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Arnaldo N S Silva, Jordy Coffa, Varsha Menon, Lindsay C Hewitt, Kakoli Das, Yohei Miyagi, Dan Bottomley, Hayley Slaney, Toru Aoyama, Wolfram Mueller, Tomio Arai, Iain B Tan, Niantao Deng, Xiu B Chan, Patrick Tan, Akira Tsuburaya, Kentaro Sakamaki, Jeremy D Hayden, Takaki Yoshikawa, Ilse Zondervan, Suvi Savola, Heike I Grabsch
OBJECTIVE: To establish the gene copy number status of receptor tyrosine kinase (RTK) and downstream signaling (DSS) genes genes in primary gastric cancer (primGC) and matched lymph node metastases (LNmet). BACKGROUND: Evidence suggests that coamplification between RTKs and DSSs and conversion between primGC and LNmet are associated with resistance to targeted therapy. METHODS: DNA from 237 Japanese primGC and 103 matched LNmet was analyzed using a newly developed multiplex ligation-dependent probe amplification (MLPA) probemix to investigate RTK (EGFR, HER2, FGFR2, and MET) and DSS (PIK3CA, KRAS, MYC, and CCNE1) gene copy number status...
October 24, 2016: Annals of Surgery
Goran Cuturilo, Danijela Drakulic, Ida Jovanovic, Aleksandar Krstic, Milan Djukic, Dejan Skoric, Marija Mijovic, Igor Stefanovic, Milena Milivojevic, Milena Stevanovic
OBJECTIVE: The incidence of the 22q11.2 microdeletion among children who have at least two out of five major clinical criteria for 22q11.2 deletion syndrome. DESIGN: Prospective study. SETTING: University Childrens Hospital in Belgrade, Serbia between 2005 and 2014. PARTICIPANTS: 57 patients with clinical characteristics of 22q11.2 deletion syndrome. METHODS: Standard G-banding cytogenetic analysis was performed in all children, and the 22q11...
September 8, 2016: Indian Pediatrics
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single molecule molecular inversion probe (smMIP)-based targeted next generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
D Saxena, M Agarwal, D Gupta, S Agrawal, V Das, S R Phadke
: Background and Introduction: Chromosomal abnormality is found in about half of first-trimester abortions. Karyotype is the gold standard to detect chromosomal abnormalities. Multiplex ligation-dependent probe amplification (MLPA) offers advantage over karyotype in terms of lower failure rate, faster turnaround time, and much higher resolution than conventional karyotyping and found to be 98% concordant with conventional karyotype. AIM: We performed this study to look for the utility of MLPA in diagnosing chromosomal abnormalities in first-trimester abortions...
October 2016: Journal of Postgraduate Medicine
B P C Hoppe, E de Jongh, A Griffioen-Keijzer, J M Zijlstra-Baalbergen, E P F IJzerman, F Baboe
Human metapneumovirus (hMPV) is a paramyxovirus that causes respiratory tract infections ranging from mild upper airway infection to severe pneumonia. Patients with haematological disease, especially haematopoietic stem cell transplantation (HSCT) recipients, are more likely to develop more severe infections. We describe three cases of hMPV infection in HSCT patients. The most reliable diagnostic procedure for hMPV is multiplex ligation-dependent probe amplification (MLPA) on a nasopharyngeal swab. Sensitivity and specificity of MLPA to detect hMPV is high and time to diagnosis is short...
October 2016: Netherlands Journal of Medicine
Ciyu Yang, Angela G Arnold, Magan Trottier, Yukio Sonoda, Nadeem R Abu-Rustum, Oliver Zivanovic, Mark E Robson, Zsofia K Stadler, Michael F Walsh, David M Hyman, Kenneth Offit, Liying Zhang
PURPOSE: Mutations in PALB2 have been associated with a predisposition to breast and pancreatic cancers. This study aims to characterize a novel PALB2 exon 13 duplication in a hereditary breast and ovarian cancer family. METHODS: The PALB2 exon 13 duplication in this family was evaluated using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT™) and confirmed by multiplex ligation-dependent probe amplification (MLPA)...
October 18, 2016: Breast Cancer Research and Treatment
Eva Gross, Harm van Tinteren, Zhou Li, Sandra Raab, Christina Meul, Stefanie Avril, Nadja Laddach, Michaela Aubele, Corinna Propping, Apostolos Gkazepis, Manfred Schmitt, Alfons Meindl, Petra M Nederlof, Marion Kiechle, Esther H Lips
BACKGROUND: Triple-negative breast cancer (TNBC) with a BRCA1-like molecular signature has been demonstrated to remarkably respond to platinum-based chemotherapy and might be suited for a future treatment with poly(ADP-ribose)polymerase (PARP) inhibitors. In order to rapidly assess this signature we have previously developed a multiplex-ligation-dependent probe amplification (MLPA)-based assay. Here we present an independent validation of this assay to confirm its important clinical impact...
