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Nearly 14% of disease-causing germline variants result from the disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing are classified as variants of uncertain significance. An analytic workflow-splice effect event resolver (SPEER)-was developed and validated to use mRNA sequencing to reveal significant deviations in splicing, pinpoint the DNA variants potentially involved, and measure the deleterious effects of the altered splicing on mRNA transcripts, providing evidence for assessing the pathogenicity of the variant. SPEER was used to analyze leukocyte RNA encoding 63 hereditary cancer syndrome-related genes in 20,317 patients. Among 3563 patients (17.5%) with at least one DNA variant predicted to affect splicing, 971 (4.8%) had altered splicing with a deleterious effect on the transcript, and 40 had altered splicing due to a DNA variant located outside of the reportable range of the test. Integrating SPEER results into the interpretation of variants allowed variants of uncertain significance to be reclassified as pathogenic or likely pathogenic in 0.4%, and as benign or likely benign in 5.9%, of the 20,317 patients. SPEER-based evidence was associated with a significantly greater effect on classifications of pathogenic or likely pathogenic and benign or likely benign in nonwhite versus non-Hispanic white patients, illustrating that evidence derived from mRNA splicing analysis may help to reduce ethnic/ancestral disparities in genetic testing., (Copyright © 2023 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Objectives: Non-invasive prenatal testing requires the presence of fetal DNA in maternal plasma. Understanding how preexamination conditions affect the integrity of cell-free DNA (cfDNA) and fetal fraction (FF) are a prerequisite for test implementation. Therefore, we examined the adjusted effect that EDTA and Streck tubes have on the cfDNA quantity and FF., Methods: A total of 3,568 maternal blood samples across Canada were collected in either EDTA, or Streck tubes, and processing metrics, maternal body mass index (BMI), gestational age and fetal karyotype and sex were recorded. Plasma samples were sequenced using two different sequencing platforms in separate laboratories. Sequencing data were processed with SeqFF to estimate FF. Linear regression and multivariate imputation by chained equations were used to estimate the adjusted effect of tube type on cfDNA and FF., Results: We found a positive association between cfDNA quantity and blood shipment time in EDTA tubes, which is significantly reduced with the use of Streck tubes. Furthermore, we show the storage of plasma at -80 °C is associated with a 4.4% annual relative decrease in cfDNA levels. FF was not associated with collection tube type when controlling for confounding variables. However, FF was positively associated with gestational age and trisomy 21, while negatively associated with BMI, male fetus, trisomy 18, Turners syndrome and triploidy., Conclusions: Preexamination, maternal and fetal variables are associated with cfDNA quantity and FF. The consideration of these variables in future studies may help to reduce the number of pregnant women with inconclusive tests as a result of low FF., (© 2021 Walter de Gruyter GmbH, Berlin/Boston.)

Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review., (Copyright © 2019 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)

The anticipated impacts of climate change on aquatic biota are difficult to evaluate because of potentially contrasting effects of temperature and hydrology on lake ecosystems, particularly those closed-basin lakes within semiarid regions. To address this shortfall, we quantified decade-scale changes in chemical and biological properties of 20 endorheic lakes in central North America in response to a pronounced transition from a drought to a pluvial period during the early 21st century. Lakes exhibited marked temporal changes in chemical characteristics and formed two discrete clusters corresponding to periods of substantially different effective moisture (as Palmer Drought Severity Index, PDSI). Discriminant function analysis (DFA) explained 90% of variability in fish assemblage composition and showed that fish communities were predicted best by environmental conditions during the arid interval (PDSI <-2). DFA also predicted that lakes could support more fish species during pluvial periods, but their occurrences may be limited by periodic stress due to recurrent droughts and physical barriers to colonization. Zooplankton taxonomic assemblages in fishless lakes were resilient to short-term changes in meteorological conditions, and did not vary between drought and deluge periods. Conversely, zooplankton taxa in fish-populated lakes decreased substantially in biomass during the wet interval, likely due to increased zooplanktivory by fish. The powerful effects of such climatic variability on hydrology and the strong subsequent links to water chemistry and biota indicate that future changes in global climate could result in significant restructuring of aquatic communities. Together these findings suggest that semiarid lakes undergoing temporary climate shifts provide a useful model system for anticipating the effects of global climate change on lake food webs., (© 2013 John Wiley & Sons Ltd.)

The authors studied the effect of lovastatin on five hypercholesterolemic CAPD patients with high risk of atherosclerotic cardiovascular disease. Patients took lovastatin 20 mg once daily for a mean period of 4.5 months. Pre- and post-treatment values of LDL and VLDL totals (325 mg/dl and 292 mg/dl, respectively) and of HDL (42 mg/dl and 43 mg/dl, respectively) had no significant statistical difference. Lack of significance may be due to low number of patients and short trial time. The study did demonstrate that lovastatin is well tolerated in CAPD patients.

The efficacy of once weekly subcutaneous erythropoietin (SC EPO) was evaluated by reviewing records of twelve continuous ambulatory peritoneal dialysis (CAPD) patients age 27-66 years after achieving a goal hematocrit (hct) greater than 30%. Patients had a mean hct of 22.8% (range: 19.1-29.5) and were placed on a thrice weekly SC EPO dose of 4000 international units (IU) (37-74 IU/KG, [mean of 57 IU/kg]) until a goal hct greater than 30% was achieved. This hct ranged from 30.8-37% (mean 33.2%) and was achieved in a mean of 11.5 weeks (range: 4.1-29 weeks). Patients were then maintained on the same SC EPO dose given only once weekly. 11/12 (92%) patients have maintained a mean hct of 34% (range: 29-38.4%) on once weekly SC EPO over a mean period of 14 weeks (range: 1.4-36 weeks). The mean serum ferritin was 484; only two patients required parenteral iron dextran therapy. One patient did not reach the goal hct due to poor compliance. There was no significant increase in blood pressure or in serum potassium level. We conclude that SC EPO is effective in treating anemia in these patients and can be given once weekly to maintain a hct greater than 30%.