Holoprosencephaly (HPE), a common developmental forebrain malformation, is characterized by failure of the cerebrum to completely divide into left and right hemispheres. The etiology of HPE is heterogeneous and a number of environmental and genetic factors have been identified. Cytogenetically visible alterations occur in 25% to 45% of HPE patients and cytogenetic techniques have long been used to study copy number variants (CNVs) in this disorder. The karyotype approach initially demonstrated several recurrent chromosomal anomalies, which led to the identification of HPE-specific loci and, eventually, several major HPE genes. More recently, higher-resolution cytogenetic techniques such as subtelomeric multiplex ligation-dependent probe amplification and chromosomal microarray have been used to analyze chromosomal anomalies. By using chromosomal microarray, we sought to identify submicroscopic chromosomal deletions and duplications in patients with HPE. In an analysis of 222 individuals with HPE, a deletion or duplication was detected in 107 individuals. Of these 107 individuals, 23 (21%) had variants that were classified as pathogenic or likely pathogenic by board-certified medical geneticists. We identified multiple patients with deletions in established HPE loci as well as three patients with deletions encompassed by 6q12-q14.3, a CNV previously reported by Bendavid et al. In addition, we identified a new locus, 16p13.2 that warrants further investigation for HPE association. Incidentally, we also found a case of Potocki-Lupski syndrome, a case of Phelan-McDermid syndrome, and multiple cases of 22q11.2 deletion syndrome within our cohort. These data confirm the genetically heterogeneous nature of HPE, and also demonstrate clinical utility of chromosomal microarray in diagnosing patients affected by HPE.

Kaposiform lymphangiomatosis is a generalized lymphatic disorder complicated by consumptive coagulopathy and pericardial and pleural effusions. We present the case of a 13-year-old female adolescent given a diagnosis of a large pleural effusion by point-of-care thoracic ultrasonography, which led to further evaluation and diagnosis of this rare disorder. We review the use of point-of-care thoracic ultrasonography for the diagnosis of pleural effusion.

The CCAAT/Enhancer Binding Proteins (C/EBPs) are a family of leucine-zipper transcription factors that regulate physiological processes such as energy metabolism, inflammation, cell cycle, and the development and differentiation of several tissues including skin. Recently, a role for C/EBPs in tumor cell proliferation and differentiation has been proposed, but the incomplete characterization in the literature of multiple translational isoforms of these proteins has made interpretation of these roles difficult. Therefore, we have carefully reexamined C/EBP isoform expression in human non-melanoma skin cancers. C/EBPα, C/EBPβ, and C/EBPδ were analyzed histologically in squamous cell carcinomas (SCC). The individual isoforms of C/EBPα and C/EBPβ were examined by immunofluorescent digital imaging, western blotting and DNA binding activity (electrophoretic mobility shift analysis). Expression of all C/EBP family proteins was decreased in SCC tumors. Suppression was greatest for C/EBPα, less for C/EBPβ, and least for C/EBPδ. Western analyses confirmed that C/EBPα p42 and p30 isoforms were decreased. For C/EBPβ, only the abundant full-length isoform (C/EBPβ-1, LAP*, 55 kD) was reduced, whereas the smaller isoforms, C/EBPβ-2 (LAP, 48 kD) and C/EBPβ-3 (LIP, 20 kD), which are predominantly nuclear, were significantly increased in well- and moderately-differentiated SCC (up to 14-fold for C/EBPβ-3). These elevations correlated with increases in PCNA, a marker of proliferation. Although C/EBPβ displayed increased post-translational modifications in SCC, phosphorylation of C/EBPβ-1 (Thr 235) was not altered. C/EBP-specific DNA binding activity in nuclear and whole-cell extracts of cultured cells and tumors was predominantly attributable to C/EBPβ. In summary, two short C/EBPβ isoforms, C/EBPβ-2 and C/EBPβ-3, represent strong candidate markers for epithelial skin malignancy, due to their preferential expression in carcinoma versus normal skin, and their strong correlation with tumor proliferation.

