical Genetics and Genomics (ACMG) criteria for BAP1 variant classification. This will allow clinicians to distinguish between BAP1 pathogenic and likely benign variants reliably and may aid to quickly benchmark newly identified BAP1 germline variants. Classification of novel BAP1 germline variants allows clinicians to inform predisposed patients and relevant family members regarding potential cancer risks, with appropriate clinical interventions implemented if required. Ministry of Health (MOH) National Medical Research Council (NMRC) National Research Foundation (NRF) Published version We would like to thank the patients and research participants for their contribution to the study. This work was supported by the Khoo Postdoctoral Fellowship Award (Duke-NUS-KPFA/2019/0034 to J.H.H), the National Medical Research Council Open Fund—Young Individual Research Grant (MOH-000232 to J.H.H), the National Medical Research Council Open Fund—Individual Research Grant (MOH-000144 to B.T.T), the National Medical Research Council Singapore Translational Research Investigator Award (MOH-000248 to B.T.T.), the NRF-NSFC Joint Research Grant (Data Science) (NRF2016NRF-NSFC001–057 to B.T.T), the LKC Startup Grant (LKC MOE to J.N.), the National Research Foundation Singapore under its Clinical Scientist Award (NMRC/CSA-INV/0017/2017) and administered by the Singapore Ministry of Health’s National Medical Research Council (to J.N.). This work is also partially funded by NCC Research Fund, NCC Cancer Fund, Terry Fox and Lee Foundation supporting funds to J.N.

The rapid deployment of 5G spectrum by the telecommunication industry is intended to promote better connectivity and data integration among various industries. However, since exposures to radio frequency radiations (RFR) >2.4 GHz are still uncommon, concerns about their potential health impacts are ongoing. In this study, we used the embryonic zebrafish model to assess the impacts of a 3.5 GHz RFR on biology- a frequency typically used by 5G-enabled cell phones and lies within the 4G and 5G bandwidth. We established a plate-based exposure setup for RFRs, exposed developing zebrafish to 3.5 GHz RFR, specific absorption rate (SAR) ≈ 8.27 W/Kg from 6 h post fertilization (hpf) to 48 hpf, and measured a battery of morphological and behavioral endpoints at 120 hpf. Our results revealed no significant impacts on mortality, morphology or photomotor response and a modest inhibition of startle response suggesting some levels of sensorimotor disruptions. This suggests that the cell phone radiations at low GHz-level frequencies are likely benign, with subtle sensorimotor effects. Through this assessment, we have established a robust setup for zebrafish RFR exposures readily amenable to testing various powers and frequencies. Future developmental exposure studies in zebrafish will evaluate a wider portion of the radio frequency spectrum to discover the bioactive regions, the potential molecular targets of RFR and the potential long-term effects on adult behavior.

Objective To investigate the utility of a detailed medical history in the interpretation of chromosomal microarray results for pediatric patients with a constitutional disease. Study design A retrospective review and reinterpretation of test results from chromosomal microarrays performed from 2011 to 2013. Previously reported genetic variants were reanalyzed after review of the patient's complete electronic medical record (cEMR). A 3-tier system was used for reclassification of variants: pathogenic or likely pathogenic (P/LP); variant of uncertain significance (VUS); or benign or likely benign (B/LB). Results Over an 18-month period, 998 patients with chromosomal microarray results were identified. The most common reasons for chromosomal microarray testing were developmental delay (n = 336), autism spectrum disorder (n = 241), and seizures (n = 143). Chromosomal microarray testing identified 1 or more variants in 48% (482 of 998) of patients; 516 patients had a negative report. For the 482 patients with variants, the original interpretations were composed of 19.3% P/LP (93 of 482), 44.8% VUS (216 of 482), and 35.9% B/LB (173 of 482) variants. After review of the cEMR, 34% of patient results (164 of 482) were changed in interpretation. One case changed from B/LB to VUS, 7 VUS were upgraded to P/LP, and 156 VUS were downgraded to B/LB. No P/LP variants had a change in interpretation. Conclusions Overall, 16.4% (164 of 998) of patients with chromosomal microarray testing had a change in interpretation. Access to the patient's cEMR improves the interpretation of chromosomal microarrays by decreasing the number of uncertain (VUS) interpretations.

The clinical utility of BRCA1/2 genotyping was recently extended from the selection of subjects at high risk for hereditary breast and ovary cancer to the identification of candidates for poly (ADP-ribose) polymerase (PARP) inhibitor treatment. This underscores the importance of accurate interpretation of BRCA1/2 genetic variants and of reducing the number of variants of uncertain significance (VUSs). Two recent studies by Findlay et al. and Starita et al. introduced high-throughput functional assays, and proactively analyzed variants in specific regions regardless of whether they had been previously observed. We retrospectively reviewed all BRCA1 and BRCA2 germline genetic test reports from patients with breast or ovarian cancer examined at Asan Medical Center (Seoul, Korea) between September 2011 and December 2018. Variants were assigned pathogenic or benign strong evidence codes according to the functional classification and were reclassified according to the ACMG/AMP 2015 guidelines. Among 3684 patients with available BRCA1 and BRCA2 germline genetic test reports, 429 unique variants (181 from BRCA1) were identified. Of 34 BRCA1 variants intersecting with the data reported by Findlay et al., three missense single-nucleotide variants from four patients (0.11%, 4/3684) were reclassified from VUSs to likely pathogenic variants. Four variants scored as functional were reclassified into benign or likely benign variants. Three variants that overlapped with the data reported by Starita et al. could not be reclassified. In conclusion, proactive high-throughput functional study data are useful for the reclassification of clinically observed VUSs. Integrating additional evidence, including functional assay results, may help reduce the number of VUSs.

