Rare Genetic Abnormalities Research Articles

Prenatal Diagnosis and Postnatal Outcomes of Left Brachiocephalic Vein Abnormalities: Systematic Review.

Abnormalities of the left brachiocephalic vein (LBCVA) are rare and poorly studied prenatally. An association with congenital heart defects (CHD), extracardiac and genetic abnormalities was described. The aim of our study was to estimate the rate and summarize the available evidence concerning prenatal diagnosis, associated anomalies, and outcomes of these anomalies. A systematic literature review was carried out selecting studies reporting on prenatal diagnosis of LBCVA, including unpublished cases from our experience. Frequencies were pooled from cohort studies to calculate prenatal incidence. Pooled proportions were obtained from all the studies including rates of associated CHD, extracardiac or genetic abnormalities and neonatal outcomes. The search resulted in the selection of 16 studies with 311 cases of LBCVA, with an incidence of 0.4% from six cohort studies. CHD occurred in 235/311 (75.6%) fetuses: 23 (7.4%) were major in cases of double, retroesophageal or subaortic course and 212 (68.2%) were minor in cases of absence (always associated with a persistent left superior vena cava) or intrathymic course. Data on other associated outcomes were scarce showing rare extracardiac anomalies (3.5%), rare genetic abnormalities (RASopathies and microdeletions associated with the retroesophageal course), and neonatal outcomes favorable in most cases, particularly in intrathymic forms.

59. Constellation of rare genetic abnormalities associated with MECOM rearrangement in AML

AML with inv(3)(q21q26)/t(3;3) is a distinct WHO entity with poor prognosis. This particular aberration involves rearrangement of GATA2 enhancer (3q21) with MECOM (3q26) resulting in activation of the MECOM oncogene and concurrent inactivation of the GATA2 tumor suppressor. We present a 25-year-old male with a prior history of onset orthostatic hypotension, fatigue, leukopenia, and anemia. His bone marrow (BM) biopsy was hypercellular (30% blasts) with erythroid predominant trilineage hematopoiesis, thrombocytosis, and clinical diagnosis of AML.

TMOD-20. CASE REPORT: THE ODYSSEY TO THE RIGHT DIAGNOSIS. SURPRISING GLIOBLASTOMA MIMICS

Abstract A 57-year-old female presented at the emergency room with acute onset aphasia but unremarkable cCT (incl. angiography and perfusion). Suspecting an ischemic stroke, she received thrombolysis with quick recovery of aphasia. Afterwards, myoclonic jerks of the face and right arm occurred leading to anticonvulsant therapy. Follow-up cMRI surprisingly demonstrated swollen T2w-hyperintense and Gd-enhancing left limbic, temporal and frontal lobes. Suspected herpes-simplex-encephalitis was treated with aciclovir despite unremarkable CSF results (no pleocytosis, no BBB disruption, negative HSV-PCR) on day 2 and follow-up (day 5). Due to persisting cognitive deficits, autoimmune limbic encephalitis was suspected, and intravenous immunoglobulin therapy was added. Three weeks later, she experienced new neurological symptoms (weakness, blurred vision, vomiting, headache). Follow-up brain MRI demonstrated a massive increase of multifocal Gd-enhancing lesions. Partial resection revealed the diagnosis of an IDH-wildtype glioblastoma (GB). Next generation oncogene panel testing demonstrated a GOPC-ROS1 fusion which is rarely found in GB. Due to the gliomatosis-like infiltration of both hemispheres, radiotherapy was deemed to be too toxic. Instead, she received two cycles of lomustine in absence of a MGMT-promotor methylation. Two months later cMRI showed a symptomatic second multilocular progression. 2nd-line therapy with a ROS-inhibitor was rejected, whereupon she died five weeks later. Our case is in several aspects peculiar: It demonstrates that rare GB-mimics (i.e. HSV- and autoimmune limbic encephalitis) can only be ruled out in a fast manner by brain biopsy. Watchful waiting may neglect fast progression of GB leading to the inability to provide optimal treatment (i.e. radiotherapy). Thrombolysis is strictly contraindicated in primary brain tumors, but was unharmful in our case most probably to the early tumor stage without relevant neoangiogenesis. Rare genetic abnormalities like ROS1-fusions which are reported mostly in childhood glioblastoma may be present and serve as a therapeutic target also in adult GB.

