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Lockwood W.W.,British Columbia Cancer Research Center | Stack D.,National Childrens Research Center | Morris T.,National Center for Medical Genetics | O'Keane C.,Materials Misericordiae University Hospital | And 6 more authors.
Journal of Molecular Diagnostics | Year: 2011

Osteosarcoma is a genetically complex malignancy, predominantly afflicting the adolescent population and associated still with relatively poor long-term outcomes. Although there has been some improvement in the understanding of osteosarcoma biology, this has not yet translated particularly well into therapeutic advances. By using a whole-genome tiling path array for comparative genomic hybridization analysis, we sought to evaluate DNA copy number changes in 22 osteosarcoma tumor samples. Regions of most frequent gains or losses generated by Genomic Identification of Significant Targets in Cancer analysis were evaluated for genes of interest. Correlation of the copy number data with preexisting expression data for these genes yielded not only targets known to be important in osteosarcoma but also novel targets, notably cyclin E1. Fluorescence in situ hybridization and immunohistochemical analysis confirmed the findings. Overexpression of cyclin E1 has potential prognostic and therapeutic implications that are discussed herein.


PubMed | Biochimie Metabolique Hopital Bichat Claude Bernard, University of Amsterdam, University Hospitals Leuven, Kinderklinik Villingen and 18 more.
Type: Journal Article | Journal: Journal of inherited metabolic disease | Year: 2016

Alpha-1,3-glucosyltransferase congenital disorder of glycosylation (ALG6-CDG) is a congenital disorder of glycosylation. The original patients were described with hypotonia, developmental disability, epilepsy, and increased bleeding tendency.Based on Euroglycan database registration, we approached referring clinicians and collected comprehensive data on 41 patients.We found hypotonia and developmental delay in all ALG6-CDG patients and epilepsy, ataxia, proximal muscle weakness, and, in the majority of cases, failure to thrive. Nine patients developed intractable seizures. Coagulation anomalies were present in <50% of cases, without spontaneous bleedings. Facial dysmorphism was rare, but seven patients showed missing phalanges and brachydactyly. Cyclic behavioral change, with autistic features and depressive episodes, was one of the most significant complaints. Eleven children died before the age of 4years due to protein losing enteropathy (PLE), sepsis, or seizures. The oldest patient was a 40year-old Dutch woman. The most common pathogenic protein alterations were p.A333V and p.I299Del, without any clear genotype-phenotype correlation.ALG6-CDG has been now described in 89 patients, making it the second most common type of CDG. It has a recognizable phenotype and a primary neurologic presentation.


Bryce R.M.,King's College London | Salas A.,Central University of Venezuela | Acosta D.,Pedro Henríquez Ureña National University | Jimenez-Velazquez I.Z.,University of Puerto Rico at San Juan | And 7 more authors.
British Journal of Haematology | Year: 2013

Anaemia among older people is increasingly recognized as a matter of public health concern. Data from low- and middle-income countries are sparse. We surveyed 10915 people aged 65 years and over (8423 with blood tests) in catchment areas in Cuba, Dominican Republic, Puerto Rico, Venezuela and Mexico, to assess prevalence and correlates of anaemia and impact on disability. Prevalence varied widely between sites, from 6·4% in rural Mexico to 9·2% in urban Mexico, 9·8% in Venezuela, 19·2% in Cuba, 32·1% in Puerto Rico and 37·3% in Dominican Republic. Prevalence was higher in men and increased with age, but sociodemographic composition did not account for prevalence differences between sites. Standardized morbidity ratios indicated a much higher prevalence in Cuba (173), Puerto Rico (280) and Dominican Republic (332) compared with USA National Health and National Examination Surveys. Anaemia was associated with undernutrition, physical impairments, and serum creatinine. There was an association with greater African admixture in Dominican Republic but not in Cuba. African admixture is therefore unlikely to fully explain the high prevalence in the Caribbean islands, which may also arise from environmental, possibly dietary factors. Given an important independent contribution of anaemia to disability, more research is needed to identify preventable and treatable causes. © 2012 Blackwell Publishing Ltd.


