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Ligation-dependent Probe Amplification (ligation-dependent + probe_amplification)
Kinds of Ligation-dependent Probe Amplification Selected AbstractsAnalysis of RET, ZEB2, EDN3 and GDNF Genomic Rearrangements in Central Congenital Hyperventilation Syndrome Patients by Multiplex Ligation-dependent Probe AmplificationANNALS OF HUMAN GENETICS, Issue 4 2010Alexandre Serra Summary Central congenital hypoventilation syndrome (CCHS) is an autonomous control disease producing hypoventilation, high PaCO2, and low PaO2 during quiet sleep. The main gene variants detected in CCHS are mutations in the PHOX2b gene in up to 97% of isolated cases. However, CCHS is sometimes associated with autonomic diseases such as Hirschsprung disease (HSCR). Since genomic rearrangements in particularly sensitive areas of the RET protooncogene and/or associated genes may account for the CCHS/HSCR phenotype in patients without other detectable RET variants, the aim of the present study was to identify rearrangements in the coding sequence of RET as well as in three HSCR-associated genes (ZEB2, EDN3 and GDNF) in CCHS/HSCR patients by using Multiplex Ligation-dependent Probe Amplification (MLPA). We have screened 27 CCHS and 11 CCHS/HSCR patients for genomic rearrangements in RET, ZEB2, EDN3 and GDNF and did not identify any deletion or amplification in these four genes in all patients. We conclude that genomic rearrangements in RET are rare and were not responsible for the CCHS/HSCR phenotype in individuals without identifiable germline RET variants in our group of patients, yet this possibility cannot be excluded altogether given the size of the cohort. [source] Analysis of RET, ZEB2, EDN3 and GDNF Genomic Rearrangements in 80 Patients with Hirschsprung Disease (Using multiplex ligation-dependent probe amplification)ANNALS OF HUMAN GENETICS, Issue 2 2009A. Serra Summary Hirschsprung disease (HSCR) is transmitted in a complex pattern of inheritance and is mostly associated with variants in the RET proto-oncogene. However, RET mutations are only identified in 15,20% of sporadic HSCR cases and solely in 50% of the familial cases. Since genomic rearrangements in particularly sensitive areas of the RET proto-oncogene and/or associated genes may account for the HSCR phenotype in patients without other detectable RET variants, the aim of the present study was to identify rearrangements in the coding sequence of RET as well as in three HSCR-associated genes (ZEB2, EDN3 and GDNF) in HSCR patients by using Multiplex Ligation-dependent Probe Amplification (MLPA). We have screened 80 HSCR patients for genomic rearrangements in RET, ZEB2, EDN3 and GDNF and did not identify any deletion or amplification in these four genes in all patients. We conclude that genomic rearrangements in RET are rare and were not responsible for the HSCR phenotype in individuals without identifiable germline RET variants in our group of patients, yet this possibility cannot be excluded altogether because the confidence to identify variation in at least two percent of the individuals was only 95%. [source] Universal multiplex PCR and CE for quantification of SMN1/SMN2 genes in spinal muscular atrophyELECTROPHORESIS, Issue 7 2009Chun-Chi Wang Abstract We established a universal multiplex PCR and CE to calculate the copy number of survival motor neuron (SMN1 and SMN2) genes for clinical screening of spinal muscular atrophy (SMA). In this study, one universal fluorescent primer was designed and applied for multiplex PCR of SMN1, SMN2 and two internal standards (CYBB and KRIT1). These amplicons were separated by conformation sensitive CE. Mixture of hydroxyethyl cellulose and hydroxypropyl cellulose were used in this CE system. Our method provided the potential to separate two 390-bp PCR products that differ in a single nucleotide. Differentiation and quantification of SMN1 and SMN2 are essential for clinical screening of SMA patients and carriers. The DNA samples included 22 SMA patients, 45 parents of SMA patients (obligatory carriers) and 217 controls. For evaluating accuracy, those 284 samples were blind-analyzed by this method and denaturing high pressure liquid chromatography (DHPLC). Eight of the total samples showed different results. Among them, two samples were diagnosed as having only SMN2 gene by DHPLC, however, they contained both SMN1 and SMN2 by our method. They were further confirmed by DNA sequencing. Our method showed good agreement with the DNA sequencing. The multiplex ligation-dependent probe amplification (MLPA) was used for confirming the other five samples, and showed the same results with our CE method. For only one sample, our CE showed different results with MLPA and DNA sequencing. One out of 284 samples (0.35%) belonged to mismatching. Our method provided a better accurate method and convenient method for clinical genotyping of SMA disease. [source] Automatic analysis of multiplex ligation-dependent probe amplification products (exemplified by a commercial kit for prenatal aneuploidy detection)ELECTROPHORESIS, Issue 22 2005Tommy Gerdes Dr. Abstract For use in routine prenatal diagnostics, we developed software and methods for automatic aneuploidy detection based on a commercial multiplex ligation-dependent probe amplification (MLPA) kit. Software and methods ensure a reliable, objective, and fast workflow, and may be applied to other types of MLPA kits. Following CE of MLPA amplification products, the software automatically identified the peak area for each probe, normalized it in relation to the neighboring peak areas of the test sample, computed the ratio relative to a reference created from normal samples, and compensated the ratio for a side effect of the normalization procedure that scaled all chromosomally normal DNA peak areas slightly up or down depending on the kind of aneuploidy present. For the chromosomes 13, 18, 21, X, and Y, probe reliability weighted