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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/28215484/establishment-and-characterization-of-a-new-human-acinar-cell-carcinoma-cell-line-faraz-icr-from-pancreas
#3
Marzieh Rezaei, Ahmad Hosseini, Saman Nikeghbalian, Abbas Ghaderi
OBJECTIVES: Basic research in the field of acinar cell carcinoma (ACC) as a rare neoplasm of the pancreas is dependent on the availability of pragmatic model such as new pancreatic cancer cell lines. Thus, establishment and characterization of new pancreatic cancer cell lines from ACC origin are deemed important. METHODS: Faraz-ICR cell line was derived from a 58-years old woman with pancreatic acinar cell carcinoma by the collagenase digestion protocol. We characterized the cell line by examining its morphology and cytostructural and functional profile...
February 8, 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/28196407/comprehensive-genomic-and-phenotypic-characterization-of-germline-fh-deletion-in-hereditary-leiomyomatosis-and-renal-cell-carcinoma-hlrcc
#4
Cathy D Vocke, Christopher J Ricketts, Maria J Merino, Ramaprasad Srinivasan, Adam R Metwalli, Lindsay A Middelton, James Peterson, Youfeng Yang, W Marston Linehan
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a familial cancer syndrome associated with the development of cutaneous and uterine leiomyomas, and an aggressive form of type 2 papillary kidney cancer. HLRCC is characterized by germline mutation of the FH gene. This study evaluated the prevalence and clinical phenotype of FH deletions in HLRCC patients. Patients with phenotypic manifestations consistent with HLRCC who lacked detectable germline FH intragenic mutations were investigated for FH deletion...
February 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28176767/intragenic-fmr1-disease-causing-variants-a-significant-mutational-mechanism-leading-to-fragile-x-syndrome
#5
Angélique Quartier, Hélène Poquet, Brigitte Gilbert-Dussardier, Massimiliano Rossi, Anne-Sophie Casteleyn, Vincent des Portes, Claire Feger, Elsa Nourisson, Paul Kuentz, Claire Redin, Julien Thevenon, Anne-Laure Mosca-Boidron, Patrick Callier, Jean Muller, Gaetan Lesca, Frédéric Huet, Véronique Geoffroy, Salima El Chehadeh, Matthieu Jung, Benoit Trojak, Stéphanie Le Gras, Daphné Lehalle, Bernard Jost, Stéphanie Maury, Alice Masurel, Patrick Edery, Christel Thauvin-Robinet, Bénédicte Gérard, Jean-Louis Mandel, Laurence Faivre, Amélie Piton
Fragile-X syndrome (FXS) is a frequent genetic form of intellectual disability (ID). The main recurrent mutagenic mechanism causing FXS is the expansion of a CGG repeat sequence in the 5'-UTR of the FMR1 gene, therefore, routinely tested in ID patients. We report here three FMR1 intragenic pathogenic variants not affecting this sequence, identified using high-throughput sequencing (HTS): a previously reported hemizygous deletion encompassing the last exon of FMR1, too small to be detected by array-CGH and inducing decreased expression of a truncated form of FMRP protein, in three brothers with ID (family 1) and two splice variants in boys with sporadic ID: a de novo variant c...
February 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28165654/identification-of-proteasomal-catalytic-subunit-psma6-as-a-therapeutic-target-for-lung-cancer
#6
Tomohiko Kakumu, Mitsuo Sato, Daiki Goto, Toshio Kato, Naoyuki Yogo, Tetsunari Hase, Masahiro Morise, Takayuki Fukui, Kohei Yokoi, Yoshitaka Sekido, Luc Girard, John D Minna, Lauren A Byers, John V Heymach, Kevin R Coombes, Masashi Kondo, Yoshinori Hasegawa
To identify potential therapeutic targets for lung cancer, we performed semi-genome-wide shRNA screening combined with the utilisation of genome-wide expression and copy number data. shRNA screening targeting 5,043 genes in NCI-H460 identified 51 genes as candidates. Pathway analysis revealed that the 51 genes were enriched for the five pathways, including ribosome, proteasome, RNA polymerase, pyrimidine metabolism and spliceosome pathways. We focused on the proteasome pathway that involved six candidate genes because its activation has been demonstrated in diverse human malignancies, including lung cancer...