Abstract 2260: Evaluating a rare t(X;14)(q28;q32) translocation reveals MTCP1 as a driving factor in chronic lymphocytic leukemia

Abstract Chronic lymphocytic leukemia (CLL) is the most prevalent adult leukemia in Western countries and is spelled by substantial genetic and clinical heterogeneity. During CLL transformation, loss or gain of genetic material appears to be a key determinant of disease phenotype and clinical outcome, with major chromosome aberrations observed in up to 80% of patients. Alternatively, balanced translocations, specifically those resulting in constitutive over-expression of various proto-oncogenes under the immunoglobulin heavy chain locus (IGH; 14q32), occur far less frequently. Despite their infrequence, molecular profiling of these rare rearrangements have revealed broad importance of un-recognized genes critical to the pathogenesis of CLL. Employing this strategy, we identified a young CLL patient with a previously undescribed t(X;14)(q28;q32) translocation, co-localization of the mature T cell proliferation 1 (MTCP1; Xq28) coding region with the IGH locus, triggering overexpression of MTCP1 in the CLL cells. Translocations involving MTCP1 are a driving factor in T-prolymphocytic leukemia; however, a role for MTCP1 in CLL has not been described. Inspired by this observation, we screened >1700 suspected CLL cases and evaluated gene expression data for further evidence of MCTP1 aberrations. This query identified seven additional Xq28 rearrangements, revealed MTCP1 mRNA was globally over-expressed in CLL cells compared to normal B-cells, and increased MTCP1 mRNA expression portends a poor response to chemoimmunotherapy. To establish a role for MTCP1 as an oncogene in B cell malignancies, we generated a mouse model with B cell-specific MTCP1 overexpression (Eµ-MTCP1). Longitudinal evaluation revealed a majority of Eµ-MTCP1 mice developed a lethal hematologic malignancy between 5-12 months of age, highlighted by the progressive emergence of clonally related CLL-like B lymphocytes (CD19+/CD5+ B cells) in the blood and accumulating in the spleen and lymph nodes. To support the use of the newly generated Eµ-MTCP1 mouse as a tool for pre-clinical evaluation of CLL therapeutics, we demonstrate that continuous ibrutinib administration in Eµ-MTCP1 mice was sufficient to delay the onset of the CLL-like disease and significantly prolonged survival. In summary, we report Xq28 translocations as rare genetic abnormalities in CLL, yet being one mechanism by which CLL cells amplify expression of MTCP1 compared to normal B cell subsets. Further, the Eµ-MTCP1 mouse model should be considered as an alternative tool for both biologic assessment of co-expressed genes and pre-clinical evaluation of novel CLL therapeutics. Lastly, relevant to all cancer types, successful application of a strategy pursuing the functional consequence of genes involved in rare translocations contributed to the understanding of this disease and identified a novel target for future therapeutic consideration. Citation Format: Janek S. Walker, Zachary A. Hing, Steven Sher, James Cronin, Katie Williams, Bonnie Harrington, Jordan N. Skinner, Casey B. Cempre, Charles T. Gregory, Max Yano, Larry P. Beaver, Brandi R. Walker, Jadwiga M. Labanowska, Nyla A. Heerema, Krzysztof Mrozek, Jennifer A. Woyach, Amy S. Ruppert, Amy Lehman, Hatice Gulcin Ozer, Vincenzo Coppola, John C. Byrd, James S. Blachly, Rosa Lapalombella. Evaluating a rare t(X;14)(q28;q32) translocation reveals MTCP1 as a driving factor in chronic lymphocytic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2260.

Insights from the genetic characterization of central precocious puberty associated with multiple anomalies.

Is there an (epi)genetic basis in patients with central precocious puberty (CPP) associated with multiple anomalies that unmasks underlying mechanisms or reveals novel genetic findings related to human pubertal control? In a group of 36 patients with CPP associated with multiple phenotypes, pathogenic or likely pathogenic (epi)genetic defects were identified in 12 (33%) patients, providing insights into the genetics of human pubertal control. A few studies have described patients with CPP associated with multiple anomalies, but without making inferences on causalities of CPP. Genetic-molecular studies of syndromic cases may reveal disease genes or mechanisms, as the presentation of such patients likely indicates a genetic disorder. This translational study was based on a genetic-molecular analysis, including genome-wide high throughput methodologies, for searching structural or sequence variants implicated in CPP and DNA methylation analysis of candidate regions. A cohort of 197 patients (188 girls) with CPP without structural brain lesions was submitted to a detailed clinical evaluation, allowing the selection of 36 unrelated patients (32 girls) with CPP associated with multiple anomalies. Pathogenic allelic variants of genes known to cause monogenic CPP (KISS1R, KISS1, MKRN3 and DLK1) had been excluded in the entire cohort (197 patients). All selected patients with CPP associated with multiple anomalies (n = 36) underwent methylation analysis of candidate regions and chromosomal microarray analysis. A subset (n = 9) underwent whole-exome sequencing, due to presenting familial CPP and/or severe congenital malformations and neurocognitive abnormalities. Among the 36 selected patients with CPP, the more prevalent associated anomalies were metabolic, growth and neurocognitive conditions. In 12 (33%) of them, rare genetic abnormalities were identified: six patients presented genetic defects in loci known to be involved with CPP (14q32.2 and 7q11.23), whereas the other six presented defects in candidate genes or regions. In detail, three patients presented hypomethylation of DLK1/MEG3:IG-DMR (14q32.2 disruption or Temple syndrome), resulting from epimutation (n = 1) or maternal uniparental disomy of chromosome 14 (n = 2). Seven patients presented pathogenic copy number variants: three with de novo 7q11.23 deletions (Williams-Beuren syndrome), three with inherited Xp22.33 deletions, and one with de novo 1p31.3 duplication. Exome sequencing revealed potential pathogenic variants in two patients: a sporadic female case with frameshift variants in TNRC6B and AREL1 and a familial male case with a missense substitution in UGT2B4 and a frameshift deletion in MKKS. The selection of patients was based on a retrospective clinical characterization, lacking a longitudinal inclusion of consecutive patients. In addition, future studies are needed, showing the long-term (mainly reproductive) outcomes in the included patients, as most of them are not in adult life yet. The results highlighted the relevance of an integrative clinical-genetic approach in the elucidation of mechanisms and factors involved in pubertal control. Chromosome 14q32.2 disruption indicated the loss of imprinting of DLK1 as a probable mechanism of CPP. Two other chromosomal regions (7q11.23 and Xp22.33) represented new candidate loci potentially involved in this disorder of pubertal timing. This work was supported by grant number 2018/03198-0 (to A.P.M.C.) and grant number 2013/08028-1 (to A.C.V.K) from the São Paulo Research Foundation (FAPESP), and grant number 403525/2016-0 (to A.C.L.) and grant number 302849/2015-7 (to A.C.L.) and grant number 141625/2016-3 (to A.C.V.K) from the National Council for Scientific and Technological Development (CNPq). The authors have nothing to disclose. N/A.