Campos D.,National Center for Medical Genetics | Monaga M.,National Center for Medical Genetics
Metabolic Brain Disease | Year: 2012

Mucopolysaccharidosis type I is one of the most frequent lysosomal storage diseases. It has a high morbidity and mortality, causing in many cases severe neurological and somatic damage in the first years of life. Although the clinical phenotypes have been described for decades, and the enzymatic deficiency and many of the mutations that cause this disease are well known, the underlying pathophysiological mechanisms that lead to its development are not completely understood. In this review we describe and discuss the different pathogenic mechanisms currently proposed for this disease regarding its neurological damage. Deficiency in the lysosomal degradation of heparan sulfate and dermatan sulfate, as well as its primary accumulation, may disrupt a variety of physiological and biochemical processes: the intracellular and extracellular homeostasis of these macromolecules, the pathways related to gangliosides metabolism, mechanisms related to the activation of inflammation, receptor-mediated signaling, oxidative stress and permeability of the lysosomal membrane, as well as alterations in intracellular ionic homeostasis and the endosomal pathway. Many of the pathogenic mechanisms proposed for mucopolysaccharidosis type I are also present in other lysosomal storage diseases with neurological implications. Results from the use of methods that allow the analysis of multiple genes and proteins, in both patients and animal models, will shed light on the role of each of these mechanisms and their combination in the development of different phenotypes due to the same deficiency. © Springer Science+Business Media, LLC 2012.


Dobson M.G.,National Center for Medical Genetics | Dobson M.G.,Our Ladys Childrens Hospital | Darlow J.M.,National Center for Medical Genetics | Darlow J.M.,Our Ladys Childrens Hospital | And 10 more authors.
Kidney International | Year: 2013

ROBO2, the receptor of SLIT2, is one of many genes/proteins that regulate the outgrowth of the ureteric bud, which is the first step in the development of the metanephric urinary system. Non-synonymous variants in ROBO2 have been found in a small proportion of patients with primary vesicoureteric reflux (VUR) in various countries. Here we sequenced 1 kb of promoter and all exons of ROBO2b with intronic margins in 227 index cases with primary VUR in an Irish population and found 55 variants, of which 20 were novel. We assessed the variants for evolutionary conservation and investigated novel and uncommon known conserved variants in 23 further index cases and family members of all index cases (to check for segregation with VUR), and then in healthy controls if we found segregation of the variants with VUR. Apart from one non-synonymous variant that was previously found in controls, we did not find any of the six other previously reported non-synonymous variants, but found four new non-synonymous variants. Of those, only two segregated with the disorder (p.Pro522Thr and p.Val799Ile). The former was not present in any of 592 healthy controls; the latter was present in one control. There are now 35 reported non-synonymous coding variants of ROBO2b. The predicted pathogenicity of those that have so far been found exclusively in VUR patients does not differ from that predicted for those variants also found in controls. Thus, our finding does not completely rule out that some variants may be the sole cause of VUR, but it is clear from the overall frequency that most of them cannot be. However, it is possible that some of these variants may cause VUR in combination with a mutation in another gene. © 2013 International Society of Nephrology.


Teruel B.M.,National Center for Medical Genetics | Rodriguez J.J.L.,Higher Institute of Medical science of Havana | McKeigue P.,University of Edinburgh | Mesa T.C.,National Center for Medical Genetics | And 6 more authors.
BMC Medical Genetics | Year: 2011

