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https://www.readbyqxmd.com/read/28545022/a-high-throughput-method-to-detect-rna-profiling-by-integration-of-rt-mlpa-with-next-generation-sequencing-technology
#1
Jing Wang, Xue Yang, Haofeng Chen, Xuewei Wang, Xiangyu Wang, Yi Fang, Zhenyu Jia, Jidong Gao
RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544683/comprehensive-genetic-study-of-cystic-fibrosis-in-slovak-patients-in-25-years-of-genetic-diagnostics
#2
Andrea Soltysova, Eva Tothova Tarova, Andrej Ficek, Marian Baldovic, Helena Polakova, Hana Kayserova, Ludevit Kadasi
INTRODUCTION: Cystic fibrosis (CF) has one of the longest histories in hereditary disease molecular diagnostics. However, identification of causative mutations in the CFTR gene is complicated by over two thousand currently identified mutations; with more still being discovered. Knowledge of mutation spectrum may improve effective routine diagnostics and is obligatory in mutation-specific treatment. OBJECTIVES: This study presents comprehensive mutation screening of the CFTR gene; with 275 unrelated, clinically confirmed and treated cystic fibrosis (CF) patients diagnosed in 25 years genetic testing in Slovakia...
May 20, 2017: Clinical Respiratory Journal
https://www.readbyqxmd.com/read/28542379/disease-related-gene-module-detection-based-on-a-multi-label-propagation-clustering-algorithm
#3
Xue Jiang, Han Zhang, Xiongwen Quan, Zhandong Liu, Yanbin Yin
Detecting disease-related gene modules by analyzing gene expression data is of great significance. It is helpful for exploratory analysis of the interaction mechanisms of genes under complex disease phenotypes. The multi-label propagation algorithm (MLPA) has been widely used in module detection for its fast and easy implementation. The accuracy of MLPA greatly depends on the connections between nodes, and most existing research focuses on measuring the similarity between nodes. However, MLPA does not perform well with loose connections between disease-related genes...
2017: PloS One
https://www.readbyqxmd.com/read/28525906/copy-number-variations-of-circulating-cell-free-dna-in-urothelial-carcinoma-of-the-bladder-patients-treated-with-radical-cystectomy-a-prospective-study
#4
Armin Soave, Felix K-H Chun, Timo Hillebrand, Michael Rink, Lars Weisbach, Bettina Steinbach, Margit Fisch, Klaus Pantel, Heidi Schwarzenbach
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency...
May 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28486310/vitrectomy-assisted-biopsy-for-molecular-prognostication-of-choroidal-melanoma-2-mm-or-less-in-thickness-with-a-27-gauge-cutter
#5
Aaron Nagiel, Colin A McCannel, Christian Moreno, Tara A McCannel
PURPOSE: Fine-needle aspiration biopsy of small choroidal melanomas 2 mm or less in thickness may be associated with a low biopsy yield. This report describes our center's experience using the 27-gauge vitreous cutter to perform tumor sampling in these small melanomas. METHODS: This was a retrospective analysis of all patients who underwent a 27-gauge vitreous cutter biopsy for molecular prognostication at the time of iodine-125 plaque placement for local treatment of choroidal melanoma ≤2...
October 31, 2016: Retina
https://www.readbyqxmd.com/read/28486243/mgmt-methylation-correlates-with-melphalan-pelvic-perfusion-survival-in-stage-iii-melanoma-patients-a-pilot-study
#6
Stefano Guadagni, Giammaria Fiorentini, Marco Clementi, Giancarlo Palumbo, Francesco Masedu, Marcello Deraco, Giovanni De Manzoni, Alessandro Chiominto, Marco Valenti, Cristina Pellegrini
Approximately 25% of melanoma patients with locoregional metastases are nonresponsive to new molecular target therapy and immunotherapy. When metastases are located in the pelvis, melphalan hypoxic perfusion can be an optional treatment. Because methylation of MGMT promoter increases the efficacy of alkylating agents, studies on melanoma outcome of patients treated with melphalan regional chemotherapy should consider this epigenetic change. This study aims to evaluate whether the survival of stage III melanoma patients treated with melphalan regional chemotherapy may be correlated with MGMT methylation status...