American Journal of Medical Genetics Part AVolume 155, Issue 8 p. 2042-2043 Correspondence Patients with VACTERL association deserve careful scrutiny: Response to Jenetzky et al.†‡ Benjamin D. Solomon, Corresponding Author Benjamin D. Solomon solomonb@mail.nih.gov Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandNational Institutes of Health, MSC 3717, Building 35, Room 1B-207, Bethesda, MD 20892.Search for more papers by this authorManu S. Raam, Manu S. Raam Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorDaniel E. Pineda-Alvarez, Daniel E. Pineda-Alvarez Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorDerek A.T. Cummings, Derek A.T. Cummings Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MarylandSearch for more papers by this author Benjamin D. Solomon, Corresponding Author Benjamin D. Solomon solomonb@mail.nih.gov Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandNational Institutes of Health, MSC 3717, Building 35, Room 1B-207, Bethesda, MD 20892.Search for more papers by this authorManu S. Raam, Manu S. Raam Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorDaniel E. Pineda-Alvarez, Daniel E. Pineda-Alvarez Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MarylandSearch for more papers by this authorDerek A.T. Cummings, Derek A.T. Cummings Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MarylandSearch for more papers by this author First published: 07 July 2011 https://doi.org/10.1002/ajmg.a.33982 † This article is a US Government work and, as such, is in the public domain in the United States of America. ‡ How to Cite this Article: Solomon BD, Raam MS, Pineda-Alvarez DE, Cummings DAT. 2011. Patients with VACTERL association deserve careful scrutiny: Response to Jenetzky et al. Am J Med Genet Part A 155:2042–2043. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume155, Issue8August 2011Pages 2042-2043 RelatedInformation

The goal of this study was to describe a novel pattern of genitourinary (GU) anomalies in VACTERL association, which involves congenital anomalies affecting the vertebrae, anus, heart, trachea and esophagus, kidneys, and limbs. We collected clinical data on 105 patients diagnosed with VACTERL association and analyzed a subset of 89 patients who met more stringent inclusion criteria. Twenty-one percent of patients have GU anomalies, which are more severe (but not more frequent) in females. Anomalies were noted in patients without malformations affecting the renal, lower vertebral, or lower gastrointestinal systems. There should be a high index of suspicion for the presence of GU anomalies even in patients who do not have spatially similar malformations.

Context Holoprosencephaly affects 1 in 8,000 live births and is the most common structural anomaly of the developing forebrain, resulting in facial dysmorphism, neurologic impairment, and additional clinical sequelae. Given the increasing relative contribution of genetic diseases to perinatal morbidity and mortality in India, proper recognition and management of holoprosencephaly can improve care for a significant number of affected Indian children. Evidence Acquisition We used the PubMed database (search terms: “holoprosencephaly,” “HPE,” “holoprosencephaly India”) and cross-referenced articles regarding holoprosencephaly, using our research group’s extensive experience as a guide for identifying seminal papers in the field. Results Holoprosencephaly is classified into four types based on the nature of the brain malformations as seen on neuroimaging and/or pathologic examination, with typically recognizable craniofacial phenotypes. Despite the identification of several genetic loci and other etiologic agents involved in pathogenesis, additional causes are elusive. Moreover, satisfactory explanations for phenomena such as incomplete penetrance and variable expressivity are lacking. Conclusions For each patient, pediatricians should follow a diagnostic protocol including dysmorphology examination, complete family history and ascertainment of risk factors, and neuroimaging. Many medical issues, including hypothalamic dysfunction, endocrinologic dysfunction, motor impairment, respiratory issues, seizures, and hydrocephalus should be prioritized in management. Pediatricians should work with genetic specialists to identify syndromic forms and to perform cytogenetic investigation, molecular screening, and genetic counseling in order to fully characterize prognosis and recurrence risk.