Clinical impact of parental consanguineous marriage in idiopathic nonobstructive azoospermia

ObjectiveTo determine the frequency of parental consanguineous marriages (PCMs) in men with diagnosed idiopathic nonobstructive azoospermia (INOA) and to compare clinical and pathological parameters between azoospermic men with and without PCM.DesignRetrospective.SettingA private clinic.Patient(s)Two hundred forty-six men with INOA. Patients were divided into two groups: group 1 with PCM and group 2 without PCM. Clinical parameters, surgical sperm retrieval rates, and pathological findings were compared between the groups.Intervention(s)Surgical sperm retrieval.Main Outcome Measure(s)PCM and clinical parameters.Result(s)Among the 246 patients with INOA, 81 had PCM. Men with PCM had lower follicle-stimulating hormone (13.7 vs. 21.9 mIU/mL), higher testosterone (3.8 vs. 3.4 ng/mL), and larger testes (14.1 vs. 11.8 mL). In parallel with the clinical findings, the most common pathological pattern in men with PCM was maturation arrest. However, there was no difference in surgical sperm retrieval rate between men with (23.4%) and without (32.1%) PCM.Conclusion(s)Our data showed that PCM was present for 33% of men with INOA. The clinical parameters of men with PCM and INOA were significantly different than those without PCM, primarily demonstrating maturation arrest in testicular pathology. Further genetic research in families who have infertile male siblings may elucidate underlying rare genetic abnormalities in spermatogenesis.

Molecular Mechanisms and Targeted Therapies Including Immunotherapy for Non-Small Cell Lung Cancer

Lung cancer is the leading cause of cancer death worldwide. Molecular targeted therapy has greatly advanced the field of treatment for non-small cell lung cancer (NSCLC), which accounts for the majority of lung cancers. Indeed, gefitinib, which was the first molecular targeted therapeutic agent, has actually doubled the survival time of NSCLC patients. Vigorous efforts of clinicians and researchers have revealed that lung cancer develops through the activating mutations of many driver genes including the epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), c-ros oncogene 1 (ROS1), v-Raf murine sarcoma viral oncogene homolog B (BRAF), and rearranged during transfection (RET) genes. Although ALK, ROS1, and RET are rare genetic abnormalities, corresponding tyrosine kinase inhibitors (TKIs) can exert dramatic therapeutic effects. In addition to anticancer drugs targeting driver genes, bevacizumab specifically binds to human vascular endothelial growth factor (VEGF) and blocks the VEGF signaling pathway. The VEGF signal blockade suppresses angiogenesis in tumor tissues and inhibits tumor growth. In this review, we also explore immunotherapy, which is a promising new NSCLC treatment approach. In general, antitumor immune responses are suppressed in cancer patients, and cancer cells escape from the immune surveillance mechanism. Immune checkpoint inhibitors (ICIs) are antibodies that target the primary escape mechanisms, immune checkpoints. Patients who respond to ICIs are reported to experience longlasting therapeutic effects. A wide range of clinical approaches, including combination therapy involving chemotherapy or radiation plus adjuvant therapy, are being developed.

Comparison of Tumor- and Bone Marrow-Derived Mesenchymal Stromal/Stem Cells from Patients with High-Grade Osteosarcoma

Osteosarcoma (OS) is suspected to originate from dysfunctional mesenchymal stromal/stem cells (MSC). We sought to identify OS-derived cells (OSDC) with potential cancer stem cell (CSC) properties by comparing OSDC to MSC derived from bone marrow of patients. This study included in vitro characterization with sphere forming assays, differentiation assays, cytogenetic analysis, and in vivo investigations of their tumorigenicity and tumor supportive capacities. Primary cell lines were isolated from nine high-grade OS samples. All primary cell lines demonstrated stromal cell characteristics. Compared to MSC, OSDC presented a higher ability to form sphere clones, indicating a potential CSC phenotype, and were more efficient at differentiation towards osteoblasts. None of the OSDC displayed the complex chromosome rearrangements typical of high grade OS and none of them induced tumors in immunodeficient mice. However, two OSDC demonstrated focused genomic abnormalities. Three out of seven, and six out of seven OSDC showed a supportive role on local tumor development, and on metastatic progression to the lungs, respectively, when co-injected with OS cells in nude mice. The observation of OS-associated stromal cells with rare genetic abnormalities and with the capacity to sustain tumor progression may have implications for future tumor treatments.