PurposeEfforts have been made by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology to make variant classification more uniform, but many limitations remain. Reclassification of a variant of uncertain significance (VUS) is expected, but other more certain calls, like pathogenic or benign, can also be reclassified once additional information is gathered. Variant reclassification can create difficult circumstances for both patients and clinicians.MethodsRetrospective review of all variant reclassifications in genes associated with hereditary cancer syndromes at one clinic between September 2013 and February 2017 was completed. All variant reclassifications were completed and reported by the original testing laboratory.ResultsA total of 1,103 hereditary cancer tests were ordered. Fewer than 5% (40/1,103) of the initial reports were updated during that time period. Most reclassifications (29/40) were downgrades of VUS to likely benign. Only three reclassifications could potentially alter medical management.ConclusionThe majority of variant reclassifications do not impact medical management. Upgrading a variant call to pathogenic could be important for a patient's care and shows the importance of open communication between laboratories and clinicians. A variant downgrade from pathogenic can be a significant reclassification as well, especially if prophylactic surgery has been completed.

BACKGROUND In pregnant women with advanced maternal age (AMA) and fetuses with ultrasonographic (USG) soft markers it is always challenging to decide whether to implement chromosomal microarray analysis (CMA) or not. It is unclear whether CMA should be used in the fetuses with isolated USG soft markers, and there is still a lack of extensive sample research. MATERIAL AND METHODS We enrolled 1521 cases in our research and divided them into 3 groups as follows: pregnant women with isolated AMA (group 1, n=633), pregnant women whose fetuses had isolated USG soft markers (group 2, n=750), and pregnant women with AMA whose fetuses had isolated USG soft markers (group 3, n=138). All pregnant women underwent prenatal ultrasound and amniocentesis, and fetal cells in the amniotic fluid were used for genetic analysis of CMA. All participants signed a written informed consent prior to CMA. RESULTS Abnormal findings were detected by CMA in 330 (21.70%) fetuses, including 37 (2.43%) clinically significant copy number variations (CNVs), 52 (3.42%) benign or likely benign CNVs, and 240 (15.78%) variants of unknown significance. The frequency of clinically significant CNVs in group 1 and group 2 were significantly lower than that in group 3 (2.37% and 2.0% vs 5.07%, P

Lung cancer remains one of the most common cancers worldwide. Temporal evaluation is a useful tool for analyzing the malignant behavior of a lesion during treatment or that of indeterminate lesions which may be benign. Thereby, this work proposes a methodology for analysis, quantification and visualization of unsupervised changes in lung lesions, through principal component analysis. From change regions, we extracted texture features for lesion classification as benign or malignant. To reach this purpose, two databases with distinct behavior were used, one of which concerning malign under treatment and another indeterminate, but likely benign, lesions. The results have shown that the lesion’s density changes in a public database of malignant lesions under treatment were greater than the private database of benign lung nodules. From the texture analysis of the regions where the density changes occurred, we were able to discriminate lung lesions with an accuracy of 98.41 %, showing that these changes could point out the nature of the lesion. Other contribution was visualization of changes occurring in the lesions over time. Besides, we quantified these changes and analyzed the entire set through volumetry, the most commonly used technique to evaluate progression of lung lesions.

Background The sources and variants types of the copy number variations (CNVs) in prenatal fetal, and the critical role of parental origin on the interpretation of fetal CNVs are unclear. Methods One hundred and forty‐one prenatal core families with abnormal CNVs were selected and performed by low‐coverage massively parallel CNV sequencing (CNV‐seq). Results The data showed that 72.3% of fetal CNVs were derived from parents, and 27.7% were new variations. Sixty‐three cases were heterozygous deletion, 70 cases were threefold duplication, six cases were complex deletion and duplication, and two cases were fourfold repeats. That means the rate of heterozygous deletion and duplication was approximate one. In addition, in parental‐derived fetal abnormal CNVs reports, before validating parental origin, 62 CNVs were variants of uncertain significance (VUS), 15 CNVs were likely benign, 20 CNVs were likely pathogenic, and 5 CNVs were pathogenic. However, after validating parental origin, the total clinical significance changed into 12 VUS, 89 likely benign, 1 likely pathogenic, and 0 pathogenic. The clinical interpretation of 78.4% fetal CNVs was changed and tended to be benign after parental CNVs were detected. Besides, we followed up all families. 93.3% parental‐derived fetal and 30.3% fetus in new mutation group were born healthy. Conclusion Parental origin verification has an important significance for interpretation on the clinical significance of fetal CNVs.

