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https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#1
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28231309/improving-molecular-diagnosis-of-aniridia-and-wagr-syndrome-using-customized-targeted-array-based-cgh
#2
Fiona Blanco-Kelly, María Palomares, Elena Vallespín, Cristina Villaverde, Rubén Martín-Arenas, Camilo Vélez-Monsalve, Isabel Lorda-Sánchez, Julián Nevado, María José Trujillo-Tiebas, Pablo Lapunzina, Carmen Ayuso, Marta Corton
Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus...
2017: PloS One
https://www.readbyqxmd.com/read/28220018/germline-variants-in-familial-pituitary-tumour-syndrome-genes-are-common-in-young-patients-and-families-with-additional-endocrine-tumours
#3
Sunita Mc De Sousa, Mark J McCabe, Kathy Wu, Tony Roscioli, Velimir Gayevskiy, Katelyn Brook, Lesley Rawlings, Hamish S Scott, Tanya J Thompson, Peter Earls, Anthony J Gill, Mark J Cowley, Marcel E Dinger, Ann I McCormack
Objective: Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design: We undertook a nation-wide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes...
February 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28219127/-sanger-sequencing-for-the-diagnosis-of-spinal-muscular-atrophy-patients-with-survival-motor-neuron-gene-1-compound-heterozygous-mutation
#4
L Yang, Y Y Cao, Y J Qu, J L Bai, H Wang, Y W Jin, Y L Han, F Song
Objective: To detect the subtle variant of survival motor neuron gene 1(SMN1) by Sanger sequencing, and to assess the value of Sanger sequencing for the diagnosis of spinal muscular atrophy(SMA) with compound heterozygous mutation of SMN1. Methods: Fifty-two patients suspected SMA were recruited by the Capital Institute of Pediatrics from Jan.2014 to June.2016. PCR was used for amplifying exon7 of SMN1 and SMN2 in 52 patients. Natural different base peaks on the sequencing chromatogram in the SMN1 and SMN2 within the amplified segments were identified with Sanger DNA sequencing to detect the homozygous deletion or heterozygous deletion of SMN1...
February 14, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28212807/prevalence-of-brca1-and-brca2-large-genomic-rearrangements-in-tunisian-high-risk-breast-ovarian-cancer-families-implications-for-genetic-testing
#5
Aouatef Riahi, Habiba Chabouni-Bouhamed, Maher Kharrat
Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Thus, large genomic rearrangements (LGRs) in BRCA1 and BRCA2 are responsible for 4-28% of all inherited BRCA mutations. In this study, Multiplex ligation-dependent probe amplification (MLPA) assay was used for detection of large rearrangements of BRCA1 and BRCA2 genes in 36 unrelated high-risk breast/ovarian cancer patients negative for BRCA1/2 point mutations...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28211676/electrochemical-genetic-profiling-of-single-cancer-cells
#6
Josep L Acero Sanchez, Hamdi Joda, Olivier Yves Henry, Beata W Solnestam, Linda Kvastad, Pelin S Akan, Joakim Lundeberg, Nadja Laddach, Dheeraj Ramakrishnan, Ian Riley, Carmen Schwind, Daniel Latta, Ciara K O' Sullivan
Recent understandings in the development and spread of cancer have lead to the realisation of novel single cell analysis platforms focused on circulating tumour cells (CTCs). A simple, rapid and inexpensive analytical platform capable of providing genetic information of these rare cells is highly desirable to support clinicians and researchers alike to either support the selection or adjustment of therapy or provide fundamental insights into cell function and cancer progression mechanisms. We report on the genetic profiling of single cancer cells, exploiting a combination of multiplex ligation-dependent probe amplification (MLPA) and electrochemical detection...
February 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28205367/multiplex-ligation-dependent-probe-amplification-as-first-mutation-screening-for-large-deletions-and-duplications-in-haemophilia
#7
D Belvini, R Salviato, P Radossi, G Tagariello
INTRODUCTION: Molecular characterization has shown a wide mutational spectrum underlying haemophilia A (HA) and haemophilia B (HB). Different molecular assays have allowed laboratories to perform genetic testing for F8 and F9 mutations. AIM: Recently, multiplex ligation-dependent probe amplification (MLPA), a simple technique for relative quantitation of targeted genomic regions, has been introduced in HA and HB for detection of large deletions and duplications...