Molecular approaches identify a cryptic MECOM rearrangement in a child with a rapidly progressive myeloid neoplasm

Myeloid neoplasms are a heterogeneous group of hematologic disorders with divergent patterns of cell differentiation and proliferation, as well as divergent clinical courses. Rare recurrent genetic abnormalities related to this group of cancers are associated with poor outcomes. One such abnormality is the MECOM gene rearrangement that typically occurs in cases with chromosome 7 abnormalities. MECOM encodes a transcription factor that plays an essential role in cell proliferation and maintenance and also in epigenetic regulation. Aberrant expression of this gene is associated with reduced survival. Hence, its detailed characterization provides biological and clinical information relevant to the management of pediatric myeloid neoplasms. In this work, we describe a rare karyotype harboring three copies of MECOM with overexpression of the gene in a child with a very aggressive myeloid neoplasm. Cytogenetic studies defined the karyotype as 46,XX,der(7)t(3;7)(q26.2;q21.2). Array comparative genomic hybridization (aCGH) revealed a gain of 26.04 Mb in the 3q26.2-3qter region and a loss of 66.6 Mb in the 7q21.2-7qter region. RT-qPCR analysis detected elevated expression of the MECOM and CDK6 genes (458.5-fold and 35.2-fold, respectively). Overall, we show the importance of performing detailed molecular cytogenetic analysis of MECOM to enable appropriate management of high-risk pediatric myeloid neoplasms.

Screening for obstructive sleep apnea in children with syndromic cleft lip and/or palate

Craniofacial malformations including cleft lip and/or palate (CL/P) increase risk for obstructive sleep apnea (OSA). While 30% of CL/P occurs in the context of underlying genetic syndromes, few studies have investigated the prevalence of OSA in this high-risk group. This study aims to determine the incidence and risk factors of positive screening for OSA in this complex patient population. The Pediatric Sleep Questionnaire (PSQ) was prospectively administered to all patients cared for by the cleft lip and palate clinic at the Children's Hospital of Philadelphia between January 2011 and August 2013. The PSQ is a 22-item, validated screening tool for OSA with a sensitivity and specificity of 0.83 and 0.87 in detecting an apnea-hypopnea index (AHI) >5/hour in healthy children. The Fisher exact and Chi-square tests were used for purposes of comparison. 178 patients with syndromic CL/P completed the PSQ. Mean cohort age was 8.1 ± 4.4 years. Patients were predominately female (53.9%), Caucasian (78.1%), and had Veau Class II cleft (50.6%). Craniofacial syndromes included isolated Pierre Robin Sequence (PRS) (29.8%), 22q11.2 deletion syndrome (14.6%), Van der Woude syndrome (6.7%), and other rare genetic abnormalities (28.8%). The overall incidence of positive OSA screening was 32.0%. Males were at increased risk for positive OSA screening (P = 0.030), as were non-Caucasians (P = 0.044). Symptoms with the highest positive predictive value for OSA were "others comment on child appearing sleepy" (76.2%) and "stops breathing during the night" (75.0%). Notably, patients with 22q11.2 deletion syndrome were at highest risk for positive screens (50.0%, P = 0.042). Nearly a third of our patients with syndromic CL/P screened positively for OSA (32.0%), highlighting the importance of screening in this at-risk population. Future work will correlate screening results with polysomnograms to help validate these findings. Diagnostic, III.

Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone.

Craniosynostosis, the premature fusion of one or more skull sutures, occurs in approximately 1 in 2500 infants, with the majority of cases non-syndromic and of unknown etiology. Two common reasons proposed for premature suture fusion are abnormal compression forces on the skull and rare genetic abnormalities. Our goal was to evaluate whether different sub-classes of disease can be identified based on total gene expression profiles. RNA-Seq data were obtained from 31 human osteoblast cultures derived from bone biopsy samples collected between 2009 and 2011, representing 23 craniosynostosis fusions and 8 normal cranial bones or long bones. No differentiation between regions of the skull was detected, but variance component analysis of gene expression patterns nevertheless supports transcriptome-based classification of craniosynostosis. Cluster analysis showed 4 distinct groups of samples; 1 predominantly normal and 3 craniosynostosis subtypes. Similar constellations of sub-types were also observed upon re-analysis of a similar dataset of 199 calvarial osteoblast cultures. Annotation of gene function of differentially expressed transcripts strongly implicates physiological differences with respect to cell cycle and cell death, stromal cell differentiation, extracellular matrix (ECM) components, and ribosomal activity. Based on these results, we propose non-syndromic craniosynostosis cases can be classified by differences in their gene expression patterns and that these may provide targets for future clinical intervention.