This study aimed to obtain a quantitative assessment of the occurrence of contradictory evidence in functional classification of genetic variation, according to the American College of Medical Genetics and Genomics (ACMG) guidelines. We analyzed 140,883 genetic variation in the Human Gene Mutation Database (HGMD). The 2014 release of the HGMD dataset before the publication of the ACMG guidelines was used for its independence from the ACMG guidelines. Evidence for benign classification, BS2 (0.37%), was identified among variants classified as pathogenic. For likely pathogenic variation, BP1 (2.99%) and BS2 (0.37%) were identified. PM1 is commonly observed among variants classified as benign (28.45%), while PM2 and PM1 are commonly identified among variants classified as likely benign (48.91% and 42.95%, respectively). Taken together, these observations will inform better approaches to apply the ACMG guidelines.

Purpose To evaluate for stability of perifissural nodules (PFNs) in a dedicated oncologic population. Methods A retrospective review of 500 computed tomography (CT) chests from oncologic patients at our tertiary care cancer center with at least a three year follow up yielded 76 patients with PFNs. Patients with metastases on baseline CT chest were excluded (n = 14) as the presence of a PFN would not be clinically relevant, thus our final patient cohort was 62 patients with a total of 112 PFNs. PFN features, clinical features, and ancillary information was recorded from the CT and the electronic medical record for all patients. The two patient cohorts—stable or decreased PFN vs. increased PFN—were then compared. Results 112 PFNs were examined in 62 patients with a median follow up interval of 5.7 years. Of 62 patients, 59 (95.2%, 95% CI: 86.5, 99.0) had decreased/stable PFNs on follow up scan (median follow up 5.6 years) and 3 (4.8%, 95% CI: 1.0, 13.5%) had enlarged PFNs (median follow up 6.3 years). None of the PFN features, clinical features, nor ancillary information from the CT proved to be statistically significant. Conclusions Despite the lack of statistically significant distinguishing features to predict growth, our results are reassuring, since the majority of PFNs in our oncology patients were decreased or unchanged in size which is comparable to previously published data on PFNs in non-oncologic patients. Thus, we can similarly presume these nodules are most likely benign and can provide reassurance to our oncologic colleagues and our patients. Larger studies are warranted to further evaluate PFNs in the oncologic population which also examines the nodules by cancer type.

Trisomy 9p is one of the most common chromosomal partial trisomies in newborns. However, reports on prenatal 9p microduplications are rare in the clinic. This study aimed to examine the genotype–phenotype correlation and assess the clinical significance of 9p24.3 microduplication encompassing the DOCK8 gene. Eight pregnant women underwent amniocentesis for cytogenetic and genetic testing for various indications for prenatal diagnosis from January 2019 to January 2020. Chromosomal karyotypic analysis was performed on G-band metaphases that were prepared from cultured amniotic fluid cells. Chromosomal microarray analysis was carried out to detect chromosomal copy number variations. We also performed a literature review on clinical data on similar 9p24.3 microduplications to determine the genotype–phenotype correlation. We detected 123–248-kb microduplications in the region of 9p24.3 (chr9: 208454–469022), involving part of or the entire DOCK8 gene. The indications for prenatal diagnosis mainly focused on the risk of maternal serum screening for trisomy 21/18, advanced maternal age, and increased nuchal translucency. No evident structural abnormalities were observed for all fetuses, except for case 5 who presented with increased nuchal translucency in prenatal ultrasound findings. Follow-up of postnatal health was performed and showed no apparent abnormalities for cases 1 to 6 after birth. The parents of case 7 chose to terminate the pregnancy while the parents of case 8 chose to continue the pregnancy. We propose that 9p24.3 microduplications that encompass part of or the entire DOCK8 gene are variants that might be benign. However, further large-scale studies are necessary to evaluate the clinical pathogenicity. For prenatal cases with 9p24.3 microduplication, postnatal health and growth should be followed up and assessed regularly from childhood to adulthood.

Highlights • An 84-year-old Japanese woman with a history of multiple primary meningiomas (PPMs) we first reported. • Histologically confirmed for a right-sided slowly growing lung nodule for 20 years. • Long-term follow-up CT scans reveal multiple lung nodules. • Multiple PPMs are most effectively treated with surgical resection and follow-up examinations. • The tumors prove to be benign by morphology with a relatively long, asymptomatic clinical course., Introduction Primary pulmonary meningiomas (PPMs) are very rare neoplasms, and we reported the first multiple case of PPMs in 1998. Usually, PPMs are slow-growing tumors with a good prognosis. Herein, we reported a rare multiple case of PPMs with an extremely long clinical course. Presentation of the case An 84-year-old Japanese woman with a history of multiple PPMs histologically confirmed as having a right-sided slowly growing lung nodule for 20 years. In 2010, we also reported the additional clinical course in the initial case 10 years after surgery implying a benign biological nature. Subsequent to that report, new lesions appeared in the bilateral lung fields with quite a slow growth rate. She was asymptomatic, and no tumor was observed in the cranial cavity during the course of her disease. Discussion and conclusion This case illustrates rare multiple PPMs and highlights their biological behavior with very slow progression from a most likely benign tumor over a 20-year period.