February 15, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28186602/-analysis-of-isodicentric-ph-chromosomes-in-chronic-myeloid-leukemia-blast-crisis
#8
Qian Li, Xiaoji Lin, Ying Lin, Rongxin Yao, Wu Huang, Handong Mei, Jian Gong, Hui Chen, Ningyan Teng
OBJECTIVE: To explore the genetic and clinical characteristics of isodicentric Ph chromosomes [idic(Ph)] in lymphoid blast crisis of chronic myeloid leukemia (CML-BLC). METHODS: Bone marrow aspirates of 2 patients with CML-BLC were analyzed by R banding after 24 hours of culturing. Genomic copy number variations (CNV) were analyzed by single nucleotide polymorphism array (SNP array) in case 1. The results were confirmed with fluorescence in situ hybridization (FISH)...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28186601/-analysis-of-the-cause-of-pregnancy-failure-with-combined-mlpa-assay-for-subtelomeric-regions-and-ultrasonography
#9
Ying Zhao, Jiwu Lou, Manna Sun, Youqing Fu, Yanhui Liu
OBJECTIVE: To explore the value of multiplex ligation-dependent probe amplification (MLPA) for the detection of chromosome abnormalities in miscarriage tissues, and to correlate the result with ultrasound findings. METHODS: A total of 421 cases of spontaneous abortions and fetal deaths were detected with the MLPA method. RESULTS: Among the 421 samples, 232 (55.11%) had an abnormal MLPA result. For the 286 cases derived from < 13 weeks pregnancy, 206 (72...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28186583/-combined-g-banded-karyotyping-and-multiplex-ligation-dependent-probe-amplification-for-the-detection-of-chromosomal-abnormalities-in-fetuses-with-congenital-heart-defects
#10
Yang Liu, Jiansheng Xie, Qian Geng, Zhiyong Xu, Weiqin Wu, Fuwei Luo, Suli Li, Qin Wang, Wubin Chen, Hongxi Tan, Hu Zhang
OBJECTIVE: To assess the value of G-banded karyotyping in combination with multiplex ligation-dependent probe amplification (MLPA) as a tool for the detection of chromosomal abnormalities in fetuses with congenital heart defects. METHODS: The combined method was used to analyze 104 fetuses with heart malformations identified by ultrasonography. Abnormal findings were confirmed with chromosomal microarray analysis (CMA). RESULTS: Nineteen (18%) fetuses were found to harbor chromosomal aberrations by G-banded karyotyping and MLPA...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28181689/prenatal-diagnosis-of-duchenne-muscular-dystrophy-in-131-chinese-families-with-dystrophinopathy
#11
Huanhuan Wang, Yan Xu, Xiaoqing Liu, Lei Wang, Wenting Jiang, Bing Xiao, Wei Wei, Yingwei Chen, Weiping Ye, Xing Ji
OBJECTIVES: To report 6-year clinical prenatal diagnosis experience of Duchenne muscular dystrophy (DMD)-affected families evaluated at a single prenatal diagnosis center in China and establish a reliable and rational prenatal diagnosis procedure for DMD families. METHODS: The prenatal diagnosis data of 146 at-risk pregnancies in 131 DMD families referred to our center from 2010 to 2016 were retrospectively reviewed. RESULTS: The mutation detection rate of the probands was greater than 99%...