A case of reticulate acropigmentation of kitamura: dowling degos disease overlap with unusual clinical manifestations.

Reticulate hyperpigmentary disorders are a group of rare genetic pigmentary abnormalities which includes reticulate acropigmentation of Kitamura (RAPK), Dowling-Degos disease (DD), reticulate acropigmentation of Dohi (RAPD), Haber's syndrome, and Galli-Galli disease. A 25-year-old male presented with asymptomatic dark-colored lesions on his hands and feet with light-colored skin lesions involving the trunk since three years. Dermatological examination revealed hyperpigmented macules in a reticulate pattern involving the dorsa of the hands and feet, front and sides of the neck, axillae, periorbital region, and groin. Multiple pits were present over both palms, with breaks in dermatoglyphics. He also had multiple nonacne facial scars predominantly on the nose and malar areas. The patient had overlapping features of RAPK and DDD. In addition, he also had hypopigmented macules and acneiform facial scars. Such an overlap of features of reticulate pigmentation has not been previously reported in the literature.

Modeling Myelodysplastic Syndromes In Mice By Altered Hoxa1 Spliceform Expression

Myelodysplastic syndromes (MDS) are a heterogeneous group of blood cell diseases with 30% of the patients developing acute myeloid leukemia (AML). The etiology of MDS is largely unknown and as a result there are no curative therapies. Mouse models that faithfully represent MDS are based on rare genetic abnormalities and currently represent only a very small subset of MDS patients.Using in silico analysis we have identified that homeobox A1 (HOXA1) mRNA is significantly upregulated in 50% of MDS patients (1.8-fold increase, n=183 MDS, 17 controls, P<0.05). Importantly, the upregulation was observed across all subsets of patients, including those with a normal karyotype. Both human HOXA1 and mouse Hoxa1 are expressed as two different spliceforms generated by alternative splicing within exon 1 of the wildtype Hoxa1 (WT-Hoxa1). These spliceforms encode a full-length (Hoxa1-FL) and a truncated form (Hoxa1-T), the latter lacking the homeobox domain. Given that mutations in splicing machinery have been identified in up to 85% of MDS patients we hypothesised that deregulated HOXA1 spliceforms may contribute to MDS.We identified that the Hoxa1 isoforms were differentially expressed in murine hematopoietic stem cells (HSCs) and progenitors. Retroviral overexpression of either WT-Hoxa1 (which generates both Hoxa1-FL and Hoxa1-T) or Hoxa1-T in murine bone marrow (BM) cells showed opposing effects on in vitro cell proliferation and colony forming cell (CFC) production respectively, suggesting that Hoxa1-T may negatively regulate Hoxa1-FL. We therefore generated a mutant Hoxa1 (MUT-Hoxa1), which expresses normal Hoxa1-FL but not Hoxa1-T, by oligomutagenesis at the splice site of Hoxa1-T. We transplanted recipient mice (n>28 per group) with bone marrow (BM) overexpressing either MUT-Hoxa1, WT-Hoxa1 or empty vector (MXIE) control.All recipients of MUT-Hoxa1 BM developed peripheral blood (PB) macrocytic anemia (mean ± SEM: Hb (g/L): MUT-Hoxa1: 126±2.9**; WT-Hoxa1: 134±2.7; MXIE: 135±1.4; **P<0.01 vs MXIE), without leukocytosis. Furthermore, thrombocytopenia was also observed in MUT-Hoxa1 and WT-Hoxa1 recipients (PB platelets (x 106/ml): MUT-Hoxa1: 738±88*; WT-Hoxa1: 777±57*; MXIE: 922 ± 37, *P<0.05 vs MXIE). Overexpression of MUT-Hoxa1 or WT-Hoxa1 was associated with significant apoptosis in BM erythroid cells (% apoptosis in GFP+ Ter119+ cells: MUT-Hoxa1: 20.7±4.9*; WT-Hoxa1: 25.3±5.2** MXIE: 13.6±2.5, *P<0.05, **P<0.01 vs MXIE). We also observed numerous dysplastic erythroid cells and micromegakaryocytes in the MUT-Hoxa1-overexpressing cells.Strikingly, 88% of recipients of MUT-Hoxa1 BM, but no WT-Hoxa1 recipients, developed AML with a median time of 10.5 months post-transplant, independent of retroviral integration site (Kaplan-Meier survival curve, P<0.05 vs MXIE). Therefore, overexpression of MUT-Hoxa1 or WT-Hoxa1 in BM cells results in clinical features of MDS, with MUT-Hoxa1 overexpression resulting in a more aggressive MDS that spontaneously progresses to AML.Analysis of BM from non-leukemic mice identified that MUT-Hoxa1 and WT-Hoxa1 recipients had significantly decreased HSC-containing lineage -ve, c-kit+, Sca-1+ (LKS+) cells (% of lin- GFP+ BM: MUT-Hoxa1 1.72 ± 0.28#; WT-Hoxa1: 2.08 ± 0.37#; MXIE: 5.09 ± 0.56%; #P<0.0001 vs MXIE, n>12). This was accompanied by increased progenitor cell-containing LKS- (% of lin- GFP+ BM: MUT-Hoxa1: 53.32 ± 5.65*; WT-Hoxa1: 47.42 ± 4.50; MXIE: 38.37 ± 4.13; *P<0.05 vs MXIE, n>12). Strikingly, granulocyte/monocyte progenitors were significantly reduced in the MUT-Hoxa1 LKS- cells, accompanied by a marked accumulation of megakaryocyte/erythroid progenitors (MEPs). We have identified deregulated gene pathways in the MUT-Hoxa1 BM MEPs by microarray analyses. We are currently testing drug candidates identified from these screens for their effects on BM obtained from our MUT-Hoxa1 and WT-Hoxa1 mouse models and MDS patients.Taken together, these results suggest that overexpression of Hoxa1-FL results in MDS, and that concurrently inhibiting splicing of Hoxa1-T (MUT-Hoxa1) forms a more aggressive MDS phenotype. Preliminary analysis of CD34+ BM cells from MDS patients reveal significant numbers of patients with elevated HOXA1-FL mRNA compared to lower or absent levels of HOXA1-T. Our MUT-Hoxa1 and WT-Hoxa1 mouse models will therefore be highly valuable in identifying better therapies for a significant subset of MDS patients. Disclosures:No relevant conflicts of interest to declare.