Background:Tumour necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS) is one of the best-known monogenic auto-inflammatory disorders resulting from an autosomal dominant variation in the TNF super family receptor 1A (TNFRSF1A) gene (1).Objectives:To define best treatment approach in patients with TRAPS and effect on long-term outcomes.Methods:We reviewed all data on patients with TRAPS enrolled in the Eurofever international registry according the INSAID gene variant classification and the new Eurofever/PRINTO classification criteria (EPCC).Results:Data on 226 patients were available. Patients not fulfilling the EPCC carrying likely benign/benign variants (21 patients, 9%) or VOUS/not classified variants (40 patients, 18%) displayed a milder disease than the patients fulfilling the EPCC with VOUS/not classified variants (38 patients, 17%) or pathogenic/likely pathogenic variants (127 patients, 56%). In particular, in patients not fulfilling the EPCC, less frequent abdominal pain and skin rashes, higher efficacy rate of colchicine and no development of AA amyloidosis have been reported. Almost 90% of patients fulfilling the EPCC required maintenance therapy and anti-interleukin (IL)-1 drugs were the most frequently used, with the highest efficacy rate (>85% complete response), while Etanercept was less effectively used and discontinued in 65% of patients.Conclusion:Anti-IL-1 drugs are the best maintenance treatment in TRAPS with potential to reverse the most serious disease complications of AA amyloidosis and infertility. The diagnosis of TRAPS should be considered very carefully in patients carrying VOUS/not classified variants not fulfilling the EPCC.References:[1]Lachmann HJ, Papa R, Gerhold K, Obici L, Touitou I, Cantarini L, et al. The phenotype of TNF receptor-associated autoinflammatory syndrome (TRAPS) at presentation: a series of 158 cases from the Eurofever/EUROTRAPS international registry. Annals of the rheumatic diseases 2014;73:2160-7.Acknowledgments:RP would like to thank the European Federation of Immunology (EFIS) for the short-term bursary and HL for her continuous support and guidance during the fellowship at the National Amyloidosis Centre in London.Disclosure of Interests:Riccardo Papa: None declared, Thirusha Lane: None declared, Francesca Bovis: None declared, Kirsten Minden Consultant of: GlaxoSmithKline, Sanofi, Speakers bureau: Roche, Isabelle Touitou: None declared, Luca Cantarini: None declared, Marco Cattalini: None declared, Laura Obici: None declared, Annette Jansson: None declared, Alexander Belot: None declared, Beata Woska-Kuśnierz: None declared, Rainer Berendes: None declared, Agustin Remesal: None declared, Marija Jelusic: None declared, Graciela Espada: None declared, Irina Nikishina: None declared, Esther Hoppenreijs: None declared, Maria Cristina Maggio: None declared, Taryn Youngstein: None declared, Tamer Rezk: None declared, Charalampia Papadopoulou: None declared, Paul Brogan Grant/research support from: Roche, Novartis, SOBI, Chemocentryx, Novimmune, Consultant of: Roche, SOBI, UCB, Novartis, Speakers bureau: Roche, SOBI, UCB, Novartis, Philip N Hawkins: None declared, Patricia Woo: None declared, Nicolino Ruperto Grant/research support from: Bristol-Myers Squibb, Eli Lily, F Hoffmann-La Roche, GlaxoSmithKline, Janssen, Novartis, Pfizer, Sobi (paid to institution), Consultant of: Ablynx, AbbVie, AstraZeneca-Medimmune, Biogen, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lily, EMD Serono, GlaxoSmithKline, Hoffmann-La Roche, Janssen, Merck, Novartis, Pfizer, R-Pharma, Sanofi, Servier, Sinergie, Sobi, Takeda, Speakers bureau: Ablynx, AbbVie, AstraZeneca-Medimmune, Biogen, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lily, EMD Serono, GlaxoSmithKline, Hoffmann-La Roche, Janssen, Merck, Novartis, Pfizer, R-Pharma, Sanofi, Servier, Sinergie, Sobi, Takeda, Marco Gattorno Consultant of: Sobi, Novartis, Speakers bureau: Sobi, Novartis, Helen J. Lachmann: None declared

Based on a homozygous missense variant p.Pro311Ala found in three siblings of a consanguineous family, mutations in the STYXL1 gene were suggested to cause moderate intellectual disability, epilepsy and complex behavioural abnormalities. We have detected this variant via whole exome sequencing in a homozygous state in two families. Segregation analyses in our families and thorough validation in international genetic databases provides evidence that this variant is most likely benign. This is important information for genetic counselling. The role of STYXL1 variants in human disease needs to be established.

Family studies are an important but underreported source of information for reclassification of variants of uncertain significance (VUS). We evaluated outcomes of a patient-driven framework that offered familial VUS reclassification analysis to any adult with any clinically ascertained VUS from any laboratory in the United States. With guidance from FindMyVariant.org, participants recruited their own relatives for study participation. We genotyped relatives, calculated quantitative cosegregation likelihood ratios, and evaluated variant classifications using Tavtigian’s unified framework for Bayesian analysis with American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria. We report participation and VUS reclassification rates from the 50 families enrolled for at least one year and reclassification results for 112 variants from the larger 92-family cohort. For the 50-family cohort, 6.7 relatives per family were invited to participate and 67% of relatives returned samples for genotyping. Sixty-one percent of VUS were reclassified, 84% of which were classified as benign or likely benign. Genotyping relatives identified a de novo variant, phase variants, and relatives with phenotypes highly specific for or incompatible with specific classifications. Motivated families can contribute to successful VUS reclassification at substantially higher rates than those previously published. Clinical laboratories could consider offering family studies to all patients with VUS.