mean ratio values and corresponding SDs were calculated, and the significance for being outside a reference interval around ratio 1.0 was tested. p,,,1% suggested aneuploidy and 1,<,p,,,5% suggested potential aneuploidy. Individual peaks, where the normalized area was situated more than 4 SD from the corresponding reference, suggested possible partial deletion or gain. Sample quality was automatically assessed. Control probes were not required. Having used the software and methods for two years, we conclude that a reliable, objective, and fast workflow is obtained. [source] ORIGINAL ARTICLE Laboratory science: Spectrum of F8 gene mutations in haemophilia A patients from a region of Italy: identification of 23 new mutationsHAEMOPHILIA, Issue 5 2010F. RICCARDI Summary., Haemophilia A (HA) is an X-linked recessive bleeding disorder caused by a lack or decrease of coagulation factor VIII activity. The molecular diagnosis of HA is challenging and a variety of different mutations have been identified throughout the F8 gene. Our aim was to detect the causative mutation in 266 HA patients from Emilia-Romagna region (Italy) and in all suspected carriers. Molecular analysis of F8 in 201 HA patients (152 index cases) was performed with a combination of several indirect and direct molecular approaches, such as long distance polymerase chain reaction, multiplex ligation-dependent probe amplification, denaturing high performance liquid chromatography and direct sequencing. The analysis revealed 78 different mutations, 23 of which were novel, not having been reported in national or international databases. The detection rate was 100%, 86% and 89% in patients with severe, moderate and mild HA, respectively. The information provided by this registry will be helpful for monitoring the treatment of HA patients in Emilia-Romagna and also for reliable genetic counselling of affected families in the future. [source] Deletions of SCN1A 5, genomic region with promoter activity in Dravet syndrome,HUMAN MUTATION, Issue 7 2010Tojo Nakayama Abstract Mutations involving the voltage-gated sodium channel ,I gene SCN1A are major genetic causes of childhood epileptic disorders, as typified by Dravet syndrome. Here we investigated the upstream regions of the SCN1A 5, noncoding exons and found two major regions with promoter activity. These two major promoters were simultaneously active in various brain regions and in most neurons. Using multiplex ligation-dependent probe amplification (MLPA) assays with probes for the 5, noncoding exons, their upstream regions, and all coding exons of SCN1A, we investigated 130 epileptic patients who did not show any SCN1A mutations by sequence analysis of all coding exons and exon,intron boundaries. Among 71 Dravet syndrome patients, we found two patients with heterozygous microdeletions removing the 5, noncoding exons and regions with promoter activity but not affecting the coding exons. We also identified four patients with deletions/duplication in the coding region. One patient with symptomatic focal epilepsy also showed a deletion in the coding region. This study provides the first case of microdeletion limited to the SCN1A 5, promoter region with the coding sequence preserved, and indicates the critical involvement of this upstream region in the molecular pathology of Dravet syndrome. Hum Mutat 31:,11, 2010. © 2010 Wiley-Liss, Inc. [source] Deletions removing the last exon of TACSTD1 constitute a distinct class of mutations predisposing to Lynch syndrome,HUMAN MUTATION, Issue 2 2009Marietta E. Kovacs Abstract Several different genetic alterations in the etiology of Lynch syndrome (hereditary nonpolyposis colorectal cancer [HNPCC]) are known, mostly point mutations and genomic rearrangements in 1 of at least 3 mismatch-repair (MMR) genes. However, no susceptibility factor has yet been identified in a significant part (30,50%) of clinicopathologically well-defined HNPCC families, suggesting the presence of other predisposing mechanisms. In a set of probands from 27 Lynch syndrome families who lacked evidence of a germline mutation in either the MSH2 or MLH1 gene, we performed genomic deletion screening with the use of multiplex ligation-dependent probe amplification (MLPA) and sequencing. We used immunohistochemistry (IHC) and microsatellite instability (MSI) analyses on samples of the probands of all families. Comparative analysis of mRNA transcripts was performed on blood leukocyte,derived samples from mutation carriers and noncarrier controls. We report that large germline deletions encompassing the last exons of the TACSTD1 gene, upstream of MSH2, cosegregate with the HNPCC phenotype in 19% (5/27) of families tested. The tumors of the carriers show high-level MSI and MSH2 protein loss. We show that these deletions, by removing the transcriptional termination sequences of the upstream gene, give rise to multiple TACSTD1/MSH2 fusion transcripts. Our results provide evidence that deletions removing the last exon of TACSTD1 constitute a distinct class of mutations predisposing to Lynch syndrome. Thus, analysis of the 3, region of the TACSTD1 gene should be included in the routine mutation screening protocols for HNPCC. Hum Mutat 30, 197,203, 2009. © 2009 Wiley-Liss, Inc. [source] High-resolution mapping of the 8p23.1 beta-defensin cluster reveals strictly concordant copy number variation of all genes,HUMAN MUTATION, Issue 10 2008Marco Groth Abstract One unexpected feature of the human genome is the high structural variability across individuals. Frequently, large regions of the genome show structural polymorphisms and many vary in their abundance. However, accurate methods for the characterization and typing of such copy number variations (CNV) are needed. The defensin cluster at the human region 8p23.1 is one of the best studied CNV regions due to its potential clinical relevance for innate immunity, inflammation, and cancer. The region can be divided into two