October 19, 2016: BMC Cancer
Marcin Braun, Agata Pastorczak, Wojciech Fendler, Joanna Madzio, Bartlomiej Tomasik, Joanna Taha, Marta Bielska, Lukasz Sedek, Tomasz Szczepanski, Michal Matysiak, Katarzyna Derwich, Monika Lejman, Jerzy Kowalczyk, Bernarda Kazanowska, Wanda Badowska, Jan Styczynski, Nina Irga-Jaworska, Joanna Trelinska, Beata Zalewska-Szewczyk, Filip Pierlejewski, Iwona Wlodarska, Wojciech Młynarski
The inactivation of tumor suppressor genes located within 9p21 locus (CDKN2A, CDKN2B) occurs in up to 30% of children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but its independent prognostic significance remains controversial. In order to investigate the prognostic impact of deletions and promoter methylation within 9p21, 641 children with newly diagnosed BCP-ALL using methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) were investigated. A total of 169 (26.4%) microdeletions in 9p21 were detected, of which 71 were homozygous...
October 18, 2016: Leukemia & Lymphoma
Liang Li, Wan-Jun Zhou, Ping Fang, Ze-Yan Zhong, Jian-Sheng Xie, Ti-Zhen Yan, Jian Zeng, Xu-Hui Tan, Xiang-Min Xu
BACKGROUND: Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA. METHODS: A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays...
October 18, 2016: Clinical Chemistry and Laboratory Medicine: CCLM
Jingzi Zhong, Tiantian Xu, Gang Chen, Haixia Liao, Jiapeng Zhang, Dan Lan
Introduction Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked myopathies caused by mutations of the dystrophin gene. Methods Multiplex ligation-dependent probe amplification (MLPA) combined with next-generation sequencing (NGS) of the exons of the dystrophin gene were performed in 92 suspected DMD/BMD patients. Patients with negative results were subjected to additional muscle diseases panel tests. Results DNA rearrangements were detected in 65(70.65%) patients using MLPA. The deletions primarily clustered at exons 45-55, followed by exons 2-19...
October 17, 2016: Muscle & Nerve
Concetta Scimone, Placido Bramanti, Alessia Ruggeri, Luigi Donato, Concetta Alafaci, Concetta Crisafulli, Massimo Mucciardi, Carmela Rinaldi, Antonina Sidoti, Rosalia D'Angelo
BACKGROUND: Cerebral cavernous malformations (CCMs) are vascular anomalies of the nervous system mostly located in the brain presenting sporadically or familial. Causes of familial forms are mutations in CCM1 (Krit1), CCM2 (MGC4607) and CCM3 (PDCD10) genes. Sporadic forms with no affected relative most often have only one lesion and no germ line mutations. However, a number of sporadic cases with multiple lesions have been reported and are indeed genetic cases with a de novo mutation or a mutation inherited from an asymptomatic parent...
October 13, 2016: BMC Medical Genetics
Jose Maria Bastida Bermeja, Jose Ramon González-Porras, Cristina Jiménez, Rocio Benito, Gonzalo R Ordoñez, Maria Teresa Álvarez-Román, M Elena Fontecha, Kamila Janusz, David Castillo, Rosa María Fisac, Luis Javier García-Frade, Carlos Aguilar, María Paz Martínez, Nuria Bermejo, Sonia Herrero, Ana Balanzategui, Jose Manuel Martin-Antorán, Rafael Ramos, Maria Jose Cebeiro, Emilia Pardal, Carmen Aguilera, Belen Pérez-Gutierrez, Manuel Prieto, Susana Riesco, Maria Carmen Mendoza, Ana Benito, Ana Hortal Benito-Sendin, Víctor Jiménez-Yuste, Jesus Maria Hernández-Rivas, Ramon García-Sanz, Marcos González-Díaz, Maria Eugenia Sarasquete
Currently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes...
October 13, 2016: Thrombosis and Haemostasis
Chunyan Chen, Xiaomei Zhang, Deqiang Wang, Fangyu Wang, Jian Pan, Zhenkai Wang, Chang Liu, Lin Wu, Heng Lu, Nan Li, Juan Wei, Hui Shi, Haijun Wan, Ming Zhu, Senqing Chen, Yun Zhou, Xin Zhou, Liu Yang, Jiong Liu
BACKGROUND Peutz-Jeghers syndrome (PJS) is an autosomal dominant genetic disease. It severely decreases patient quality of life and leads elevated cancer risk. Germline mutation of LKB1 is the leading cause of familial PJS. MATERIAL AND METHODS To characterize the germline mutation of LKB1 gene in Chinese familial and sporadic PJS patients, 14 PJS families, 5 sporadic PJS patients, and 250 healthy adults were collected and genomic DNAs of peripheral blood were extracted. Mutation screenings of LKB1 were performed using MLPA (multiplex ligation-dependent probe amplification), PCR, direct sequencing, and PCR-DHPLC (denaturing high-performance liquid chromatography)...