Learning diagnostic labels from image content has been the standard in computer-aided diagnosis. Most computer-aided diagnosis systems use low-level image features extracted directly from image content to train and test machine learning classifiers for diagnostic label prediction. When the ground truth for the diagnostic labels is not available, reference truth is generated from the experts diagnostic interpretations of the image/region of interest. More specifically, when the label is uncertain, e.g. when multiple experts label an image and their interpretations are different, techniques to handle the label variability are necessary. In this paper, we compare three consensus techniques that are typically used to encode the variability in the experts labeling of the medical data: mean, median and mode, and their effects on simple classifiers that can handle deterministic labels (decision trees) and probabilistic vectors of labels (belief decision trees). Given that the NIH/NCI Lung Image Database Consortium (LIDC) data provides interpretations for lung nodules by up to four radiologists, we leverage the LIDC data to evaluate and compare these consensus approaches when creating computer-aided diagnosis systems for lung nodules. First, low-level image features of nodules are extracted and paired with their radiologists semantic ratings (1= most likely benign, , 5 = most likely malignant); second, machine learning multi-class classifiers that handle deterministic labels (decision trees) and probabilistic vectors of labels (belief decision trees) are built to predict the lung nodules semantic ratings. We show that the mean-based consensus generates the most robust classi- fier overall when compared to the median- and mode-based consensus. Lastly, the results of this study show that, when building CAD systems with uncertain diagnostic interpretation, it is important to evaluate different strategies for encoding and predicting the diagnostic label.

Background The 100,000 Genomes Project is a national programme to perform whole genome sequencing (WGS) in families with an undiagnosed rare disorder or cancer. Multiple specialties from GOSH have recruited patients to the pilot study. Here we report on the outcome of the first 111 pilot cases. Methodology Total lymphocyte DNA was extracted (Chemagic Star, Chemagen) and exported to Genomics England for WGS (HiSeqX, Illumina). Prioritised variants were discussed and classified by a multidisciplinary team (MDT) of Clinical Scientists, Consultant Clinical Geneticists and the recruiting clinicians. Variants deemed to be ‘pathogenic’ or ‘likely pathogenic’ were flagged for diagnostic confirmation and clinical reporting. Results Genomics England returned results for 111 cases (probands); 95 (86%) were analysed as trios (proband and both parents). Variant interpretation has been completed for 97 cases (87%). Thirty-six percent of cases (40/111) and a total of 76 variants were discussed at an MDT meeting. Fifty-three percent of variants discussed (40/76) were classified as pathogenic or likely pathogenic, 30% (23/76) were classified as variants of unknown significance and 17% (13/76) were classified as benign or likely benign. This equated to a genetic diagnosis in 27/111 cases (25%) of which 5/111 (5%) were felt to be a partial rather than full explanation of the phenotype. Of the 97 cases where primary analysis was complete, 66/97 (68%) had no primary findings. This included cases in which variants of unknown significance have been detected. Conclusion WGS is a useful tool for rare disease diagnosis especially in patients who have undergone a fruitless diagnostic odyssey. Analysis of GOSH pilot cases has enabled us to develop infrastructure locally to support the return of main programme results. One quarter of GOSH pilot patients should expect a genetic diagnosis from the primary analysis. It is unclear whether this will be an accurate reflection of the diagnostic rate achieved in the main programme due to ongoing refinement of the recruitment and analysis pipelines.

Brain malformations are a major cause of therapy-refractory epilepsy as well as neurological and developmental disabilities in children. This study examined the frequency and the nature of copy number variations among children with structural brain malformations and refractory epilepsy. The medical records of all children born between 1990 and 2009 in the epilepsy registry at the Astrid Lindgren's Children's Hospital were reviewed and 86 patients with refractory epilepsy and various brain malformations were identified. Array-CGH analysis was performed in 76 of the patients. Pathogenic copy number variations were detected in seven children (9.2%). In addition, rearrangements of unclear significance, but possibly pathogenic, were detected in 11 (14.5%) individuals. In 37 (48.7%) patients likely benign, but previously unreported, copy number variants were detected. Thus, a large proportion of our patients had at least one rare copy number variant. Our results suggest that array-CGH should be considered as a first line genetic test for children with cerebral malformations and refractory epilepsy unless there is a strong evidence for a specific monogenic syndrome.

Background Significant numbers of variants detected in cancer patients are often left labeled only as variants of unknown significance (VUS). In order to expand precision medicine to a wider population, we need to extend our knowledge of pathogenicity and drug response in the context of VUS’s. Methods In this study, we analyzed variants from AACR Project GENIE Consortium APG (Cancer Discov 7:818-831, 2017) and compared them to the COSMIC database Forbes et al. (Nucleic Acids Res 43:D805-811, 2015) to identify recurrent variants that would merit further study. We filtered out known hotspot variants, inactivating variants in tumor suppressors, and likely benign variants by comparing with COSMIC and ExAC Lee et al. (Science 337:967-971, 2012). Results We have identified 45,933 novel variants with unknown significance unique to GENIE. In our analysis, we found on average six variants per patient where two could be considered as pathogenic or likely pathogenic and the majority are VUS’s. More importantly, we have discovered 730 recurrent variants that appear more than 3 times in GENIE but less than 3 in COSMIC. If we combine the recurrences of GENIE and COSMIC for all variants, 2586 are newly identified as occurring more than 3 times than when using COSMIC alone. Conclusions Although it would be inappropriate to blindly accept these recurrent variants as pathogenic, they may warrant higher priority than other observed VUS’s. These newly identified recurrent variants might affect the molecular profiles of approximately 1 in 6 patients. Further analysis and characterization of these variants in both research and clinical contexts will improve patient treatments and the development of new therapeutics. Electronic supplementary material The online version of this article (10.1186/s12885-019-5313-1) contains supplementary material, which is available to authorized users.