VACTERL association involves the presence of specific congenital, multi-organ malformations that tend to co-occur. Clinical and research efforts typically center on pediatric patients, and there is a scarcity of information in the literature regarding VACTERL-related issues and outcomes in adulthood. We describe here 11 adults with features of VACTERL association ascertained through our research study on the condition. In our cohort of adult patients, approximately 25% of medically significant malformations that are component features of VACTERL association, including 40% of vertebral, 50% of cardiac, and 50% of renal anomalies, were not identified during childhood. Additionally, medical sequelae of many of the primary malformations identified in infancy or early childhood persist or are first reported in adulthood. These sequelae can involve challenging medical and surgical management in adulthood. As most adults with VACTERL association are not specifically followed for VACTERL-related issues, a more uniform diagnostic work-up and a low threshold for investigation of medical sequelae of the primary disorder may enhance the quality of clinical management in these patients.

Uncommon craniosynostosis syndromes, while individually less well characterized than more common conditions such as Apert, Crouzon, Pfeiffer, Muenke, and Saethre-Chotzen syndromes, comprise a significant proportion of craniosynostosis cases when considered in sum. Thirteen of these rare syndromes are covered here with respect to nosology, associated clinical characteristics, and molecular genetics. They were selected for discussion in this chapter due to recent molecular advances therein that can significantly enhance clinicians' ability to diagnose and counsel patients with these syndromes. The syndromes discussed here include Antley-Bixler syndrome, Baller-Gerold syndrome, Beare-Stevenson cutis gyrata syndrome, Bohring-Opitz syndrome, C (Opitz trigonocephaly) syndrome, Carpenter syndrome, Crouzon syndrome with acanthosis nigricans, Jackson-Weiss syndrome, Jacobsen syndrome, Loeys-Dietz syndrome type I, osteoglophonic dysplasia, P450 oxidoreductase deficiency, and Shprintzen-Goldberg syndrome. Copyright (C) 2011 S. Karger AG, Basel

VACTERL association, a relatively common condition with an incidence of approximately 1 in 20,000-35,000 births, is a non-randomassociation of birth defects that includes vertebral defects (V), anal atresia (A), cardiac defects (C), tracheo-esophageal fistula (TE), renal anomalies (R) and limb malformations (L). Although the etiology is unknown in the majority of patients, there is evidence that it is causally heterogeneous. Several studies have shown evidence for inheritance in VACTERL, implying a role for genetic loci. Recently, patients with component features of VACTERL and a lethal developmental pulmonary disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV), were found to harbor deletions or mutations affecting FOXF1 and the FOX gene cluster on chromosome 16q24. We investigated this gene through direct sequencing and high-density SNP microarray in 12 patients with VACTERL association but without ACD/MPV. Our mutational analysis of FOXF1 showed normal sequences and no genomic imbalances affecting the FOX gene cluster on chromosome 16q24 in the studied patients. Possible explanations for these results include the etiologic and clinical heterogeneity of VACTERL association, the possibility that mutations affecting this gene may occur only in more severely affected individuals, and insufficient study sample size. Published by Elsevier Masson SAS.

BACKGROUND Tracheo-esophageal fistula (TEF) with/or without esophageal atresia (EA) is a common congenital malformation that is often accompanied by other anomalies. The causes of this condition are thought to be heterogeneous but are overall not well understood. CASE REPORT We identified a patient with a TEF/EA, as well as cardiac and genitourinary anomalies, who was found to have a 0.7 Mb de novo deletion of chromosome 20q13.33. One gene within the deleted interval, GTPBP5, is of particular interest as a candidate gene. CONCLUSIONS GTPBP5 bears further study as a cause of TEF/EA accompanied by other malformations. Birth Defects Research (Part A) 2011. © 2011 Wiley-Liss, Inc.