October 10, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Karan Rai, Robert Pilarski, Getachew Boru, Muneeb Rehman, Ahmad H Saqr, James B Massengill, Arun Singh, Meghan J Marino, Frederick H Davidorf, Colleen M Cebulla, Mohamed Abdel-Rahman
Uveal melanoma (UM) is the most commonly diagnosed primary intraocular tumor in adults. Familial UM (FUM), defined as two or more family members diagnosed with UM, is rare and estimated at less than 1% of all UM. Currently, BAP1 is the only gene known to contribute significant risk for UM. In this study we aimed to estimate the frequency of BAP1 mutation in FUM and to characterize the family and personal histories of other cancers in these families. We identified 32 families with FUM, including seven families previously reported by our group...
October 8, 2016: Genes, Chromosomes & Cancer
Katerina Hirschfeldova, Martina Florianova, Vera Kebrdlova, Marketa Urbanova, Jitka Stekrova
Heterozygous aberrations of SHOX gene have been reported to be responsible for Léri-Weill dyschondrosteosis (LWD) and small portion of idiopathic short stature. The study was established to assess effectiveness of using phenotype 'scoring form' in patients indicated for SHOX gene defect analysis. The submitted study is based on a retrospective group of 352 unrelated patients enrolled as a part of the routine diagnostic practice and analyzed for aberrations affecting the SHOX gene. All participants were scanned for deletion/duplication within the main pseudoautosomal region (PAR1) using the multiplex ligation-dependent probe amplification (MLPA) method...
October 6, 2016: Journal of Human Genetics
Laurence Baranger, Wendy Cuccuini, Christine Lefebvre, Isabelle Luquet, Christine Perot, Isabelle Radford, Marina Lafage-Pochitaloff
Cytogenetic analyses (karyotype and, if necessary, appropriate complementary FISH analyses) are mandatory at diagnosis in acute lymphoblastic leukemia (ALL) as their results are taken into account in therapeutic protocols due to their diagnostic and prognostic values. In some cases, karyotype can be completed by other techniques (RT-PCR, RQ-PCR, DNA content, SNP-array, MLPA…) that can be equally or more informative than FISH. Here, we have tempted to establish guidelines concerning karyotype and FISH analyses according to the most recent data of the litterature which is reviewed here, completing the 2008 WHO classification with the recent new cytogenomic entities such as Ph-like ALL and indicating possible therapeutic implications...
October 1, 2016: Annales de Biologie Clinique
Zubeyde Yalniz, Semra Demokan, Burak Karabulut, Murat Ulusan, Yusufhan Suoglu, Nejat Dalay
BACKGROUND: Sensitive and reliable new biomarkers are needed in head and neck cancer to predict the outcome and for therapy that is more effective. Copy number alterations are frequent and play a critical role in cancer. METHODS: Copy number alterations of 24 tumor suppressor genes in head and neck cancer were analyzed simultaneously in matched tumor and normal samples from 93 patients using multiplex ligation-dependent probe amplification (MLPA). RESULTS: Chromosomes 3p and 9p displayed the most common alterations...
October 3, 2016: Head & Neck
Sanjay Konakondla, Mayur Jayarao, Jami Skrade, Caterina Giannini, Michael J Workman, Chad J Morgan
INTRODUCTION: The well-described entity of Subependymal Giant Cell Astrocytoma (SEGA) in the setting of Tuberous Sclerosis Complex (TSC) is profound in current literature. It has been described in children as well as adults with or without identifiable clinical presentations of tuberous sclerosis. To our knowledge there has not been any report of a negative genetic workup of Tuberous Sclerosis Complex in an adult patient presenting with an isolated SEGA. CASE REPORT: We present a case of a 25-year-old female with no medical history who presented to the emergency room for headaches...
November 2016: Clinical Neurology and Neurosurgery
Federica Incani, Carla Cossu, Alessandra Meloni, Valeria Faà, Maria Luisa Serra, Federico Dettori, Antonella Meloni, Maria Cristina Rosatelli
OBJECTIVE: he aim of this study was to investigate whether a variation in the genomic copy number (CNV) of the β-defensin cluster could be associated with the predisposition to Chronic Mucocutaneous Candidiasis (CMC) in Sardinian APECED patients. SUBJECTS AND METHODS: The β-defensin copy number variation was determined by MLPA analysis in 18 Sardinian APECED patients with CMC and in 21 Sardinian controls. Statistical analyses were performed with ANOVA-one way test...
September 28, 2016: Journal of Oral Pathology & Medicine
Gil M Novo-Filho, Marília M Montenegro, Évelin A Zanardo, Roberta L Dutra, Alexandre T Dias, Flavia B Piazzon, Taís V M M Costa, Amom M Nascimento, Rachel S Honjo, Chong A Kim, Leslie D Kulikowski
The most prevalent structural variations in the human genome are copy number variations (CNVs), which appear predominantly in the subtelomeric regions. Variable sizes of 4p/4q CNVs have been associated with several different psychiatric findings and developmental disability (DD). We analyzed 105 patients with congenital anomalies (CA) and developmental and/or intellectual disabilities (DD/ID) using MLPA subtelomeric specific kits (P036 /P070) and 4 of them using microarrays. We found abnormal subtelomeric CNVs in 15 patients (14...
September 24, 2016: Cytogenetic and Genome Research
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