The widespread use of abdominal imaging techniques has increased the detection of solid renal masses over the past years. Imaging plays a crucial role in the management and surveillance and in determining which lesions need treatment. The "classical angiomyolipoma" is the only benign solid renal mass that can be characterized with confidence by imaging through the detection of a fat-containing lesion without calcifications. There is a large overlap of imaging features between benign and malignant renal masses that often makes difficult a correct characterization of these lesions. In this review, we discuss the imaging features of the main solid renal masses that may suggest a likely benign diagnosis.

Key Clinical Message BRCA1, c.4096+3A>G was identified in a consanguineous Danish family with several cases of breast/ovarian cancer. In silico analysis and splicing assays indicated that the variant caused aberrant splicing. However, based on segregation data and the finding of a healthy homozygous carrier, we classify the BRCA1 c.4096+3A>G variant as likely benign.

Among the detected small nodules sized from 3 to 30mm in CT images, a significant portion is undetermined in terms of malignancy which needs biopsy or other follow-up means, resulting in excessive risk and cost. Therefore, predicting the malignancy of the nodules becomes a clinically desirable task. Based on the previous study of texture features extracted from gray-tone spatial-dependence matrices, this study aims to find more efficient texture features or image texture markers in discriminating the nodule malignancy. Two new image texture markers (median and variance) are proposed to classify the small nodules into different malignant levels, thus the risk prediction could be performed through image analysis. These two new image texture markers can minimize the effect of outliers in the feature series, thus can reduce the noise influence to the feature classification. Total 1,353 nodule samples selected from the Lung Image Database Consortium were used to evaluate the efficiency of the proposed new features. All the classification results are shown in the ROC curves and tabulated by the AUC values. The classification outcomes from (1) the most likely and likely benign nodules vs. the most likely and likely malignant nodules, (2) the most likely vs. likely benign nodules, and (3) the most likely vs. likely malignant nodules, are 0.9125±0.0096, 0.9239±0.0147, and 0.8888±0.0197, respectively, in terms of the largest AUC values. From the experimental outcomes on different malignant levels, the two new image texture markers from nodule volumetric CT image data have shown encouraging performance for the risk prediction.

INTRODUCTION The TET2 (Ten‐Eleven Translocation 2) gene, located at chromosome 4q24.1, belongs to TET family of proteins that possesses the capacity of catalyzing the conversion of 5‐methylcytosine into 5‐hydroxymethylcytosine. It is considered to be a putative tumor suppressor gene during cancer initiation and development. TET2 mutations are extensively studied and reported in a variety of human hematological malignancies including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), suggesting a crucial role of TET2 in the pathogenesis of blood cancers. The landscape of rare TET2 variants which may be of potential clinical relevance is not fully described. The landscape of TET2 variants from a large cohort of MDS and AML patients was explored. METHODS We analyzed data from bone marrow samples of 2634 patients with AML or MDS who presented at MD Anderson between the years 2012-2016. Seven hundred seventy seven patients were found to have TET2 variants that were not classifiable as known mutations. Two hundred sixty-three patients were diagnosed with MDS, 144 with secondary AML transformed from MDS, and 370 with AML without prior history of MDS. The coding regions of TET2 gene was analyzed by next-generation sequencing in the molecular diagnostics laboratory. Non-mutation variants were classified into 2 groups: 1) those reported as germline polymorphisms (GP) in population studies, literature or matched tumor-normal analysis on patients at MDACC; and 2) variants for which a germline versus somatic origin could not be determined unequivocally (variants of uncertain origin, VUO). Very common GP variants (defined as those with a population frequency of over 20% in laboratory sample cohort) were not evaluated. Variants' predicted frequency in the population according to gnomAD Exomes 2.0.2, and classification according to American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation of sequence variants, were assessed using the VarSome platform by Saphetor. RESULTS Two-hundred and twenty-eight unique variants were identified. The amino acid substitutions from missense variants were widely distributed throughout TET2. Fifty-four unique variants were classified as GP and several of these recurrent variants were found to be present in our population at a significantly higher frequency (p CONCLUSIONS The landscape of rare TET2 variants in a large group of MDS and AML patients was frequent, diverse, and included both GP and VUO. GP variants were more likely benign by ACMG classification and found in both MDS and AML patients. A large number of singleton VUO were found among MDS patients, and many were predicted to be pathogenic or had uncertain significance. VUO's also contained many fs and nonsense variants. These result support the idea that rare pathogenic variants in TET2 are currently underrecognized as contributory, although they are likely to help drive leukemogenesis. Greater understanding of the importance of individual TET2 variants and additional classification metrics are needed. Disclosures DiNardo: Karyopharm: Honoraria; Abbvie: Honoraria; Agios: Consultancy; Medimmune: Honoraria; Celgene: Honoraria; Bayer: Honoraria. Daver:Karyopharm: Research Funding; Incyte: Consultancy; Novartis: Consultancy; ImmunoGen: Consultancy; Sunesis: Consultancy; Pfizer: Consultancy; Daiichi-Sankyo: Research Funding; Kiromic: Research Funding; Alexion: Consultancy; Otsuka: Consultancy; Sunesis: Research Funding; Incyte: Research Funding; ARIAD: Research Funding; BMS: Research Funding; Karyopharm: Consultancy; Novartis: Research Funding; Pfizer: Research Funding. Kadia:Celgene: Research Funding; Takeda: Consultancy; BMS: Research Funding; Abbvie: Consultancy; Novartis: Consultancy; Novartis: Consultancy; Amgen: Consultancy, Research Funding; Jazz: Consultancy, Research Funding; Abbvie: Consultancy; Pfizer: Consultancy, Research Funding; Takeda: Consultancy; Amgen: Consultancy, Research Funding; BMS: Research Funding; Pfizer: Consultancy, Research Funding; Jazz: Consultancy, Research Funding; Celgene: Research Funding. Konopleva:Stemline Therapeutics: Research Funding; abbvie: Research Funding; cellectis: Research Funding; Immunogen: Research Funding. Andreeff:Amgen: Consultancy, Research Funding; Astra Zeneca: Research Funding; Jazz Pharma: Consultancy; Oncolyze: Equity Ownership; Aptose: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Oncoceutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; SentiBio: Equity Ownership; United Therapeutics: Patents & Royalties: GD2 inhibition in breast cancer ; Reata: Equity Ownership; Celgene: Consultancy; Eutropics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Consultancy, Patents & Royalties: MDM2 inhibitor activity patent, Research Funding.