subclusters, which harbor predominantly either alpha- or beta-defensin genes. Previous studies assessing individual copy numbers gave different results regarding whether the complete beta-defensin cluster varies or only particular genes therein. We applied multiplex ligation-dependent probe amplification (MLPA) to measure defensin locus copy numbers in 42 samples. The data show strict copy number concordance of all 10 loci typed within the beta-defensin cluster in each individual, while seven loci within the alpha-defensin cluster are consistently found as single copies per chromosome. The exception is DEFA3, which is located within the alpha-defensin cluster and was found to also differ in copy number interindividually. Absolute copy numbers ranged from two to nine for the beta-defensin cluster and zero to four for DEFA3. The CNV-typed individuals, including HapMap samples, are publicly available and may serve as a universal reference for absolute copy number determination. On this basis, MLPA represents a reliable technique for medium- to high-throughput typing of 8p23.1 defensin CNV in association studies for diverse clinical phenotypes. Hum Mutat 0,1,8, 2008. © 2008 Wiley-Liss, Inc. [source] Myoclonus-dystonia: significance of large SGCE deletions,,HUMAN MUTATION, Issue 2 2008A. Grünewald Abstract Myoclonus-dystonia (M-D) is an autosomal-dominant movement disorder caused by mutations in SGCE. We investigated the frequency and type of SGCE mutations with emphasis on gene dosage alterations and explored the associated phenotypes. We tested 35 M-D index patients by multiplex ligation-dependent probe amplification (MLPA) and genomic sequencing. Mutations were found in 26% (9/35) of the cases, all but three with definite M-D. Two heterozygous deletions of the entire SGCE gene and flanking DNA and a heterozygous deletion of exon 2 only were detected, accounting for 33% (3/9) of the mutations found. Both large deletions contained COL1A2 and were additionally associated with joint problems. Further, we discovered one novel small deletion (c.771_772delAT, p.C258X) and four recurrent point mutations (c.289C>T, p.R97X; c.304C>T, p.R102X; c.709C>T, p.R237X; c.1114C>T, p.R372X). A Medline search identified 22 articles on SGCE mutational screening. Sixty-four unrelated M-D patients were described with 41 different mutations. No genotype,phenotype association was found, except in patients with deletions encompassing additional genes. In conclusion, a rigorous clinical preselection of patients and careful accounting for non-motor signs should precede mutational tests. Gene dosage studies should be included in routine SGCE genetic testing. © 2007 Wiley-Liss, Inc. [source] Array-MLPA: comprehensive detection of deletions and duplications and its application to DMD patients,HUMAN MUTATION, Issue 1 2008Fanyi Zeng Abstract Multiplex ligation-dependent probe amplification (MLPA) is widely used to screen genes of interest for deletions and duplications. Since MLPA is usually based on size-separation of the amplification products, the maximum number of target sequences that can be screened in parallel is usually limited to ,40. We report the design of a robust array-based MLPA format that uses amplification products of essentially uniform size (100,120,bp) and distinguishes between them by virtue of incorporated tag sequences. We were thus able to increase probe complexity to 124, with very uniform product yields and signals that have a low coefficient of variance. The assay designed was used to screen the largest set studied so far (249 patients) of unrelated Duchenne muscular dystrophy (DMD) cases from the Chinese population. In a blind study we correctly assigned 98% of the genotypes and detected rearrangements in 181 cases (73%); i.e., 163 deletions (65%), 13 duplications (5%), and five complex rearrangements (2%). Although this value is significantly higher for Chinese patients than previously reported, it is similar to that found for other populations. The location of the rearrangements (76% in the major deletion hotspot) is also in agreement with other findings. The 96-well flow-through microarray system used in this research provides high-throughput and speed; hybridization can be completed in 5 to 30,minutes. Since array processing and data analysis are fully automated, array-MLPA should be easy to implement in a standard diagnostic laboratory. The universal array can be used to analyze any tag-modified MLPA probe set. Hum Mutat 29(1), 190,197, 2008. © 2007 Wiley-Liss, Inc. [source] Low proportion of whole exon deletions causing phenylketonuria in Denmark and Germany,,HUMAN MUTATION, Issue 2 2007Lisbeth Birk Møller Abstract Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by mutations of the gene encoding phenylalanine hydroxylase (PAH). More than 500 different PAH mutations have been identified and about 90% of these are single base mutations. Although the identification rate of the PAH mutations is generally very high, some variants remain unidentified. A fraction of these mutations are the result of genomic deletions or duplications, which are not recognized with standard PCR-based methods. Here we present the results of exon deletion or duplication analysis in a total of 34 families, in which two mutations had not been identified using conventional diagnostic screening techniques. Using multiplex ligation-dependent probe amplification (MLPA), we found a deletion covering exon 1 and exon 2 (c.1-?_168+?del) in one patient, a deletion of exon 3 (c.169-?_352+?del) in four patients, and a deletion of exon 5 (c.442-?