February 9, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28174603/mlpa-analysis-in-a-cohort-of-patients-with-autism
#12
Sara Peixoto, Joana B Melo, José Ferrão, Luís M Pires, Nuno Lavoura, Marta Pinto, Guiomar Oliveira, Isabel M Carreira
BACKGROUND: Autism is a global neurodevelopmental disorder which generally manifests during the first 2 years and continues throughout life, with a range of symptomatic variations. Epidemiological studies show an important role of genetic factors in autism and several susceptible regions and genes have been identified. The aim of our study was to validate a cost-effective set of commercial Multiplex Ligation dependent Probe Amplification (MLPA) and methylation specific multiplex ligation dependent probe amplification (MS-MLPA) test in autistic children refered by the neurodevelopmental center and autism unit of a Paediatric Hospital...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28164568/methylation-analysis-of-brca1-and-apc-in-breast-cancer-and-it-s-relationship-to-clinicopathological-features
#13
Halaleh Shakeri, Ashraf Fakhrjou, Alireza Nikanfar, Seyyed M Mohaddes-Ardebili
BACKGROUND: Promoter methylation of tumor suppressor genes is an important epigenetic alteration that occurs in the primary stages of human tumors, including breast cancer. Identification of methylated genes and their relationship to clinical features can contribute to the prognosis and early detection of tumors. In this study, we explored the methylation status of APC and BRCA1 genes and their relationship to clinical factors in breast cancer patients. METHODS: BRCA1 and APC promoter methylation was examined by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay in formalin-fixed paraffin embedded (FFPE) breast tissue from 75 patients...
December 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28160324/molecular-diagnosis-of-%C3%AE-thalassemia-in-a-multi-ethnic-population
#14
Oded Gilad, Orna Steinberg Shemer, Michal Nevo, Orly Dgany, Tanya Krasnov, Sharon Noy-Lotan, Ron Rabinowicz, Nofar Amitai, Shifra Ben-Dor, Isaac Yaniv, Joanne Yacobovich, Hannah Tamary
OBJECTIVE: α-Thalassemia, one of the most common genetic diseases, is caused by deletions or point mutations affecting one to four α-globin genes. Molecular diagnosis is important to prevent the most severe forms of the disease. However, the diagnosis of α-thalassemia is complex due to a high variability of the genetic defects involved, with over 250 described mutations. We summarize herein the findings of genetic analyses of DNA samples referred to our laboratory for the molecular diagnosis of α-thalassemia, along with a detailed clinical description...
February 3, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/28122887/expanding-the-genetic-spectrum-of-anos1-mutations-in-patients-with-congenital-hypogonadotropic-hypogonadism
#15
C I Gonçalves, F Fonseca, T Borges, F Cunha, M C Lemos
STUDY QUESTION: What is the prevalence and functional consequence of ANOS1 (KAL1) mutations in a group of men with congenital hypogonadotropic hypogonadism (CHH)? SUMMARY ANSWER: Three of forty-two (7.1%) patients presented ANOS1 mutations, including a novel splice site mutation leading to exon skipping and a novel contiguous gene deletion associated with ichthyosis. WHAT IS KNOWN ALREADY: CHH is characterized by lack of pubertal development and infertility, due to deficient production, secretion or action of GnRH, and can be associated with anosmia/hyposmia (Kallmann syndrome, KS) or with a normal sense of smell (normosmic CHH)...
January 24, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28122725/optimal-fixation-conditions-and-dna-extraction-methods-for-mlpa-analysis-on-ffpe-tissue-derived-dna
#16
Lilit Atanesyan, Maryvonne J Steenkamer, Anja Horstman, Cathy B Moelans, Jan P Schouten, Suvi P Savola
OBJECTIVES: Molecular genetic analysis of formalin-fixed, paraffin-embedded (FFPE) tissues is of great importance both for research and diagnostics. Multiplex ligation-dependent probe amplification (MLPA) is a widely used technique for gene copy number determination, and it has been successfully used for FFPE tissue-extracted DNA analysis. However, there have been no studies addressing the effect of tissue fixation procedures and DNA extraction methods on MLPA. This study therefore focuses on selecting optimal preanalytic conditions such as FFPE tissue preparation conditions and DNA extraction methods...