Dancers frequently present to the sports medicine clinic with a variety of lower extremity complaints ranging from acute and traumatic injuries to more chronic, overuse injuries. This case series depicts a similar and unique incidental radiographic finding found in 2 young dancers seen at the same sports medicine clinic. While the findings are likely benign and unrelated to both patients’ initial presentation, the finding of acroosteolysis can be found in more serious systemic and genetic processes as well an early finding in repetitive trauma.

BACKGROUND AND PURPOSE: DWI has been increasingly used to characterize orbital masses and provides quantitative information in the form of the ADC, but studies of DWI of orbital masses have shown a range of reported sensitivities, specificities, and optimal threshold ADC values for distinguishing benign from malignant lesions. Our goal was to determine the optimal use of DWI for imaging orbital masses through aggregation of data from multiple centers. MATERIALS AND METHODS: Source data from 3 previous studies of orbital mass DWI were aggregated, and additional published data points were gathered. Receiver operating characteristic analysis was performed to determine the sensitivity, specificity, and optimal ADC thresholds for distinguishing benign from malignant masses. RESULTS: There was no single ADC threshold that characterized orbital masses as benign or malignant with high sensitivity and specificity. An ADC of less than 0.93 × 10 −3 mm 2 /s was more than 90% specific for malignancy, and an ADC of less than 1.35 × 10 −3 mm 2 /s was more than 90% sensitive for malignancy. With these 2 thresholds, 33% of this cohort could be characterized as “likely malignant,” 29% as “likely benign,” and 38% as “indeterminate.” CONCLUSIONS: No single ADC threshold is highly sensitive and specific for characterizing orbital masses as benign or malignant. If we used 2 thresholds to divide these lesions into 3 categories, however, a majority of orbital masses can be characterized with >90% confidence.

The 2010 consensus statement on diagnostic chromosomal microarray (CMA) testing recommended an array resolution ≥400 kb throughout the genome as a balance of analytical and clinical sensitivity. In spite of the clear evidence for pathogenicity of large copy-number variants (CNVs) in neurodevelopmental disorders and/or congenital anomalies, the significance of small, nonrecurrent CNVs (

Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype–genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype–genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation.

In selected patients, our Unit has recently moved from handheld ultrasound-guided vacuum-assisted core biopsy (VACB) piecemeal acquisition of tissue to the handheld Intact Breast Lesion Excision System (Intact). Intact removes a single piece of tissue, potentially allowing radiologists to excise the entire lesion as well as allowing pathologists to visualise lesion architecture more easily and to calculate margins. We evaluated our early experience of excising benign or likely benign breast lesions using the 20 mm Intact.