_509+?del) in two patients. A deletion was thus detected in about 20% (7/34) of the families tested. Out of a combined cohort of 570 independent PKU patients from Denmark and Germany, exon deletions were identified in a total of four patients. The estimated allelic frequency of exon deletions in PKU patients in these two populations is therefore below 0.5%. © 2007 Wiley-Liss, Inc. [source] A new multiparameter assay to assess HPV 16/18, viral load and physical status together with gain of telomerase genes in HPV-related cancersINTERNATIONAL JOURNAL OF CANCER, Issue 4 2010Wendy Theelen Abstract Oncogenic human papillomavirus (HPV) is the most important risk factor for cancer of the uterine cervix and a subgroup of head and neck cancers. Viral load has been associated with persistence of infection, whereas integration of HPV into the host cell genome is associated with transition to invasive disease. Viral integration is frequently correlated with loss of viral E2 and gain of the telomerase-related genes TERC and TERT. The objective of this study was to develop a rapid and sensitive multiplex ligation-dependent probe amplification (MLPA) assay for the simultaneous analysis of viral load, integration and copy number gain of TERC and TERT in HPV16/18-associated lesions. The performance of the assay was tested for HPV vs. human gene copy number ratios ranging from 0.1 to 100 and for percentages of integration ranging from 0 to 100%. The model systems used include plasmid mixtures and the HPV-positive cell lines SiHa, HeLa and CaSki described to contain a range of 2,600 viral copies per cell. In samples with low-viral load, viral integration can be reliably determined when more than 30% of the virus is integrated. Gain of the telomerase-related genes in the cell lines as determined by our MLPA assay was in accordance with data reported in the literature. Our study demonstrates that within a single MLPA-reaction viral type, load, integration and gain of TERC and TERT can be reliably determined, which will improve risk assessment for patients suspected for HPV infection. [source] Deletion of the OPHN1 gene detected by aCGHJOURNAL OF INTELLECTUAL DISABILITY RESEARCH, Issue 3 2008I. Madrigal Abstract Background The oligophrenin 1 gene (OPHN1) is an Rho-GTPase-activating protein involved in the regulation of the G-protein cycle required for dendritic spine morphogenesis. Mutations in this gene are implicated in X-linked mental retardation (XLMR). Methods We report a deletion spanning exons 21 and 22 of the OPHN1 gene identified by a tiling path X-chromosome array comparative genomic hybridization (CGH) and multiplex ligation-dependent probe amplification, confirmed by polymerase chain reaction (PCR), in a family with four males with intellectual disabilities. Results Patients harbouring mutations in this gene share the same clinical manifestations reinforcing the idea of a syndromic XLMR. The most important neurological findings are cerebellar hypoplasia and ventriculomegaly. Conclusions We recommend screening of the OPHN1 gene in male patients with XLMR and cerebellar anomalies. This case highlights the value of high-resolution techniques as Multiplex Ligation Probe Amplification (MLPA) and CGH array for a better characterization of copy number changes and suggests that MLPA technology may be very useful for an initial screening of small deletions and duplications in XLMR patients. [source] Detection of large deletion mutations in the SERPINC1 gene causing hereditary antithrombin deficiency by multiplex ligation-dependent probe amplification (MLPA)JOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 4 2008S.-T. LEE [source] Holoprosencephaly: An update on cytogenetic abnormalities,AMERICAN JOURNAL OF MEDICAL GENETICS, Issue 1 2010Claude Bendavid Abstract Holoprosencephaly (HPE), the most common developmental defect of the forebrain and midface, is caused by a failure of midline cleavage early in gestation. Isolated HPE, which is highly genetically heterogeneous, can be due to major chromosomal abnormalities. Initially, karyotype approach led to the identification of several recurrent chromosomal anomalies predicting different HPE loci. Subsequently, several genes were isolated from these critical HPE regions, but point mutations and deletions in these genes were found only in 25% of the genetic cases. In order to identify other HPE genes, a more accurate investigation of the genome in HPE patients was necessary. To date, high-resolution cytogenetic techniques such as subtelomeric multiplex ligation-dependent probe amplification (MLPA) and microarray-based comparative genomic hybridization (array CGH) have enhanced chromosomal aberration analysis. In this article, we have updated the cytogenetic anomalies associated with HPE in a map listing all the subtelomeric and interstitial deletions that have been characterized either by karyotype, MLPA, or array CGH. The accumulation of recurrent genomic imbalances will lead to the further delineation of minimal critical HPE loci, which is the first step to the identification of new HPE genes. © 2010 Wiley-Liss, Inc. [source] Diagnostic yield by supplementing prenatal metaphase karyotyping with MLPA for microdeletion syndromes and subtelomere imbalancesPRENATAL DIAGNOSIS, Issue 10 2010S. Kjaergaard Abstract Objective The aim of the study was to retrospectively assess the relevance of using multiplex ligation-dependent probe amplification (MLPA) for detection of selected microdeletion syndromes (22q11, Prader,Willi/Angelman, Miller,Dieker, Smith,Magenis, 1p-, Williams), the reciprocal microduplication syndromes and imbalance at the subtelomere regions of chromosomes in a routine prenatal setting. Method A total of 530 prenatal samples were analysed by commercial MLPA kits (SALSA P064, P036 and P069) in addition to rapid aneuploidy testing and G-band karyotyping. Results Among the prenatal samples with a normal metaphase karyotype, nine submicroscopic imbalances were detected: seven 22q11 deletions (Velocardiofacial/DiGeorge syndrome), one 15q11deletion (Prader,Willi syndrome) and one terminal deletion of the short arm of chromosome 4 (Wolf,Hirschhorn syndrome). All imbalances were found in amniocentesis (AC) taken due to fetal structural malformation and/or other ultrasound scan (US) detected abnormality. The