Quantification of Discordant Variant Interpretations in a Large Family-Based Study of Li-Fraumeni Syndrome

PURPOSE The use of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines has improved germline variant classification concordance, but discrepancies persist, sometimes directly affecting medical management. We evaluated variant discordance between and within families with germline TP53 variants in the National Cancer Institute's Li-Fraumeni syndrome longitudinal cohort study. MATERIALS AND METHODS Germline TP53 genetic testing results were obtained from 421 individuals in 140 families. A discordant test result was defined as a report of pathogenicity that differed between two clinical testing laboratories, between a testing laboratory and the ClinVar database, or between either the laboratory or ClinVar database and variant classification by internal study review. RESULTS There were 141 variants in 140 families (one family had two different TP53 variants). Fifty-four families had discordant interpretations (54 of 140, 39%). Sixteen families had discordant classifications leading to clinically important differences in medical management (16 of 140, 11%). Interfamilial discordance was observed between four families (two different variants). Intrafamilial discordance was observed within six families. One family experienced both intrafamilial and interfamilial discordance. CONCLUSION This large single-gene study found discordant germline TP53 variant interpretations in 39% of families studied; 11% had a variant with the potential to significantly affect medical management. This finding is especially concerning in patients with Li-Fraumeni syndrome because of their exceedingly high risks of multiple cancers and intensive cancer screening and risk-reducing recommendations. Centralized data sharing, gene-specific variant curation guidelines, and provider education for consistent variant interpretation are essential for optimal patient care.

The characteristics of breast cancer research using big data analysis techniques: recurrence gene study or utilization behavior of hospital but sample statistic error

Breast cancer is a major cause of female death, and various big data analysis methods have been applied to breast cancer. This study lists cases in which big data analysis was applied to breast cancer research. In addition, statistics and percentages from each specific sample were proposed. However, research on the use of big data has a blind spot that relies on sample characteristics. Therefore, before sampling big data, statistical inference should be discussed more precisely through pre-examination and sample statistical errors should be reduced by professional statistical evaluation of the analysis method.

Efficacy of Immunohistochemistry for SDHB in the Screening of Hereditary Pheochromocytoma–Paraganglioma

The most common genetic backgrounds of hereditary paraganglioma and pheochromocytoma (PPGL) are SDHx germline mutations. Given the fact that the immunohistochemistry (IHC) result for SDHB is always negative regardless of the type of SDHx mutation, we aimed to evaluate the efficacy of using SDHB IHC for screening SDHx mutations in PPGL cases. In total, 52 patients who underwent surgery for PPGL treatment between 2006 and 2020 and underwent genetic analysis at diagnosis were included. Tissue microarrays (TMAs) were constructed with PPGL tissues and IHC for SDHB was performed on TMA sections. All 10 patients with SDHB-negative IHC contained SDHB or SDHD mutations. The genetic test results of patients with SDHB-weakly positive IHC varied (one SDHB, two RET, one VHL, and three unknown gene mutations). There were no SDHx mutations in the SDHB-positive IHC group. Six patients with weakly positive SDHB IHC with primarily unknown genetic status were re-called and underwent next-generation sequencing. None of them had SDHx mutations. In conclusion, SDHB-negative IHC is a cost-effective and reliable method to predict SDHx mutations. However, in the case of weakly positive SDHB staining, an additional gene study should be considered.

Evaluation of Reference Genes and Expression Level of Genes Potentially Involved in the Mode of Action of Cry1Ac and Cry1F in a Susceptible Reference Strain of Chrysodeixis includens

Soybean looper (SBL), Chrysodeixis includens (Walker), is one of the major lepidopteran pests of soybean in the American continent. SBL control relies mostly on the use of insecticides and genetically modified crops expressing Bacillus thuringiensis (Bt) insecticidal Cry proteins. Due to the high selection pressure exerted by these control measures, resistance has developed to different insecticides and Bt proteins. Nevertheless, studies on the mechanistic background are still scarce. Here, the susceptibility of the laboratory SBL-Benzon strain to the Bt proteins Cry1Ac and Cry1F was determined in diet overlay assays and revealed a greater activity of Cry1Ac than Cry1F, thus confirming results obtained for other sensitive SBL strains. A reference gene study across larval stages with four candidate genes revealed that RPL10 and EF1 were the most stable genes for normalization of gene expression data obtained by RT-qPCR. Finally, the basal expression levels of eight potential Bt protein receptor genes in six larval instars were analyzed, including ATP-binding cassette (ABC) transporters, alkaline phosphatase, aminopeptidases, and cadherin. The results presented here provide fundamental knowledge to support future SBL resistance studies.