Introduction (purpose of the study): The objective of this study was to assess whether dual-time-point ¹⁸F-fluoro-2-deoxyglucose (¹⁸F-FDG)-PET/CT imaging improved the evaluation of suspected malignancy and if there was any resulting change in management. Methods: A total of 53 patients with suspected malignancy were investigated by performing two static acquisitions started at mean times t = 64 and t = 155 min after the tracer injection. The total number of malignant lesions was 133 and the total number of benign lesions was 61. Visual and semiquantitative analysis was performed on both the early and delayed images. Results: Overall, there was a significant improvement (P < 0.001) in the sensitivity of delayed imaging (94%) compared with early imaging (77%) in detecting malignant lesions, without a reduction in specificity. In 10 patients, 13 malignant lesions were undetected on early imaging alone but detected on delayed imaging. In seven patients, 10 malignant lesions were incorrectly classified as 'likely benign' on early imaging but correctly reported as 'likely malignant' on delayed imaging. Management was altered in 2 out of 17 patients. Overall, delayed imaging altered management in 2 out of 53 studied patients. Dual-time-point ¹⁸FDG-PET/CT imaging was useful in differentiating malignant from benign intra-abdominal lesions but did not improve the evaluation of pulmonary lesions. Conclusions:¹⁸F-FDG-PET/CT imaging should be performed as late as reasonably possible after tracer administration in order to increase tumour-to-background contrast and thereby improve the sensitivity of demonstrating additional sites of disease. Dual-time-point ¹⁸FDG-PET/CT may be of benefit in the evaluation of intra-abdominal lesions but does not improve the overall evaluation of pulmonary lesions.

With continued improvement of high-resolution multidetector computed tomography imaging, there is an increasing number of unsuspected thoracic findings. Although many of these findings are of little clinical significance, other findings such as small incidental lung nodules require additional imaging to exclude more worrisome causes, often resulting in greater exposure to ionizing radiation, increased cost, and patient anxiety. Although greater uniformity among radiologists regarding likely benign findings may help reduce unnecessary imaging studies, the lack of clear follow-up guidelines for many findings suggests that further investigation is needed in some areas.

Ophthalmologists may be the first to hear about formed visual hallucinations in the setting of visual loss. Although such hallucinations are likely benign and occur in association with the Charles Bonnet syndrome, it is important to be aware of the strong association of hallucinations with dementia with Lewy bodies because the latter diagnosis is associated with significant prognostic and therapeutic implications for the patient.Single case report.A patient with macular disease was presumed to have formed hallucinations due to the Charles Bonnet syndrome and was subsequently diagnosed with dementia with Lewy bodies after being admitted to a psychiatric facility.Both patients with the Charles Bonnet syndrome and patients with dementia with Lewy bodies can present with formed visual hallucinations. Ophthalmologists and retina specialists, in particular, should be familiar with the features of dementia with Lewy bodies because the diagnosis of this condition can allow appropriate intervention and help prevent drug-related side effects. If there is any suspicion of early dementia in such patients, they may benefit from neuropsychiatric evaluation.

Ciliated muconodular papillary tumors (CMPTs) are rare peripheral nodules of the lung first described in 2002. Because of their rarity and nonstandardized diagnostic terminology, CMPTs have been poorly recognized among pathologists. To better characterize these lesions, we undertook a detailed clinicopathologic and immunohistochemical study of 10 archival cases. Ten CMPTs occurred in 7 men and 3 women with a median age of 62 years. All were small peripheral nonendobronchial nodules with a mean diameter of 1.0 cm. All but 1 tumor were incidentally detected by computed tomography-based screening, all of which were radiologically interpreted as adenocarcinomas. Although limited surgery treated all but 1 CMPT, they followed a benign course with no recurrence at a mean follow-up of 43 months (range: 2 to 88 mo). Histologically, CMPTs showed glandular and/or papillary architecture, comprising a vaguely organized mixture of nonatypical ciliated columnar cells, mucous cells, and basal cells, often enveloped by copious intra-alveolar mucin. Micropapillary tufts of ciliated cells and seemingly discontinuous growth along alveolar walls were occasionally present, mimicking adenocarcinomas. Ciliated cells and basal cells were immunopositive for TTF-1 and p40, respectively, whereas mucous cells lacked HNF4α expression. CMPTs are rare, likely benign, underrecognized processes of the lung that should be distinguished from adenocarcinomas.

• Clinical examination of the breast is the weakest test of the “triple diagnostic assessment”, but may be decisive to solve many common symptoms as breast pain, inflammatory changes, acute enlargement of cysts, and many more. • The basic goal of clinical breast examination is to identify a palpable dominant mass, which by definition is a three-dimensional distinct mass that is different from the remainder of the breast tissue and from the tissue of the other breast (not symmetrical). • A dominant breast mass should be definitively diagnosed in a timely manner (old or already recorded, newly or firstly discovered, changing over time, etc.). • Even though a dominant mass in a woman under the age of 40 is most likely benign, a new dominant mass in a postmenopausal woman is most likely malignant.

Purpose To determine the radiological technologist's performance in detecting abnormalities in film-screen mammographic images. Methods Fifty sets of 2-view bilateral mammographic images wereread and judged to be either benign, likely benign, suspicious of abnormality or highly suggestive of malignancy. Seven readers, 5 radiological technologists and 2 radiologists currently working in the field of mammography participated in this study. Results The sensitivity of three-fifths of the technologists in detecting abnormalities that were likely to be a sign of breast cancer was 100%, which was comparable to the 2 participating radiologists. Specificity was also high amongst the technologists, with three-fifths being equal to (88.37%) or better (93.02%) than that of the radiologists (88.37%). Conclusion Of those participating in this study, the findings indicate that the sensitivity and specificity of the majority of individual technologists to detect mammographic abnormalities is comparable to that of the radiologists when compared to the gold standard.