diagnostic yield was 4.1% in the subgroup with structural malformation and 1.6% in the subgroup with other US abnormality. Conclusion The data set substantiates that additional MLPA analyses for selected microdeletions and subtelomere imbalances are valuable in routine prenatal diagnostics, when a malformation(s) and/or other abnormalities are detected by US. In contrast, the additional MLPA analyses gave no diagnostic yield in case of increased nuchal translucency (NT). Copyright © 2010 John Wiley & Sons, Ltd. [source] MLPA as a screening method of aneuploidy and unbalanced chromosomal rearrangements in spontaneous miscarriagesPRENATAL DIAGNOSIS, Issue 8 2007Dan Diego-Alvarez Abstract Objective The present study aims to validate multiplex ligation-dependent probe amplification (MLPA) technique with subtelomeric probe mixes as a screening method to detect aneuploidy and unbalanced terminal chromosomal rearrangements in spontaneous abortions (SAs). Methods MLPA with P036B and P070 probe mixes was performed on 221 miscarriage DNA samples between the 5th and 24th week of gestation. Cytogenetic culture was attempted on 178 miscarriages. Karyotyped miscarriages served as controls in this blinded study. Results were confirmed by quantitative fluorescent-PCR (QF,PCR). Results Among the karyotyped miscarriages, MLPA was able to detect all the expected aneuploidies, as well as an unbalanced product from a reciprocal translocation, and revealed cryptic deletions and duplications not visible at the 550-band resolution level. In addition, chromosomal anomalies were found in ,37% of cases that failed to grow or could not be cultivated. As expected, ploidy changes were not detected. Copy number variation was found for target sequences of P036B (CYFIP1, MRPL41, CAB45) and P070 (DECR2, TNFRSF18) probe mixes. Conclusions We propose the use of MLPA with subtelomeric probe mixes as a reliable, rapid and economical first approach to detect aneuploidy and unbalanced terminal chromosomal rearrangements in SAs. Copyright © 2007 John Wiley & Sons, Ltd. [source] External quality assessment of rapid prenatal detection of numerical chromosomal aberrations using molecular genetic techniques: 3 years experiencePRENATAL DIAGNOSIS, Issue 5 2007S. C. Ramsden Abstract Objectives Prenatal diagnosis using rapid molecular genetic techniques is now a widely used method for detecting the most prevalent chromosomal aneuploidies. The object of this work was to develop a methodology for delivering external quality assessment (EQA) appropriate to the needs of routine diagnostic testing laboratories. Methods We have provided three rounds of EQA using 15 different samples over 3 years. The scheme has developed to assess both the genotyping accuracy of the results and the appropriateness of the clinical reports issued to the referring clinician. Results Participation in the EQA scheme has increased from 9 to 27 laboratories from across Europe over the three sample distributions. All laboratories have used quantitative fluorescence-PCR (QF-PCR) to analyse these samples except for a sole participant in 2006 who used multiplex ligation-dependent probe amplification (MLPA). In total 265 samples have been distributed, of which four (1.5%) were not reported due to technical failures and one (0.4%) was reported incorrectly and must be regarded as a genotyping error. Conclusions We have demonstrated a significant and increasing demand for EQA in the rapid detection of aneuploidies in UK and other European laboratories. Using the methodologies described, we have had a very low rate of technical failures and demonstrated a high level of genotyping accuracy. However, the quality of the clinical reports was variable and suggestions are made for improvement. Copyright © 2007 John Wiley & Sons, Ltd. [source] ORIGINAL ARTICLE: Leukocyte Activation and Circulating Leukocyte-Derived Microparticles in PreeclampsiaAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 5 2009Christianne A.R. Lok Problem, Preeclampsia shows characteristics of an inflammatory disease including leukocyte activation. Analyses of leukocyte-derived microparticles (MP) and mRNA expression of inflammation-related genes in leukocytes may establish which subgroups of leukocytes contribute to the development of preeclampsia. Method of Study, Blood samples were obtained from preeclamptic patients, normotensive pregnant and non-pregnant controls. sL-selectin and elastase were measured by ELISA. mRNA was isolated from leukocytes and gene expression was determined by multiplex ligation-dependent probe amplification (MLPA). MP were characterized by flow cytometry. Results, Altered concentrations of sL-selectin and elastase confirmed leukocyte activation in preeclampsia. These leukocytes showed up-regulation of Nuclear Factor of Kappa light chain gene enhancer in B Cells inhibitor (NF,B-1A) and cyclin-dependent kinase inhibitor (CDKN)-1A compared with normotensive pregnant women. interleukin-1 Receptor Antagonist (IL-1RA) and tumor necrosis factor (TNF)-R1 were increased compared with those in non-pregnant controls. Monocyte-derived MP were elevated in preeclamptic patients compared with pregnant women. The numbers of cytotoxic T-cell-derived and granulocyte-derived MP were elevated compared with those of non-pregnant women. Conclusion, Leukocytes are activated in preeclampsia. A pro-inflammatory gene expression profile is not prominent, although differences in mRNA expression can be detected. Increased levels of particular subsets of leukocyte-derived MP reflect activation of their parental cells in preeclampsia. [source] Analysis of RET, ZEB2, EDN3 and GDNF Genomic Rearrangements in 80 Patients with Hirschsprung Disease (Using multiplex ligation-dependent probe amplification)ANNALS OF HUMAN GENETICS, Issue 2 2009A. Serra Summary Hirschsprung disease (HSCR) is transmitted in a complex pattern of inheritance and is mostly associated with variants in the RET