Psychiatric Onset Alexander Disease: An Important Challenge in Neuropsychiatric Diagnosis

Introduction: Alexander disease is a heterogenous group of diseases with various manifestations based on age of disease onset. This rare leukodystrophy syndrome with mutations in GFAP Gene could present with developmental delay and seizure in infantile form to ataxia and bulbar palsy in adulthood. However psychiatric symptoms are not well-defined and usually evaluate after disease diagnosis not before disease investigations. Case report: Our patient is a fifty-two-year-old Iranian woman with history of depression from about 17 years ago, suicidal attempt two years ago and ingestion a large amount of opium with the intention of suicide 2 months ago who was presented with disorientation and probably delirious state in the last interview. Eventually in comprehensive investigations, white matter hyperintensity and leukodystrophy was diagnosed and ultimately to determine the cause of these changes with gene study, whole and Exon deletion of GFAP Gene Late Onset Alexander disease was determined. Conclusion: Neurological-onset manifestation of Alexander disease specifically late onset form is the most common clinical picture of disease and was seen in about 90% of patients but psychiatric symptoms are not well-known and psychiatric- onset disease was not described yet. On the other hand, various Gene Mutation were described in Late Onset Alexander Disease, however large whole Exon deletion which was revealed in our patient is a novel mutation and significantly need to be declared. Here authors describe a late onset Alexander disease with psychiatric onset symptoms and novel large Exon deletion in GFAP Gene.

“Epidemiology of Short QT Interval in Phase I of Kherameh Cohort Study: A Population-based Study on 4,363 Subjects in Southern Iran”

Aims: Short QT-interval is a condition that bear the suspicion of short QT syndrome (SQTS). SQTS is known to increase risk of life-threatening arrythmias and sudden cardiac death (SCD). Due to the insufficient population-based studies and use of various QT cut-off values it accounts for as an undiagnosed condition. In this study, we sought for prevalence of short QT interval in Kherameh cohort study, one of the southern sectors of the Prospective Epidemiological Research Studies in Iran (PERSIAN).Methods: Data of 4,363 adult subjects were analyzed from phase 1 of the cohort during 2014-2017. The corrected QT (QTc) intervals were calculated and electrocardiograms (ECGs) with QTc of less than 370 milliseconds (msec) were reanalyzed for bradycardia, early repolarization, atrial fibrillation (AF), arrhythmias, and other electrical conduction abnormalities. Results: Seventy-two subjects (1.65%) had a QTc of less than 370msec (mean QTc of 360.72±11.72). A male predominance and a lower mean heart rate observed in SQTS susceptible group (M/F of 1/0.26 vs. 1/1.145, p-value<0.0001; 58.389±9.787 vs. 70.899±11.775; p-value<0.0001) compare to the subjects with normal QTc. At least, 2 subjects with high-probability SQTS and 3 with intermediate-probability SQTS identified. The frequency of AF, syncope, bradycardia, early repolarization, low voltage ECG, and infantile SCD in first- and second-degree relatives were 16.67, 4.17, 33.33, 11.11, 6.94, 11.11%, respectively.Conclusion: The prevalence of short QT interval in our cohort was in line with previous studies. The higher proportions of cardiac symptoms, familial SCDs and ECG derived specific findings amongst SQTS-susceptible index persons than non-short QT interval normal population might implicate in gene study and family screening.

MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula

Although RNA sequencing has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labelling and organization of samples, to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation.

Knockout of Formyl Peptide Receptor-1 Attenuates Cigarette Smoke–Induced Airway Inflammation in Mice

Objective: The formyl peptide receptor-1 (FPR-1) has been reported to be implicated in the regulation of inflammatory disorders, while its role in cigarette smoke (CS)–induced airway inflammation has not been fully explained. In this study, we investigated the role of FPR-1 in CS-induced airway inflammation and the possible mechanism through gene knockout (KO) technology and transcriptional study.Methods: FPR-1 KO or wild-type C57BL/6 mice were exposed to mainstream CS to establish an airway inflammation model. Cell counts and pro-inflammatory cytokines were measured in bronchoalveolar lavage fluid (BALF). Lung tissues were collected for histological examination, polymerase chain reaction, Western blot, transcriptomic gene study, and related bioinformatics analysis.Results: CS exposure induced significant histological inflammatory changes, increased neutrophils, and pro-inflammatory cytokines in the BALF of wild-type mice, which were all attenuated by KO of FPR-1. The transcriptomic gene study showed a total of 198 up-regulated genes and 282 down-regulated genes in mouse lungs. Bioinformatics analysis including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested these differentiated expressed genes were significantly related to the immune, chemotaxis responses, and cross-talked with a complicated network of signaling pathways including NF-κB. Western blot validated that KO of FPR-1 inhibited CS-induced NF-κB activation.Conclusion: Knockout of FPR-1 significantly ameliorates CS-induced airway inflammation in mice, possibly via its related immune-chemotaxis responses and inhibition of NF-κB activation.