February 6, 2017: Cancer Science
https://www.readbyqxmd.com/read/28161066/genomic-profile-in-gestational-and-non-gestational-choriocarcinomas
#7
Julia Bette Homem de Mello, Priscila Daniele Ramos Cirilo, Odair Carlito Michelin, Maria Aparecida Custódio Domingues, Marilza Vieira Cunha Rudge, Silvia Regina Rogatto, Izildinha Maestá
INTRODUCTION: Gestational (GC) (derived from the placenta) and non-gestational (NGC) choriocarcinomas are trophoblastic diseases originated from abnormal proliferation of trophoblastic cells. These rare tumors share similar morphology and pathological features and differ on chemotherapy response, genetic origin and prognosis. In this study, the genomic profile of choriocarcinomas was performed according to their origin (GC or NGC) aiming to better understand these poorly characterized diseases...
February 2017: Placenta
https://www.readbyqxmd.com/read/28159702/a-case-of-feingold-type-2-syndrome-associated-with-keratoconus-refines-keratoconus-type-7-locus-on-chromosome-13q
#8
Fabio Sirchia, Eleonora Di Gregorio, Gabriella Restagno, Enrico Grosso, Patrizia Pappi, Flavia Talarico, Elisa Savin, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Barbara Pasini, Jodhbir S Mehta, Alfredo Brusco
We report on a 58-year old woman with microcephaly, mild dysmorphic features, bilateral keratoconus, digital abnormalities, short stature and mild cognitive delay. Except for keratoconus, the phenotype was suggestive for Feingold syndrome type 2 (FGLDS2, MIM 614326), a rare autosomal dominant disorder described in six patients worldwide, due to the haploinsufficiency of MIR17HG, a micro RNA encoding gene. Karyotype showed a de novo deletion on chromosome 13q, further defined by array-Comparative Genomic Hybridization (a-CGH) to a 17...
January 31, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28140512/lineal-and-cyclic-depsipeptidomimetics-with-a-beta-lactam-core-a-class-of-new-alphavbeta3-integrin-receptor-inhibitors
#9
José Ignacio Ganboa, Nerea Zabala, José Ignacio Miranda, Antonio Laso, Claudio Palomo
The αvβ3 integrin receptor plays an important role in tumor metastasis and tumor-induced angiogenesis. The inhibition of this receptor using diverse ligands, antibodies or cyclic peptides, is a promising research field for the treatment of a variety of tumors. The replacement of N(Me)V amino acid residue by a β-lactam ring in Cilengitide leads to new products that show higher inhibitory activity respect to native cyclopeptide. In particular, substitution of a peptide bond β-lactam-NH-Arg by one β-lactam-O-Arg ester linkage, increases the activity of the new cyclodepsipeptide...
January 31, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28138844/haplotyping-a-non-meiotic-diploid-fungal-pathogen-using-induced-aneuploidies-and-snp-cgh-microarray-analysis
#10
Judith Berman, Anja Forche
The generation of haplotype information has recently become very attractive due to its utility for identifying mutations associated with human disease and for the development of personalized medicine. Haplotype information also is crucial for studying recombination mechanisms and genetic diversity, and for analyzing allele-specific gene expression. Classic haplotyping methods require the analysis of hundreds of meiotic progeny. To facilitate haplotyping in the non-meiotic human fungal pathogen Candida albicans, we exploited trisomic heterozygous chromosomes generated via the UAU1 selection strategy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28133555/familial-case-of-pelizaeus-merzbacher-disorder-detected-by-oligoarray-comparative-genomic-hybridization-genotype-to-phenotype-diagnosis
#11
Kimia Najafi, Roxana Kariminejad, Kaveh Hosseini, Azadeh Moshtagh, Gole Maryam Abbassi, Neda Sadatian, Masood Bazrgar, Ariana Kariminejad, Mohamad Hassan Kariminejad
Introduction. Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive hypomyelinating leukodystrophy characterized by nystagmus, spastic quadriplegia, ataxia, and developmental delay. It is caused by mutation in the PLP1 gene. Case Description. We report a 9-year-old boy referred for oligoarray comparative genomic hybridization (OA-CGH) because of intellectual delay, seizures, microcephaly, nystagmus, and spastic paraplegia. Similar clinical findings were reported in his older brother and maternal uncle...