proto-oncogene. However, RET mutations are only identified in 15,20% of sporadic HSCR cases and solely in 50% of the familial cases. Since genomic rearrangements in particularly sensitive areas of the RET proto-oncogene and/or associated genes may account for the HSCR phenotype in patients without other detectable RET variants, the aim of the present study was to identify rearrangements in the coding sequence of RET as well as in three HSCR-associated genes (ZEB2, EDN3 and GDNF) in HSCR patients by using Multiplex Ligation-dependent Probe Amplification (MLPA). We have screened 80 HSCR patients for genomic rearrangements in RET, ZEB2, EDN3 and GDNF and did not identify any deletion or amplification in these four genes in all patients. We conclude that genomic rearrangements in RET are rare and were not responsible for the HSCR phenotype in individuals without identifiable germline RET variants in our group of patients, yet this possibility cannot be excluded altogether because the confidence to identify variation in at least two percent of the individuals was only 95%. [source] Absence of large intragenic rearrangements in the DPYD gene in a large cohort of colorectal cancer patients treated with 5-FU-based chemotherapyBRITISH JOURNAL OF CLINICAL PHARMACOLOGY, Issue 2 2010Laia Paré WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT , Dihydropyrimidine dehydrogenase (DPD) is the enzyme responsible for the elimination of approximately 80% of the administered dose of 5-fluorouracil (5-FU). , Mutations in the DPD-coding gene have been shown to increase the risk of severe toxicity in 5-FU treated patients. , The IVS14+1G>A is the most common DPYD mutation. WHAT THIS STUDY ADDS , The intragenic rearrangements of DPYD using multiplex ligation-dependent probe amplification (MLPA) were studied for the first time in a large series of 234 colorectal cancer patients treated with 5-FU-containing chemotherapy. , No deletions or duplications of one or more DPYD exons were detected. The presence of the IVS14+1G>A mutation was also excluded. , These data show that neither the large genomic rearrangements in the DPYD gene nor the IVS14+1G>A mutation are responsible for the serious toxicity associated with a 5-FU containing regimen in this cohort of Spanish patients. AIMS To study the relationship between the toxicity associated with a 5-FU-based therapy and the presence of (i) the large intragenic rearrangements in the DPYD gene and (ii) the IVS14+1G>A mutation. METHODS We used the multiplex ligation-dependent probe amplification technique (MLPA) to study genomic DNA from 234 colorectal cancer patients treated with 5-FU-based chemotherapy. RESULTS We did not detect any deletion/duplication in the DPYD gene. The presence of the IVS14+1G>A mutation was also excluded. CONCLUSIONS Neither the large genomic rearrangements in the DPYD gene nor the IVS14+1G>A mutation play a significant role in the development of serious toxicity associated with a 5-FU containing regimen. [source] 4262: MLPA of choroidal melanomaACTA OPHTHALMOLOGICA, Issue 2010BE DAMATO Purpose To determine the genotypic profiles of choroidal melanomas using multiplex ligation-dependent probe amplification (MLPA) and to correlate findings with clinical and pathological features and metastatic death. Methods DNA samples from 452 choroidal melanomas were analyzed with MLPA evaluating 31 loci on chromosomes 1, 3, 6 and 8. The MLPA results were correlated with survival predictors and wiht metastatic death. Results The patients (194 female; 258 male) had a median age of 59.4 years and a median follow-up of 1.89 years. Metastatic death occurred in 47 patients, correlating most strongly with concurrent chromosomes 3 losses and chromosome 8q gains (Logrank analysis, p<0.001). Many small choroidal melanomas with a basal diameter of less than 10mm showed only chromosome 3 loss or chromosome 8q gain or none of these, suggesting that their tumour was 'pre-lethal' at the time of ocular treatment. Conclusion MLPA analysis of choroidal melanoma is predictive of metastatic death and, therefore, clinically useful. The findings of this study are most consistent with evolutionary clonal abnormality, suggesting that timely treatment prevents the metastatic genotype and metastatic spread in a proportion of patients. [source] 4368: Hypermethylation of tumour suppressor genes in ocular adnexal lymphomaACTA OPHTHALMOLOGICA, Issue 2010H MA Purpose Promoter hypermethylation occurs in various tumours, including ocular adnexal lymphomas (OAL), and is a mechanism by which tumour suppressor genes can be inactivated during tumourigenesis. This study aimed to investigate the levels of hypermethylation and specific genes that are hypermethylated in different subtypes of OAL using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) and pryrosequencing. Methods DNA was extracted from formalin-fixed, paraffin-embedded tissues from 33 extra-marginal zone B-cell lymphomas (EMZL) and 37 non-EMZL. Using two MS-MLPA assays (MRC-Holland) the methylation status and copy number of 36 genes was detected. MS-MLPA results were validated using pyrosequencing. Results MLPA and pyrosequencing results were comparable with 75-100% concordancy. Ten common genes were hypermethylated in the EMZL and non-EMZL, diffuse large B-cell lymphomas (DLBCL) and mantle cell lymphomas (CDH13, DAPK1, ESR1, GATA5, IGSF4, PAX6, RAR,, THBS1, TIMP3, and WT1). In non-EMZLs, a greater number of genes showed hypermethylation when diagnosed in the orbit and patients had a poorer prognosis. Deletion of the 9p21 region was seen in 7/13 DLBCLs including the p14ARF, p15 and p16 genes. Conclusion Hypermethylation is a feature of OALs suggesting a role for epigenetic deregulation in OAL development. In non-EMZLs greater epigenetic deregulation may be indicative of poorer patient prognosis. We hypothesise that EMZL, DLBCL and mantle cell lymphomas share a similar epigenetic aetiology and that genes in the 9p21 region