May 10, 2017: Melanoma Research
https://www.readbyqxmd.com/read/28484312/genetic-diagnosis-as-a-tool-for-personalized-treatment-of-duchenne-muscular-dystrophy
#7
REVIEW
Luca Bello, Elena Pegoraro
Accurate definition of genetic mutations causing Duchenne muscular dystrophy (DMD) has always been relevant in order to provide genetic counseling to patients and families, and helps to establish the prognosis in the case where the distinction between Duchenne, Becker, or intermediate muscular dystrophy is not obvious. As molecular treatments aimed at dystrophin restoration in DMD are increasingly available as commercialized drugs or within clinical trials, genetic diagnosis has become an indispensable tool in order to determine eligibility for these treatments...
December 2016: Acta Myologica: Myopathies and Cardiomyopathies: Official Journal of the Mediterranean Society of Myology
https://www.readbyqxmd.com/read/28459104/accurate-clinical-detection-of-exon-copy-number-variants-in-a-targeted-ngs-panel-using-decon
#8
Anna Fowler, Shazia Mahamdallie, Elise Ruark, Sheila Seal, Emma Ramsay, Matthew Clarke, Imran Uddin, Harriet Wylie, Ann Strydom, Gerton Lunter, Nazneen Rahman
Background: Targeted next generation sequencing (NGS) panels are increasingly being used in clinical genomics to increase capacity, throughput and affordability of gene testing. Identifying whole exon deletions or duplications (termed exon copy number variants, 'exon CNVs') in exon-targeted NGS panels has proved challenging, particularly for single exon CNVs.  Methods: We developed a tool for the Detection of Exon Copy Number variants (DECoN), which is optimised for analysis of exon-targeted NGS panels in the clinical setting...
November 25, 2016: Wellcome Open Research
https://www.readbyqxmd.com/read/28456540/azfa-microdeletions-occurrence-in-chinese-infertile-males-and-novel-deletions-revealed-by-semiconductor-sequencing
#9
Xiang-Yin Liu, Hong-Yang Zhang, Da-Xin Pang, Lin-Tao Xue, Xiao Yang, Yu-Shuai Li, Rui-Zhi Liu
OBJECTIVE: To evaluate the frequency of AZFa microdeletions among infertile males, and establish a new high-throughput sequencing method to detect novel deletion types. METHODS: A total of 3,731 infertile men were included. Karyotype analysis was performed using G-band staining of peripheral blood lymphocytes. Polymerase chain reaction (PCR) amplification using specific sequence-tagged sites (STS) was performed to screen for AZF region microdeletions of the Y chromosome...
April 26, 2017: Urology
https://www.readbyqxmd.com/read/28444874/prognostic-impact-of-chromosomal-aberrations-and-gnaq-gna11-and-bap1-mutations-in-uveal-melanoma
#10
Kjersti M Staby, Karsten Gravdal, Sverre J Mørk, Steffen Heegaard, Olav K Vintermyr, Jørgen Krohn
PURPOSE: To evaluate clinico-pathological and molecular prognostic factors in a well-defined series of posterior uveal melanoma (UM) with focus on chromosomal aberrations and mutations in the GNAQ, GNA11 and BRCA1-associated protein 1 (BAP1) genes. METHODS: Formalin-fixed paraffin-embedded (FFPE) tissue samples were obtained from 50 consecutive eyes enucleated for UM between 1993 and 2005. The material was tested for loss of chromosome 3 and gain of chromosome 8q gene signatures by selective molecular gene markers using multiplex ligation-dependent probe amplification (MLPA), and for DNA mutations in the GNAQ, GNA11 and BAP1 genes...