January 24, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28116794/genetic-profile-of-brazilian-patients-with-dystrophinopathies
#17
Paula Abreu Ducceschi de Almeida, Marcela Câmara Machado-Costa, Gabrielle Novais Manzoli, Leticia Sauma Ferreira, Maria do Carmo de Souza Rodrigues, Larissa Souza Mario Bueno, Jonas Alex Morales Saute, Filippo Pinto Vairo, Ursula da Silveira Matte, Marina Siebert, Silvia Liliana Cossio, Gabriel S Macedo, Pablo Brea Winckler, Michele Michelin Becker, Lucas Vilas Boas Magalhães, Marcus Vinicius Magno Gonçalves, Carlo Domenico Marrone, Anamarli Nucci, Marcondes C França
Different types of mutations in the DMD gene underlie Duchenne (DMD) and Becker (BMD) muscular dystrophies. Large deletions and duplications are the most frequent causative genetic alterations worldwide, but little is known about DMD/BMD genetic profile in Brazil. Hence, we recruited patients with DMD and BMD from 8 neuromuscular reference centers along the country, and performed a comprehensive molecular investigation that included MLPA and NGS analyses. We evaluated 199 patients from 177 unrelated families: 166 with DMD, 32 with BMD and one 1...
January 24, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28110336/new-territory-for-an-old-disease-5-alpha-reductase-type-2-deficiency-in-bulgaria
#18
Silvia Andonova, Ralitsa Robeva, Radoslava Vazharova, Susanne Ledig, Liliana Grozdanova, Elisaveta Stefanova, Irena Bradinova, Tihomir Todorov, George Hadjidekov, Milko Sirakov, Peter Wieacker, Philip Kumanov, Alexey Savov
Disorders/differences of sexual development (DSD) are a group of conditions, some of which can be clinically indistinguishable mainly due to their phenotypic variability. Defining the molecular basis of their wide spectrum is still in progress. The diagnosis of 5-alpha-reductase type 2 (5α-reductase-2) deficiency is difficult especially in newborns and pre-pubertal individuals, and as a result its frequency might be underestimated. In the present study, we describe the clinical characteristics and molecular defects in 3 nonrelated 5α-reductase-2 deficiency patients of Bulgarian descent...
21, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/28087349/combination-of-multiple-ligation-dependent-probe-amplification-and-illumina-miseq-amplicon-sequencing-for-tsc1-tsc2-gene-analyses-in-patients-with-tuberous-sclerosis-complex
#19
Nur Farrah Dila Ismail, Abdul Qawee Rani, Nik Mohd Ariff Nik Abdul Malik, Chia Boon Hock, Siti Nabilahuda Mohd Azlan, Salmi Abdul Razak, Wee Teik Keng, Lock Hock Ngu, Abdul Rashid Silawati, Nor AzniYahya, Narazah Mohd Yusoff, Teguh Haryo Sasongko, Zabidi Azhar Mohd Hussin
Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous disorder characterized by tumor growth in multiple organs and caused by mutations in either TSC1 or TSC2 genes. Because of their relatively large genomic sizes, absence of hotspots, and common type of mutations, mutation detection in TSC1 and TSC2 genes has been challenging. We devised a combination of multiple ligation-dependent probe amplification (MLPA) and amplicon sequencing (AS) to simplify the detection strategy, yet we come up with reasonably high detection rate...
January 10, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28079318/duchenne-muscular-dystrophy-and-becker-muscular-dystrophy-confirmed-by-multiplex-ligation-dependent-probe-amplification-genotype-phenotype-correlation-in-a-large-cohort
#20
Seena Vengalil, Veeramani Preethish-Kumar, Kiran Polavarapu, Manjunath Mahadevappa, Deepha Sekar, Meera Purushottam, Priya Treesa Thomas, Saraswathi Nashi, Atchayaram Nalini
BACKGROUND AND PURPOSE: Studies of cases of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) confirmed by multiplex ligation-dependent probe amplification (MLPA) have determined the clinical characteristics, genotype, and relations between the reading frame and phenotype for different countries. This is the first such study from India. METHODS: A retrospective genotype-phenotype analysis of 317 MLPA-confirmed patients with DMD or BMD who visited the neuromuscular clinic of a quaternary referral center in southern India...
January 2017: Journal of Clinical Neurology
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