American Journal of Medical Genetics Part AVolume 152A, Issue 9 p. fm i-fm v Table of ContentsFree Access Table of Contents, Volume 152A, Number 9, September 2010 First published: 20 August 2010 https://doi.org/10.1002/ajmg.a.33697AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Volume152A, Issue9September 2010Pages fm i-fm v RelatedInformation

VACTERL association is a relatively common condition, though the causes remain poorly understood. We present data on 79 patients diagnosed with VACTERL association and perform statistical analysis on a selected subset of 60 patients with at least three component features, and who, after review, did not meet criteria for a likely alternate diagnosis. Considered individually, no two component features are significantly associated, but several multivariate statistical techniques suggest novel patterns of the co-occurrence of component features, and latent class cluster analysis demonstrates the presence of five major subgroups of patients. These findings have implications for both our understanding of VACTERL association and for the approach to research involving this condition.

VACTERL/VATER association is typically a sporadic disorder. We present data on inheritance in 78 probands with VACTERL association, and show that 9% of probands have a primary relative with at least one component feature of VACTERL association. The prevalence of component features in first-degree relatives is significantly higher than expected in the general population, which has implications for counseling of affected families and for research into possible etiologies.

Holoprosencephaly (HPE) and craniosynostosis are separate conditions that have occasionally been observed to occur simultaneously in the same patient. Here, we compile patients with both conditions who have been documented in the literature thus far; moreover, we report on two additional siblings who have not been previously described. We also compare the clinical features of these patients and discuss the previously hypothesized possibility of an independent association including both HPE and craniosynostosis. Published 2010 Wiley‐Liss, Inc.

Proteases are important biomarkers for many biological processes and are popular targets for therapeutics investigations. A protease can be detected by monitoring changes in the paramagnetic chemical exchange saturation transfer (PARACEST) effect of a MRI contrast agent that serves as a substrate for the protease. To translate this type of responsive PARACEST MRI contrast agent to in vivo applications, the sensitivity, timing, specificity and validation of the response of the agent must be evaluated. This report demonstrates that PARACEST MRI contrast agents can be used to detect nanomolar concentrations of proteases, can be designed to preferentially detect the protease caspase-3 relative to caspase-8, and can be detected within the 15 min time frame of typical MRI studies. The response can be validated using an unresponsive PARACEST MRI contrast agent as a control. A survey of the MEROPS database shows that this approach may also be applied to detect other proteases, and therefore may represent a new platform technology for studies of the proteasome.

The mutations in APP, PSEN1, and PSEN2 that cause early onset familial AD alter Aβ processing in a way that fosters Aβ aggregation. Risk for late–onset AD (LOAD) is, therefore, likely to be associated with common variants in these and other genes involved in Aβ processing. To evaluate this possibility, we analyzed putative functional variants in three Aβ processing genes (APP, PSEN1, BACE1). Putative functional variants in conserved regions (100 bp window, >70% match human vs. mouse) of APP, PS1, and BACE1 were mined from publicly available databases, genotyped, and tested for association in large case/control series. Previous meta–analysis of PSEN1 SNP rs16592 (Alzgene at Alzforum.org) in many Caucasian case/control series (3248 AD, 2767 Control) showed significant association with LOAD (p=0.03). This SNP, which is located in a conserved region of intron 8, had the same OR when it was genotyped in our combined Caucasian case/control series (1231 AD, 1326 CON). This association was not significant in our series alone (p=0.17), but inclusion of our series in the meta–analysis improved significance (p=0.008) supporting the validity of the previously reported association. None of six additional SNPs in conserved regions of PSEN1 was significant at the 0.05 level, but two showed more significant association than rs16592. Analysis of 7 SNPs in conserved regions of BACE1 showed that four associated at p<0.25. In many genes all common variants are on a single haplotype block where they form a small number of haplotypes that pair to form relatively few genotypes that can be analyzed individually. We analyzed 39 SNPs in conserved regions of APP, and analysis by HaploView (solid spline of LD) showed them to be distributed over 7 haplotype blocks creating a large number of complex APP genotypes. Our preliminary analysis suggests that these complex APP genotypes may substantially influence risk for AD. Collectively our findings in these three LOAD candidate genes suggest that many LOAD genes may have modest effects that will be difficult to demonstrate convincingly until large case/control series with sufficient power to show replicable association are assembled as we are now endeavoring to do.