Cochlear implantation in 13q deletion syndrome

PurposeThe advent of cochlear implantation has been followed by an explosion in surgical and technological advances with subsequent alterations in the treatment of sensorineural hearing loss management. Many individuals with rare genetic abnormalities who once may have not been considered candidates for cochlear implantation are now benefiting from cochlear implantation. One of these unusual syndromes is the 13q deletion syndrome. The clinical features of 13q deletion syndrome, a rare chromosomal abnormality, were originally described in the early 1960s, though the literature currently lacks defined phenotypic abnormalities. Patients with 13q deletion syndrome present with varying degrees of cognitive and growth delay, craniofacial dysmorphisms, and congenital malformations. The etiology of the sensorineural hearing loss has not been elucidated, and genes associated with other syndromes which include sensorineural hearing loss have been proposed as the causative agents. We describe the unique clinical and surgical considerations for 13q deletion syndrome and review the considerations when deliberating on cochlear implantation in syndromic hearing loss. Materials and MethodsCase report. ResultsSuccessful cochlear implantation in a patient with 13q deletion syndrome. ConclusionMany patients with 13q deletion syndrome suffer from sensorineural hearing loss, and when appropriately selected may likely benefit from cochlear implantation. Many other syndromic patients following careful selection may also benefit from cochlear implantation and should not be excluded from consideration until appropriately evaluated.

Liquid biopsy-based assays to monitor residual disease in cancer.

11096 Background: One of the main challenges in cancer management is monitoring the non-organ-confined disease post metastasis. Recently analysis of circulating tumor nucleic acids has generated a new paradigm for monitoring the progression and molecular pathology of the residual disease through a non-invasive test. Methods: We have developed a new sequencing workflow, which increases the sensitivity and specificity of detecting and quantifying rare tumor-derived nucleic acids among healthy fragments by at least ten-fold. Unlike conventional sequencing library preparation protocols, the majority of extracted circulating DNA fragments are hybridized to sequencing flow cells with minimal modifications. The sequencing data are processed using our proprietary bioinformatics pipelines to search for rare genetic abnormalities within the heterogeneous circulating fragments. Results: To study the performance of our technology, we first evaluated its sensitivity in analytical samples. We spiked varying amounts of LNCaP cancer cell line gDNA into a background of normal gDNA and were able to successfully detect somatic mutations down to 0.1% sensitivity. Subsequently, we investigated the correlation of circulating DNA and tumor gDNA in human xenograft models in mice. In seven different mice models of two different human tumors, we found very strong correlation between somatic mutations detected in all pairs of tumor gDNA and mouse blood cfDNA. After preclinical studies, we initiated a pilot study on human samples across different cancer types. We found more than 90% correlation between tumor mutations in stage IIIb CRC cancer patients and the mutations detected in their circulation (n=7). In a pilot study in prostate cancer patients (n=3), we detected chromosomal abnormalities in multi locations in circulating DNA genome in both advanced and post-relapse stages of the disease. Conclusions: The present work indicates the potential of using circulating nucleic acids to facilitate the integration of real-time molecular pathology into routine cancer care. Our assay will be used to identify residual disease after neoadjuvant chemotherapy and/or surgery, but may also identify a subset of patients who may benefit from alternative therapies.

Abstract 123: Hormonal and genetic risk factors of soft tissue sarcoma in Sweden.