Background: The prevalence and incidence of dementia are low in Nigeria, but high among African-Americans. In these populations there is a high frequency of the risk-conferring APOE-e4 allele, but the risk ratio is less than in Europeans. In an admixed population of older Cubans we explored the effects of ethnic identity and genetic admixture on APOE genotype, its association with dementia, and dementia prevalence.Methods: A cross-sectional catchment area survey of 2928 residents aged 65 and over, with a nested case-control study of individual admixture. Dementia diagnosis was established using 10/66 Dementia and DSM-IV criteria. APOE genotype was determined in 2520 participants, and genetic admixture in 235 dementia cases and 349 controls.Results: Mean African admixture proportions were 5.8% for 'white', 28.6% for 'mixed' and 49.6% for 'black' ethnic identities. All three groups were substantially admixed with considerable overlap. African admixture was linearly related to number of APOE-e4 alleles. One or more APOE-e4 alleles was associated with dementia in 'white' and 'black' but not 'mixed' groups but neither this, nor the interaction between APOE-e4 and African admixture (PR 0.52, 95% CI 0.13-2.08) were statistically significant. Neither ethnic identity nor African admixture was associated with dementia prevalence when assessed separately. However, considering their joint effects African versus European admixture was independently associated with a higher prevalence, and 'mixed' or 'black' identity with a lower prevalence of dementia.Conclusions: APOE genotype is strongly associated with ancestry. Larger studies are needed to confirm whether the concentration of the high-risk allele in those with African ancestry is offset by an attenuation of its effect. Counter to our hypothesis, African admixture may be associated with higher risk of dementia. Although strongly correlated, effects of admixture and ethnic identity should be distinguished when assessing genetic and environmental contributions to disease risk in mixed ancestry populations. © 2011 Teruel et al; licensee BioMed Central Ltd.


Wentzel C.,Uppsala University | Lynch S.A.,National Center for Medical Genetics | Stattin E.-L.,Umeå University | Sharkey F.H.,Western General Hospital | And 2 more authors.
Molecular Syndromology | Year: 2010

Background: Interstitial deletions of the long arm of chromosome 6 have been described in several patients with obesity and a Prader-Willi-like phenotype. Haploinsufficiency of the SIM1 gene located at 6q16.3 is suggested as being responsible for the regulation of body weight. Here we report on 2 patients with interstitial deletions at 6q14.1-q15 presenting with obesity and symptoms strikingly similar to those reported for deletions involving the SIM1 gene despite not having a deletion of this gene. Methods: Array comparative genomic hybridisation was used to diagnose 2 children with obesity and developmental delay, revealing 2 interstitial deletions at 6q14.1-q15 of 8.73 and 4.50 Mb, respectively, and a region of overlap of 4.2-Mb. Results: The similar phenotype in the 2 patients was most likely due to a 4.2-Mb common microdeletion at 6q14.1-q15. Another patient has previously been described with an overlapping deletion. The 3 patients share several features, such as developmental delay, obesity, hernia, rounded face with full cheeks, epicanthal folds, short palpebral fissures, bulbous nose, large ears, and syndactyly between toes II and III. Conclusions: Together with a previously reported patient, our study suggests that the detected deletions may represent a novel clinically recognisable microdeletion syndrome caused by haploinsufficiency of dosage-sensitive genes in the 6q14.1-q15 region. Copyright © 2010 S. Karger AG.


Lynn M.,National Childrens Research Center | Wang Y.,Harvard University | Slater J.,Harvard University | Shah N.,University College Dublin | And 8 more authors.
Diagnostic Molecular Pathology | Year: 2013

Ewing sarcoma family tumors are aggressive sarcomas of childhood and adolescence with continuing poor outcomes. Decades of research on the characteristics of the often solitaryknown oncogenic-genomic aberration in Ewing sarcoma family tumors, namely a TET-ETS fusion, have provided little advancement in the understanding of the molecular pathogenesis of Ewing sarcoma or treatment thereof. In this study, the highresolution single-nucleotide polymorphism technology was used to identify additional/secondary copy-number alterations (CNAs) in Ewing sarcoma that might elucidate the aggressive biology of this sarcoma. We compared paired constitutional and tumor DNA samples. Commonly known genomic alterations including gain of 1q and chromosome 8 were the most frequently detected changes in this study. In addition, deletions and loss of heterozygosity were identified in 10q, 11p, and 17p. Furthermore, tumor-specific CNAs were identified not only in genes previously known to be of interest, including CDKN2A, but also in genes not previously associated with Ewing sarcoma, including SOX6 and PTEN. Selected array-based findings were confirmed by fluorescence in situ hybridization, immunohistochemical studies, or sequencing. The results highlight an unexpected level of cytogenetic complexity associated with several of the samples, 2 of which contained TP53 mutations. In summary, our high-resolution genome-wide copy-number data identify several novel CNAs associated with Ewing sarcoma, which are promising targets for novel therapeutic strategies in this aggressive sarcoma. Copyright © 2013 by Lippincott Williams & Wilkins.