2017: Case Reports in Genetics
https://www.readbyqxmd.com/read/28124401/brca1-alterations-with-additional-defects-in-dna-damage-response-genes-may-confer-chemoresistance-to-brca-like-breast-cancers-treated-with-neoadjuvant-chemotherapy
#12
Mamoru Takada, Shigenori Nagai, Masayuki Haruta, Ryuichi P Sugino, Katsunori Tozuka, Hiroyuki Takei, Fumie Ohkubo, Kenichi Inoue, Masafumi Kurosumi, Masaru Miyazaki, Aiko Sato-Otsubo, Yusuke Sato, Seishi Ogawa, Yasuhiko Kaneko
The BRCA-like phenotype is a feature that some sporadic breast cancers share with those occurring in BRCA1 or BRCA2 mutation carriers. Since tumors with the phenotype have defects in the DNA damage response pathway, which may increase sensitivity to drugs such as DNA cross-linking agents and PARP inhibitors, a method to identify this phenotype is important. The prediction of chemoresistance, which frequently develops in these tumors, is also crucial for improving therapy. We examined genomic aberrations and BRCA1 promoter methylation in tumors of 73 breast cancer (20 HR-/HER2- and 53 HR+/HER2-) patients, who received neoadjuvant chemotherapy with anthracycline, cyclophosphamide, and taxane, using SNP array CGH and quantitative PCR...
January 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28119487/stag1-mutations-cause-a-novel-cohesinopathy-characterised-by-unspecific-syndromic-intellectual-disability
#13
Daphné Lehalle, Anne-Laure Mosca-Boidron, Amber Begtrup, Odile Boute-Benejean, Perrine Charles, Megan T Cho, Amanda Clarkson, Orrin Devinsky, Yannis Duffourd, Laurence Duplomb-Jego, Bénédicte Gérard, Aurélia Jacquette, Paul Kuentz, Alice Masurel-Paulet, Carey McDougall, Sébastien Moutton, Hilde Olivié, Soo-Mi Park, Anita Rauch, Nicole Revencu, Jean-Baptiste Rivière, Karol Rubin, Ingrid Simonic, Deborah J Shears, Thomas Smol, Ana Lisa Taylor Tavares, Paulien Terhal, Julien Thevenon, Koen Van Gassen, Catherine Vincent-Delorme, Marjolein H Willemsen, Golder N Wilson, Elaine Zackai, Christiane Zweier, Patrick Callier, Christel Thauvin-Robinet, Laurence Faivre
BACKGROUND: Cohesinopathies are rare neurodevelopmental disorders arising from a dysfunction in the cohesin pathway, which enables chromosome segregation and regulates gene transcription. So far, eight genes from this pathway have been reported in human disease. STAG1 belongs to the STAG subunit of the core cohesin complex, along with five other subunits. This work aimed to identify the phenotype ascribed to STAG1 mutations. METHODS: Among patients referred for intellectual disability (ID) in genetics departments worldwide, array-comparative genomic hybridisation (CGH), gene panel, whole-exome sequencing or whole-genome sequencing were performed following the local diagnostic standards...
January 24, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28119329/marker-chromosomes-can-arise-from-chromothripsis-and-predict-adverse-prognosis-in-acute-myeloid-leukemia
#14
Tilmann Bochtler, Martin Granzow, Friedrich Stölzel, Christina Kunz, Brigitte Mohr, Mutlu Kartal-Kaess, Katrin Hinderhofer, Christoph E Heilig, Michael Kramer, Christian Thiede, Volker Endris, Martina Kirchner, Albrecht Stenzinger, Axel Benner, Martin Bornhäuser, Gerhard Ehninger, Anthony D Ho, Anna Jauch, Alwin Krämer
Metaphase karyotyping is an established diagnostic standard in acute myeloid leukemia (AML) for risk stratification. One of the cytogenetic findings in AML are structurally highly abnormal marker chromosomes. In this study we have assessed frequency, cytogenetic characteristics, prognostic impact and underlying biological origin of marker chromosomes. Given their inherent gross structural chromosomal damage, we speculated that they may arise from chromothripsis, a recently described phenomenon of chromosome fragmentation in a single catastrophic event...