may be important to DLBCL development. Correlation of hypermethylation and copy number data with clinical presentation and follow-up could reveal biomarkers of diagnostic and prognostic value in OALs. [source] Heterogeneity in uveal melanoma assessed by multiplex ligation-dependent probe amplification (MLPA)ACTA OPHTHALMOLOGICA, Issue 2009J DOPIERALA Purpose To study intratumour heterogeneity in primary uveal melanoma (UM) by MLPA in microdissected formalin-fixed, paraffin-embedded (FFPE) tissues. Methods DNA was extracted from 2-9 areas microdissected from 32 FFPE UMs. Thirty-one loci on chromosomes 1p, 3, 6 and 8 were tested for copy number changes using the SALSA MLPA P027.B1 assay (MRC Holland). MLPA data were displayed as dosage quotients (DQs), which were classified to 5 ranges (0.35-0.64 deleted; 0.65-0.84 equivocal deletion; 0.85-1.14 normal; 1.15-1.35 equivocal amplification; >1.35 amplified). The tumour was considered heterogeneous at a locus, if a) the difference in DQs of any two areas was higher than 0.2 (value determined by ROC analysis), and b) the DQs of the areas belonged to different ranges. Results Genetic abnormalities were detected in all 32 UMs. Monosomy 3, the most significant metastasis predictor, and gain of 8q genes MYC or DDEF1 were detected in at least 1 microdissected area of 22 (69%) and 28 (87%) of the tumours, respectively. The comparison of MLPA data obtained from different areas of UMs showed heterogeneity in 1-24 loci across chromosomes 1p, 3, 6 and 8 in 26 (81%) tumours. Interestingly, trisomy 3 was observed in 3 (9%) UMs and these tumours showed the highest degree of heterogeneity (>23 heterogeneous loci). Intratumour heterogeneity of 3p12.2 (ROBO1) and 6p21.2 (CDKN1A) were most common and present in more than 35% of the tumours. Conclusion Heterogeneity of chromosomal abnormalities of 1p, 3, 6 and 8 is present in many UM. Taking one random tumour sample for prognostic testing, therefore, may not be representative of the whole tumour. [source] A population-based study of genotypic and phenotypic variability in children with spinal muscular atrophyACTA PAEDIATRICA, Issue 5 2009Eva Arkblad Abstract Aims: To describe the occurrence of spinal muscular atrophy (SMA) in childhood; to evaluate if any of the genes in the SMA region on chromosome 5q13 correlates with disease severity; to make genotype,phenotype correlations; to evaluate the variability of different disease alleles in carriers and the sensitivity of multiplex ligation-dependent probe amplification (MLPA) for detecting carriers. Methods: In a population-based study from Western Sweden MLPA was used to determine the copy-numbers of several genes in the SMA region (SMN1, SMN2, BIRC1, GTF2H2 and SERF1A) in SMA-patients and their parents. Results: We estimated the incidence of SMN1-related SMA in childhood at 1 in 11 800 live births and confirmed the relationship between the number of SMN2 copies and the severity of disease. No other direct relationships were found. All but one of the analysed parents were confirmed as carriers by MLPA analysis. A total of at least 30 different disease alleles were identified and no specific disease allele represented more than 15% of the total. Conclusion: The childhood incidence of SMA in the Swedish population is around 1 in 12 000 live births and it is unlikely that there is any founder effect involved in SMA in western Sweden. [source] Identification of a novel deletion in the OA1 gene: report of the first Spanish family with X-linked ocular albinismCLINICAL & EXPERIMENTAL OPHTHALMOLOGY, Issue 5 2010Monica Martinez-Garcia PhD Abstract Background:, This study was undertaken to analyse the OA1 gene (GPR143) and its involvement in a Spanish family presenting with nystagmus, a common symptom of X-linked ocular albinism (XLOA). Methods:, DNA samples from the index case and eight relatives were analysed by multiplex ligation-dependent probe amplification (MLPA). Sequence analysis and restriction assay were used to confirm the results. In addition, an analysis of a STR located in intron 1 of the OA1 gene (OA-CA) was performed. Results:, The father of the proband presented with nystagmus, a feature consistent with XLOA. Mutation screening by multiplex ligation-dependent probe amplification and sequence analysis of the exon 2 of the OA1 gene led to the identification of the novel p.Glu129fsX35 (g.5815delA) mutation in two affected males and four carrier females. Three relatives were found to be non-mutated. The deletion detected resulted in a truncated protein 35 codons downstream and generated a new restriction site for the XcmI endonuclease. Additionally, microsatellite analysis showed co-segregation with the disease in the family. Conclusions:, A novel deletion in the OA1 gene was identified in a Spanish family with ocular albinism. The mutation detected is likely a loss-of-function alteration. To the best of our knowledge, we describe the first Spanish family known to present with XLOA due to mutations in the OA1 gene. [source] De novo duplication of MECP2 in a girl with mental retardation and no obvious dysmorphic featuresCLINICAL GENETICS, Issue 2 2010P Makrythanasis Makrythanasis P, Moix I, Gimelli S, Fluss J, Aliferis K, Antonarakis SE, Morris MA, Béna F, Bottani A. De novo duplication of MECP2 in a girl with mental retardation and no obvious dysmorphic features. Loss-of-function mutations of MECP2 are responsible for Rett syndrome (RTT), an X-linked neurodevelopmental disorder affecting mainly girls. The availability of MECP2 testing has led to the identification of such mutations in girls with atypical RTT features and the recognition of milder forms. Furthermore, duplication of the entire gene has recently been described in boys with mental retardation and recurrent infections. We describe a girl with a heterozygous de novo MECP2 duplication. The patient, at the age of 19, has mental retardation with no autistic features. She is friendly but