April 26, 2017: Acta Ophthalmologica
https://www.readbyqxmd.com/read/28413448/genetic-and-epigenetic-characterization-of-the-tumors-in-a-patient-with-a-tongue-primary-tumor-a-recurrence-and-a-pharyngoesophageal-second-primary-tumor
#11
Ilda P Ribeiro, Francisco Marques, Leonor Barroso, Jorge Miguéis, Francisco Caramelo, André Santos, Maria J Julião, Joana B Melo, Isabel M Carreira
BACKGROUND: The choice of therapeutic modality for oral carcinoma in recurrent or second primary tumors remains controversial, as the treatment modalities available might be reduced by the treatment of the first tumor, and the overall survival is lower when compared with patients with a single or first tumor. Identifying biomarkers that predict the risk of relapse and the response to treatment is an emerging clinical issue. CASE PRESENTATION: A Caucasian 49-years-old man was treated with chemotherapy followed by chemoradiotherapy for a primary left side tongue tumor, achieving a complete response...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28401483/molecular-profiling-of-gene-copy-number-abnormalities-in-key-regulatory-genes-in-high-risk-b-lineage-acute-lymphoblastic-leukemia-frequency-and-their-association-with-clinicopathological-findings-in-indian-patients
#12
Prerana Bhandari, Firoz Ahmad, Bibhu Ranjan Das
Genes related to key cellular pathways are frequently altered in B cell ALL and are associated with poor survival especially in high-risk (HR) subgroups. We examined gene copy number abnormalities (CNA) in 101 Indian HR B cell ALL patients and their correlation with clinicopathological features by multiplex ligation-dependent probe amplification. Overall, CNA were detected in 59 (59%) cases, with 26, 10 and 23% of cases harboring 1, 2 or +3 CNA. CNA were more prevalent in BCR-ABL1 (60%), pediatric (64%) and high WCC (WBC count) (63%) patients...
May 2017: Medical Oncology
https://www.readbyqxmd.com/read/28397223/-analysis-of-clinical-features-and-genetic-mutations-in-a-chinese-family-affected-with-menkes-disease
#13
Xiaorong Shi, Xi Lin, Zhonglin Ke, Shuqing Chen, Bin Wu, Guiling Mo
OBJECTIVE: To delineate the clinical features and potential mutation of the ATP7A gene in a family affected with Menkes disease. METHODS: Clinical data of a patient and his family members were analyzed. Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) assays were performed to detect the mutation of the ATP7A gene. RESULTS: The patient was admitted at the age of 5 months due to severe epilepsy and marked delayed psychomotor development...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28397213/-analysis-of-genome-wide-copy-number-variations-among-fetuses-with-abnormalities-detected-by-prenatal-ultrasouography
#14
Ke Wu, Shaohua Tang, Chong Chen, Huanzheng Li, Lili Zhou, Jianxin Lyu
OBJECTIVE: To explore the genetic etiology of fetal abnormalities detected by prenatal ultrasound through single nucleotide polymorphism (SNP array) analysis. METHODS: Two hundred and eight fetuses were tested with SNP array and conventional karyotyping. Complex copy number variations (CNVs) were verified with fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and quantitative fluorescence polymerase chain reaction (QF-PCR)...
April 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28396697/efficient-and-cost-effective-genetic-analysis-of-products-of-conception-and-fetal-tissues-using-a-qf-pcr-array-cgh-strategy-five-years-of-data
#15
Celia Donaghue, Nada Davies, Joo Wook Ahn, Helen Thomas, Caroline Mackie Ogilvie, Kathy Mann
BACKGROUND: Traditional testing of miscarriage products involved culture of tissue followed by G-banded chromosome analysis; this approach has a high failure rate, is labour intensive and has a resolution of around 10 Mb. G-banded chromosome analysis has been replaced by molecular techniques in some laboratories; we previously introduced a QF-PCR/MLPA testing strategy in 2007. To improve diagnostic yield and efficiency we have now updated our testing strategy to a more comprehensive QF-PCR assay followed by array CGH...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28387648/dysmorphic-features-frontal-cerebral-cavernoma-and-hyperglycemia-in-a-girl-with-a-de-novo-deletion-of-7-23-mb-in-region-7p13-p12-1
#16
Gilberto Pérez López, Beatriz Villafuerte Quispe, María José Cabrejas Núñez, Luis Castaño, Raquel Barrio
We describe the case of a 7 year old girl referred to our Diabetes Unit for hyperglycemia associated to facial dysmorphic features, intellectual disability and cerebral cavernomas, who was initially diagnosed with type 1 diabetes mellitus (positive anti-IA2 antibody and HLA DR3/DR4/DQ2). In follow up, due to the evolution of the diabetes (very good metabolic control with low insulin dose and negative IA-2 antibodies - samples analyzed in two different laboratories-), first clinical suspicion was GCK-related Maturity-Onset Diabetes of the Young (MODY 2) by persistent mild hyperglycemia in the fasting state, which was substantiated in Multiplex Ligation-dependent Probe Amplification (MLPA)...