Abstract BACKGROUND AND METHODS. The aetiology of soft tissue sarcoma (STS) is largely unknown. Merely a handful putative risk factors such as certain genetic syndromes, a positive family history of cancer/STS, specific chemical exposures and exposure to ionizing radiation have been identified. With respect to the genetic aetiology, most STS patients do not have a clear family history of cancer. Only in rare cases heritable or germline genetic abnormalities associated with cancer predisposition syndromes that manifest as STS have been identified. We study STS and cancer morbidity in first degree relatives (FDR) together with hormone related factors in the Swedish population in the years between the years 1988 and 2009 using a population-based case-control design. RESULTS. Our study is the largest on this topic to date, including 855 cases and 2024 controls. It identified protective effects of being shorter than your peers at age eleven with a relative risk (RR) of 0.5 (0.4 - 0.7). Having used oral contraceptives (OC), RR 0.6 (0.4 - 1.0), and high parity, RR 0.6 (0.3 - 0.9) comparing three or more children to none, also appeared to reduce the risk for STS. The reduction increased further comparing use for eleven years or more to use for three years or less, RR 0.2 (0.1 - 0.6). Those with an FDR with STS and with those with an FDR with cancer had increased risks, RR 5.16 (1.03 - 25.9) and 1.31 (1.05 - 1.65), respectively. The latter varied with sex and histological subtype. In men, the familial risk was significant for malignant fibrous histiocytoma/undifferentiated pleomorphic sarcomas (MFH), RR 2.21 (1.23 - 3.97) and was higher in younger men (P=0.015). In women, there was a significant overall familial risk when stratifying on OC use, RR 1.55 (1.06 - 2.26). This risk seemed to derive from a group of rare and unclassified tumours present mainly in retroperitoneum and visceral organs, RR 6.19 (0.54 - 71.2). CONCLUSIONS. STS are a heterogeneous group of tumours with possibly very different aetiologies. However, the genesis of sarcoma seems to be influenced by both sex and growth hormones as well as genetic factors. Studies are on the way of the molecular genetic background of these associations. Citation Format: Philippe Wagner, Susanne Magnusson, Håkan Olsson. Hormonal and genetic risk factors of soft tissue sarcoma in Sweden. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 123. doi:10.1158/1538-7445.AM2013-123

A Case of Deep Vein thrombosis due to Protein C, Protein S Deficiency and Hyper-Homocystinaemia, A Rare Genetic Abnormalities

Approximately 80% of Deep Vein Thromboses (DVTs) are clinically asymptomatic, 20% of those that actually demonstrate signs and symptoms. DVT associated with protein C and protein S deficiencies are rare genetic abnormalities that cause thrombophilia and lead to thrombosis. Here we describe a case of 55-year old male who presented with recurrent DVT of left lower limb and eventually diagnosed as a case of DVT due to protein C and protein S deficiency with hyperhomocystinaemia.. The particular interest in this case report is that it is important to consider sceening for thrombophilia incase of DVT with uncertain aetiology. DOI: http://dx.doi.org/10.3329/bjmed.v22i1.13598 Bangladesh J Medicine 2011; 22: 27-29

Effect of chromosome constitution variations on the expression of Turner phenotype

Turner syndrome (TS) is a chronic disease related to haploinsufficiency of genes that are normally expressed in both X chromosomes in patients with female phenotype that is associated with a wide range of somatic malformations. We made detailed cytogenetic and clinical analysis of 65 patients with TS from the region of Recife, Brazil, to determine the effects of different chromosome constitutions on expression of the TS phenotype. Overall, patients with X-monosomy exhibited a tendency to have more severe phenotypes with higher morbidity, showing its importance in TS prognosis. Additionally, we found rare genetic and phenotypic abnormalities associated with this syndrome. To the best of our knowledge, this is the first case of 45,X,t(11;12)(q22;q22) described as a TS karyotype. Turner patients usually have normal intelligence; however, moderate to severe levels of mental retardation were found in 5 TS cases, which is considerate a very uncommon feature in this syndrome.

NOVEL Recurrent Genetic Aberrations in Pediatric AML: An AIEOP AML-2002 Study Group.