Aloraifi F.,Trinity College Dublin | Boland M.R.,St Vincents University Hospital | Green A.J.,National Center for Medical Genetics | Geraghty J.G.,St Vincents University Hospital
Surgical Oncology | Year: 2015

Breast cancer is the leading cause of cancer deaths in females worldwide occurring in both hereditary and sporadic forms. Women with inherited pathogenic mutations in the BRCA1 or BRCA2 genes have up to an 85% risk of developing breast cancer in their lifetimes. These patients are candidates for risk-reduction measures such as intensive radiological screening, prophylactic surgery or chemoprevention. However, only about 20% of familial breast cancer cases are attributed to mutations in BRCA1 and BRCA2, while a further 5-10% are attributed to mutations in other rare susceptibility genes such as TP53, STK11, PTEN, ATM and CHEK2. A multitude of genome wide association studies (GWAS) have been conducted confirming low-risk common variants associated with breast cancer in excess of 90 loci, which may contribute to a further 23% of the heritability. We currently find ourselves in "the next generation", with technologies offering deep sequencing at a fraction of the cost. Starting off primarily in a research setting, multi-gene panel testing is now utilized in the clinic to sequence multiple predisposing genes simultaneously (otherwise known as multi-gene panel testing). In this review, we focus on the hereditary breast cancer discoveries, techniques and the challenges we face in this complex disease, especially in the light of the vast amount of data we now have at hand. It has been 20 years since the first breast cancer susceptibility gene has been discovered and there has been substantial progress in unraveling the genetic component of the disease. However, hereditary breast cancer remains a challenging topic subject to common debate. © 2015 Elsevier Ltd. All rights reserved.


PubMed | University College Dublin, National Center for Medical Genetics and Trinity College Dublin
Type: Journal Article | Journal: European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology | Year: 2015

Women with inherited pathogenic mutations in the BRCA1 or BRCA2 genes have up to an 85% risk of developing breast cancer in their lifetime. However, only about 20% of familial breast cancer is attributed to mutations in BRCA1 and BRCA2, while a further 5-10% are attributed to mutations in other rare susceptibility genes such as TP53, STK11, PTEN, ATM and CHEK2. Despite extensive efforts to explain the missing heritability of this disease, the majority of familial clustering in breast cancer remains largely unexplained. We aim to analyze the pathology of familial cases of which no pathogenic mutation is yet identified.We compared the pathological phenotype of BRCA1/BRCA2 negative familial breast cancer (BRCAx) to BRCA1-positive, BRCA2-positive and sporadic cases without a family history. Age-adjusted analysis is summarized in odds ratios and confidence intervals for tumor type, grade, lymph node, ER and HER2 status.We found non-familial cases to be more likely to be ER positive (P=0.041) as compared with BRCAx tumors. More cases of lobular carcinoma were found with BRCAx as compared to BRCA1 tumors (P=0.05). After multivariate logistic regression analysis, BRCAx tumors are more likely ER positive (P=0.001) and HER2 positive (P=0.047) in comparison to BRCA1. Conversely, BRCAx cases are less likely to be ER positive (P=0.02) but more likely to be HER2 positive (P=0.021) as compared with BRCA2 tumors.Our findings suggest that BRCA1, BRCA2 and BRCAx tumors differ in phenotype from non-familial and familial BRCA1-positive and BRCA2-positive tumors. Further studies will need to be performed in this important population in order to develop strategies for early detection and prevention.

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