April 7, 2017: Journal of Clinical Research in Pediatric Endocrinology
https://www.readbyqxmd.com/read/28379443/differences-in-genetic-and-epigenetic-alterations-between-von-hippel-lindau-disease-related-and-sporadic-hemangioblastomas-of-the-central-nervous-system
#17
Shunsaku Takayanagi, Akitake Mukasa, Shota Tanaka, Masashi Nomura, Mayu Omata, Shunsuke Yanagisawa, Shogo Yamamoto, Koichi Ichimura, Hirofumi Nakatomi, Keisuke Ueki, Hiroyuki Aburatani, Nobuhito Saito
Background.: Although inactivation of the von Hippel-Lindau gene (VHL), located on chromosome 3p25, is considered to be a major cause of hemangioblastomas (HBs), the incidence of biallelic inactivation of VHL is reportedly low. The aim of this study was to determine the prevalence of VHL alterations in HBs, as well as to identify additional molecular aberrations. Methods.: Genetic and epigenetic alterations were comprehensively and comparatively analyzed in 11 VHL-related and 21 sporadic HBs...
March 30, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28344651/identification-of-a-novel-dmd-duplication-identified-by-a-combination-of-mlpa-and-targeted-exome-sequencing
#18
Beibei Wu, Liying Wang, Ting Dong, Jiahui Jin, Yili Lu, Huiping Wu, Yue Luo, Xiaoou Shan
BACKGROUND: Duchenne muscular dystrophy (DMD) is an X-linked recessive muscle-wasting disease caused by a mutation in the DMD gene. The aim of this study was to identify a de novo mutation of the DMD gene in the family of a 9-month-old Chinese male patient, as well as to describe the phenotypic characteristics of this patient. RESULTS: The patient was suspected to suffer from DMD according to physical examination, biochemical analyses, and electromyogram. We identified a duplication of exons 4-42 in DMD gene with targeted exome sequencing and multiplex ligation-dependent probe amplification (MLPA)...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28344356/methylation-status-as-a-predictor-of-intravesical-bacillus-calmette-gu%C3%A3-rin-bcg-immunotherapy-response-of-high-grade-non-muscle-invasive-bladder-tumor
#19
Petr Husek, Jaroslav Pacovsky, Marcela Chmelarova, Miroslav Podhola, Milos Brodak
BACKGROUND AND AIMS: Genetic and epigenetic alterations play an important role in urothelial cancer pathogenesis. Deeper understanding of these processes could help us achieve better diagnosis and management of this life-threatening disease. The aim of this research was to evaluate the methylation status of selected tumor suppressor genes for predicting BCG response in patients with high grade non-muscle-invasive bladder tumor (NMIBC). MATERIALS AND METHODS: We retrospectively evaluated 82 patients with high grade non-muscle-invasive bladder tumor (stage Ta, T1, CIS) who had undergone BCG instillation therapy...
March 22, 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
https://www.readbyqxmd.com/read/28336264/genomic-imbalances-in-syndromic-congenital-heart-disease
#20
Miriam Coelho Molck, Milena Simioni, Társis Paiva Vieira, Ilária Cristina Sgardioli, Fabíola Paoli Monteiro, Josiane Souza, Agnes Cristina Fett-Conte, Têmis Maria Félix, Isabella Lopes Monlléo, Vera Lúcia Gil-da-Silva-Lopes
OBJECTIVE: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). METHODS: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). RESULTS: Clinically significant copy number variations (CNVs ≥300kb) were identified in 10% (8/78) of cases...
March 21, 2017: Jornal de Pediatria
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