gets frequently anxious. She has neither dysmorphic features nor malformations. Her motor development was delayed with walking at 20 months. Speech is fluid with good pronunciation but is simple and repetitive. Diagnosis was made after single-strand conformation analysis (SSCA) and multiplex ligation-dependent probe amplification (MLPA) analysis of MECP2. Array comparative genomic hybridization (aCGH) analysis showed a duplication of 29 kb including MECP2 and part of IRAK1. Fluorescent in situ hybridization (FISH) has revealed that the duplicated region is inserted near the telomere of the short arm of chromosome 10. X-chromosome inactivation in leukocyte DNA was not skewed. We conclude that it is likely that this MECP2 duplication is responsible for the mental retardation in this patient. This case broadens the phenotypic spectrum of MECP2 abnormalities with consequent implication in diagnosis and genetic counselling of girls with non-syndromic mental retardation. [source] Novel and recurrent p14ARF mutations in Italian familial melanomaCLINICAL GENETICS, Issue 6 2010F Binni Binni F, Antigoni I, De Simone P, Majore S, Silipo V, Crisi A, Amantea A, Pacchiarini D, Castori M, De Bernardo C, Catricalà C, Grammatico P. Novel and recurrent p14ARF mutations in Italian familial melanoma. CDKN2A and CDK4 are the only known high-penetrant genes conferring proneness to cutaneous melanoma. The CDKN2A locus consists of four exons and encodes several alternate transcripts, two of which are p16INK4a and p14ARF, and originate from different open reading frames. Exon 1, is specific for p16INK4a, while exon 1, characterizes p14ARF. Most CDKN2A mutations are located in exons 1, and 2, while exon 1, variations have been identified in rare melanoma-prone pedigrees. In a previous study, we investigated 155 Italian melanoma cases, including 94 familial melanomas (FAMs) and 61 sporadic multiple primary melanomas (MPMs), for p16INK4a/CDK4 germline alterations and identified 15 p16INK4a and 1 CDK4 point mutations. In the present work, we extended our search to p14ARF mutations and CDKN2A deletions in the remaining samples. We identified the recurrent g.193+1G> A mutation in two FAM cases, while an additional pedigree displayed the previously undescribed variant g.161G> A. Multiplex ligation-dependent probe amplification (MLPA) screening for copy variations resulted negative in all cases. In Italy, the overall frequency of p14ARF mutations is 3.2% in FAM and 0% in sporadic MPM. Re-evaluation of our patients' cohort emphasizes that the chance of identifying CDKN2A/CDK4 mutations in FAM is mainly influenced by the number of affected family members and the presence of one or more MPM cases. Accordingly, mutation rate rises to 61% in selected cases. Further studies are expected in order to investigate CDKN2A rarer mutations, including atypical deletions and inherited epimutations. [source] Molecular and clinical features associated with CFTR gene rearrangements in Italian population: identification of a new duplication and recurrent deletionsCLINICAL GENETICS, Issue 4 2008V Paracchini Cystic fibrosis (CF) is mainly caused by small deletions or missense mutations in the CFTR gene. The CF mutation database lists more than 35 large rearrangements that may escape detection using polymerase chain reaction-base techniques. The Innogenetics assay, the denaturing high-performance liquid chromatography and sequencing screening showed a mutation detection rate of 92.6% in our population. We report here the results of multiplex ligation-dependent probe amplification (MLPA) screening for CFTR gene rearrangements, performed on the unidentified alleles of our CF patients. Our sample population consists of 692 non-related Italian CF patients (for a total of 1384 alleles), followed at CF Centres in the Lombardia Region. MLPA analysis was performed in 49 patients who still had one or two unidentified alleles (for a total of 52 unidentified alleles) after extensive analysis of CFTR gene. All patients who were studied had the classical form of CF. We characterized nine different deletions and a new duplication. The deletion of exons 22,23 (7/82) was the most frequent in our cohort. The search for deletion/duplications of the CFTR gene has made it possible to reach a 94.1% detection rate, with an improvement (1.6%) of the carrier detection rate in the Italian population. [source] Frequency of hereditary non-polyposis colorectal cancer among Uruguayan patients with colorectal cancerCLINICAL GENETICS, Issue 1 2005C Sarroca Few studies have investigated the frequency of hereditary non-polyposis colorectal cancer (HNPCC) in patients with colorectal cancer (CRC), and these have shown marked geographic variations. The aim of this study was to estimate the frequency of HNPCC in a cohort of Uruguayan CRC patients. We included all patients operated consecutively for CRC in the Hospital Central de las Fuerzas Armadas (Uruguay) between 1987 and 2003. Cases were classified into three groups: (i) those fulfilling Amsterdam criteria; (ii) those not fulfilling Amsterdam criteria but considered as a population at increased risk of cancer; and (iii) sporadic CRC. Genetic analysis to detect point mutations in hMLH/hMSH2/hMSH6 genes was performed in group 1 patients. Cases not showing mutations were tested by multiplex ligation-dependent probe amplification. Among 461 patients, group 1 represented 2.6%, group 2 represented 5.6%, and sporadic cases 91.8%. hMLH1/hMSH2/hMSH6 mutations were found in 25% of cases classified as HNPCC (two in hMLH1 and one in hMSH2). No mutations were detected in hMSH6 gene. The proportion of CRC patients that fulfilled Amsterdam criteria agrees with other reports. However, the percentage of HNPCC cases with identified mutations (25%) may be lower than that reported from other populations. This may reflect, among other possible causes, a different genetic profile in the Uruguayan population. [source] | |||||||||||||