Purpose Copy number variants (CNVs) have emerged as a major cause of human disease such as autism and intellectual disabilities. Because CNVs are common in normal individuals, determining the functional and clinical significance of rare CNVs in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis (CMA) as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain large CNV datasets generated through routine patient care. Methods A consortium of diagnostic laboratories was established [the International Standards for Cytogenomic Arrays (ISCA) consortium] to share CNV and phenotypic data in a central, public database. We present the largest CNV case-control study to date comprising 15,749 ISCA cases and 10,118 published controls, focusing our initial analysis on recurrent deletions and duplications involving 14 CNV regions. Results Compared to controls, fourteen deletions, and seven duplications were significantly overrepresented in cases, providing a clinical diagnosis as pathogenic. Conclusion Given the rapid expansion of clinical CMA testing, very large datasets will be available to determine the functional significance of increasingly rare CNVs. This data will provide an evidenced-based guide to clinicians across many disciplines involved in the diagnosis, management, and care of these patients and their families.

Germline mutations are the source of evolution and contribute substantially to many health-related processes. Here we use whole-genome deep sequencing data from 693 parents–offspring trios to examine the de novo point mutations (DNMs) in the offspring. Our estimate for the mutation rate per base pair per generation is 1.05 × 10−8, well within the range of previous studies. We show that maternal age has a small but significant correlation with the total number of DNMs in the offspring after controlling for paternal age (0.51 additional mutations per year, 95% CI: 0.29, 0.73), which was not detectable in the smaller and younger parental cohorts of earlier studies. Furthermore, while the total number of DNMs increases at a constant rate for paternal age, the contribution from the mother increases at an accelerated rate with age.These observations have implications related to the incidence of de novo mutations relating to maternal age.

Helicobacter pylori infection induces innate immune responses in macrophages, contributing to mucosal inflammation and damage. Macrophage apoptosis is important in the pathogenesis of mucosal infections but has not been studied with H. pylori. NO derived from inducible NO synthase (iNOS) can activate macrophage apoptosis. Arginase competes with iNOS by converting l-arginine to l-ornithine. Since we reported that H. pylori induces iNOS in macrophages, we now determined whether this bacterium induces arginase and the effect of this activation on apoptosis. NF-κB-dependent induction of arginase II, but not arginase I, was observed in RAW 264.7 macrophages cocultured with H. pylori. The time course of apoptosis matched those of both arginase and iNOS activities. Surprisingly, apoptosis was blocked by the arginase inhibitors Nω-hydroxy-l-arginine or Nω-hydroxy-nor-l-arginine, but not by the iNOS inhibitor N-iminoethyl-l-lysine. These findings were confirmed in peritoneal macrophages from iNOS-deficient mice and were not dependent on bacterial-macrophage contact. Ornithine decarboxylase (ODC), which metabolizes l-ornithine to polyamines, was also induced in H. pylori-stimulated macrophages. Apoptosis was abolished by inhibition of ODC and was restored by the polyamines spermidine and spermine. We also demonstrate that arginase II expression is up-regulated in both murine and human H. pylori gastritis tissues, indicating the likely in vivo relevance of our findings. Therefore, we describe arginase- and ODC-dependent macrophage apoptosis, which implicates polyamines in the pathophysiology of H. pylori infection.

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