AbstractAbstract 2494 Introduction.Acute myeloid leukemia (AML) is an heterogeneous disease with known specific recurrent genetic aberrations. The continuous and increasing identification of new genetic mutations has permitted to identify new subgroups with different prognosis. In the present work we evaluated the incidence of rare genetic abnormalities in pediatric AML such as del(4)(q12)FIP1L1-PDGFRA, t(16;21)(p11;q22)FUS-ERG, t(8;16)(p11;p13)MOZ-CBP, t(11;17)(q23;q12–21)MLL-AF17, t(4;11)(q35;q23)MLL-ArgB2, t(5;11)(q35;p15.5)NUP98-NSD1, t(3;5)(q25;q34)NPM1-MLF1, and MLLPTD. Methods.We selected 306 patients with AML other than acute promyelocytic leukemia, negative for known recurrent genetic abnormalities involving MLL, CBF-beta and FLT3 genes. RNA was extracted from fresh bone marrow at diagnosis, and multiplex RT-PCR was employed. Sequencing by Sanger method was applied to all positive cases to characterize breakpoints of fusion. The Kaplan-Meier method was used for estimating the probability of event-free survival (EFS). Results.We identified one patient each positive for t(16;21)(p11;q22)FUS-ERG, t(11;17)(q23;q12–21)MLL-AF17, and t(4;11)(q35;q23)MLL-ArgB2, respectively, this suggesting that these rearrangements are rare in pediatric AML. 2/306 patients had del(4)(q12)FIP1L1/PDGFRA, and 4/306 the t(8;16)(p11;p13)MOZ-CBP; both these anomalies should be investigated in larger cohorts for definining their prognostic value. Interestingly 6/306 (2%) patients had the t(3;5)(q25;q34)NPM1-MLF1, 6/306 (2%) the MLLPTD, and 8/306 (2.6%) were found to carry the t(5;11)(q35;p15.5)NUP98-NSD1. Since the t(5;11) fusion was recently associated to FLT3ITD, we enlarged the screening to 42 de novo AML harbouring FLT3ITD mutation enrolled in the AIEOP-LAM 2002 protocol finding that 6 of them (14%) had the NUP98-NSD1 fusion gene. We documented a poor EFS for patients with t(5;11)NUP98-NDS1 (n=12) as compared to patients negative for molecular lesions and enrolled in the LAM 2002-AIEOP protocol (25% vs 53.1% at 3 years, p<0.01, n=154). We did not find differences in clinical or biological features of the isolated t(5;11) and t(5;11)+FLT3ITD positive patients (Table 1). We then evaluated the prognostic impact of the t(5,11) in the FLT3ITD+ cohort of AML, finding that the NUP98/NSD1 identifies a previously unrecognized subgroup of FLt3ITD patients with worse prognosis (EFS 33.3% vs 42.7 at 8y, p= 0.2). Furthermore, to analyze whether MLLPTD might also have a role in the progression to relapse, we screened 40 AML at relapse; however, we did not find the abnormality in this cohort. By contrast, 4 patients harbored at relapse the same MLLPTD found at diagnosis, suggesting the stability of this mutation. Conclusions.We provide evidence that NUP98-NSD1 may be considered a recurrent translocation in pediatric AML with poor prognosis. Being cryptic to conventional karyotyping, we confirmed the need of using molecular approaches for a proper identification of this anomaly. We also suggest that the NUP98-NSD1 fusion gene be considered for a better evaluation of the FLT3ITD+ patients. Disclosures:No relevant conflicts of interest to declare.

Regulating Genetic Tests: Who Owns the Data?

Direct-to-consumer (DTC) genetic testing is not as dangerous as A. L. McGuire et al. suggest (“Regulating direct-to-consumer personal genome testing,” Policy Forum, 8 October, p. [181][1]). The belief that genetic information will compel consumers to behave unreasonably is unfounded. Unlike the classical genetic tests that look for rare genetic abnormalities (such as Huntington's disease), genetic tests sold directly to consumers cannot diagnose a disease. They merely provide information about DNA sequence variations, or single-nucleotide polymorphisms (SNPs). Certain SNPs can be found more often among individuals with a particular disease or condition. For example, one particular combination of two SNPs in the APOE gene occurs 3 to 20 times more frequently in individuals with Alzheimer's ([ 1 ][2]). Consequently, a person with this particular combination of SNPs could be at a greater risk to develop Alzheimer's; the mere presence of these SNPs is not diagnostic. There is no reason to require government approval before allowing a person to see his or her own genetic information. After receiving results that indicate a health-related risk, a person will likely see a doctor to determine the next appropriate step. This action would be no different from a person's response to learning that he or she has increased blood pressure, cholesterol, or weight. Should DTC sales of weight scales be regulated too? The real question is what will happen if governments, big pharma, committees, and other faceless bodies gain control of our genetic information. College admissions based on genotype? Advertising geared to those with a particular SNP? This is a question for the ethicists to ponder. 1. [↵][3] 1. L. Bertram 2. et al ., Nat. Genet. 39, 17 (2007). [OpenUrl][4][CrossRef][5][PubMed][6][Web of Science][7] [1]: /lookup/doi/10.1126/science.1194006 [2]: #ref-1 [3]: #xref-ref-1-1 View reference 1 in text [4]: {openurl}?query=rft.jtitle%253DNature%2Bgenetics%26rft.stitle%253DNat%2BGenet%26rft.aulast%253DBertram%26rft.auinit1%253DL.%26rft.volume%253D39%26rft.issue%253D1%26rft.spage%253D17%26rft.epage%253D23%26rft.atitle%253DSystematic%2Bmeta-analyses%2Bof%2BAlzheimer%2Bdisease%2Bgenetic%2Bassociation%2Bstudies%253A%2Bthe%2BAlzGene%2Bdatabase.%26rft_id%253Dinfo%253Adoi%252F10.1038%252Fng1934%26rft_id%253Dinfo%253Apmid%252F17192785%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [5]: /lookup/external-ref?access_num=10.1038/ng1934&link_type=DOI [6]: /lookup/external-ref?access_num=17192785&link_type=MED&atom=%2Fsci%2F330%2F6011%2F1626.2.atom [7]: /lookup/external-ref?access_num=000243136500012&link_type=ISI