January 24, 2017: Blood
https://www.readbyqxmd.com/read/28098801/a-novel-antihypertensive-derived-from-adlay-coix-larchryma-jobi-l-var-ma-yuen-stapf-glutelin
#15
Bin Li, Liansheng Qiao, Lingling Li, Yanling Zhang, Kai Li, Lingzhi Wang, Yanjiang Qiao
Our previous studies have shown that Coix glutelin pepsin hydrolysate can effectively inhibit angiotensin converting enzyme (ACE) activity in vitro. The main purpose of this study was to obtain potent anti-hypertensive peptides from Coix glutelin. The Coix glutelin hydrolysates (CGH) were prepared by pepsin catalysis and further separated by an ultrafitration (UF) system, gel filtration chromatography (GFC) and reversed-phase high performance liquid chromatography (RP-HPLC). As a result, the sub-fraction F5-3 had the highest ACE-inhibitory activity...
January 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28093361/neil1-is-a-candidate-gene-associated-with-common-variable-immunodeficiency-in-a-patient-with-a-chromosome-15q24-deletion
#16
Rosa Romano, Apostolos Zaravinos, Kyriaki Liadaki, Rozina Caridha, Johanna Lundin, Göran Carlsson, Jacek Winiarski, Qiang Pan-Hammarström, Lennart Hammarström
We report the first patient with an interstitial deletion of chromosome 15q24.1-q24.3 associated with common variable immunodeficiency (CVID). The 18-year old female patient's clinical and immunological phenotype was compared with 8 additional previously published patients with chr15q24 deletions. A CGH analysis estimated the deletion to be 3.767Mb in size (chr15: 74,410,916-78,178,418) and the result was confirmed using qRT-PCR. We defined an immune-related commonly deleted region (ICDR) within the chromosomal band 15q24...
January 14, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28081277/comparative-genomic-hybridization-analysis-of-rice-dwarf-mutants-induced-by-gamma-irradiation
#17
J E Hwang, S-H Kim, I J Jung, S M Han, J-W Ahn, S-J Kwon, S H Kim, S-Y Kang, D S Kim, J-B Kim
Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA-III-189 and -1052, in the M3 generation...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28075483/detecting-apc-gene-mutations-in-familial-adenomatous-polyposis-fap
#18
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary forms of colorectal cancer (CRC) account for up to 5% of total cases. Familial adenomatous polyposis (FAP) is an autosomal dominant condition affecting nearly 1 in 5000 people and accounts for only about 1% of all CRCs. It is characterized by the progressive development of hundreds to thousands of adenomatous colon polyps. The gene associated with FAP (APC) contains 15 coding exons. The mutation spectrum of the APC gene is broad in that 87% of causative mutations are point mutations (including other sequence variants) and around 10% to 15% are intragenic deletions and duplications...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28061750/genomecat-a-versatile-tool-for-the-analysis-and-integrative-visualization-of-dna-copy-number-variants
#19
Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann
BACKGROUND: The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. RESULTS: We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs...
January 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28056283/-copy-number-variants-analysis-in-whole-genome-of-patients-with-lipoma-tethered-cord-syndrome
#20
B Z Tao, X G Yu, C Cheng, R Zong, Z Y Zhao, L K Wang, A J Shang
Objective: To explore the abnormality of chromosomes of patients with lipoma tethered cord syndrome and the probable association between Copy Number Variations (CNV) and lipoma tethered cord syndrome. Methods: By using the Agilent SurePrint G3 Human CGH 8×60K Microarray Kit, we performed genome-wide screening for CNV on 11 patients with lipoma tethered cord syndrome adopted by the Neurosurgery Department of Chinese PLA General Hospital and their healthy parents from March 2015 to May 2015. We analyze CNVs got by the kit against the gene databases...
January 3, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
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