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Elisabetta Bigagli, Carlotta De Filippo, Cinzia Castagnini, Simona Toti, Francesco Acquadro, Francesco Giudici, Marilena Fazi, Piero Dolara, Luca Messerini, Francesco Tonelli, Cristina Luceri
BACKGROUND: DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study. METHODS: Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes...
October 5, 2016: Cellular Oncology (Dordrecht)
Seung-Hyun Jung, Min Sung Kim, Chan Kwon Jung, Hyun-Chun Park, So Youn Kim, Jieying Liu, Ja-Seong Bae, Sung Hak Lee, Tae-Min Kim, Sug Hyung Lee, Yeun-Jun Chung
Follicular thyroid adenoma (FTA) precedes follicular thyroid carcinoma (FTC) by definition with a favorable prognosis compared to FTC. However, the genetic mechanism of FTA to FTC progression remains unknown. For this, it is required to disclose FTA and FTC genomes in mutational and evolutionary perspectives. We performed whole-exome sequencing and copy number profiling of 14 FTAs and 13 FTCs, which exhibited previously-known gene mutations (NRAS, HRAS, BRAF, TSHR and EIF1AX) and copy number alterations (CNAs) (22q loss and 1q gain) in follicular tumors...
September 9, 2016: Oncotarget
Rabih Chaoui, Kai-Sven Heling, Yili Zhao, Elena Sinkovskaya, Alfred Abuhamad, Katrin Karl
OBJECTIVES: The cavum septi pellucidi (CSP) is an easily recognizable landmark in the fetal brain. CSP disappears after birth to form the septum pellucidum. Children with microdeletion 22q11 (del. 22q11) were, however, reported to have a persistent dilated CSP. This study was designed to examine whether the CSP is dilated in fetuses with del.22q11. METHODS: This was a case-control study where the CSP width was measured in normal fetuses from 16 to 34 weeks and in fetuses with del...
October 2016: Prenatal Diagnosis
M Brodhun, V Stahn, A Harder
Schwannomas are benign Schwann cell-derived tumors of the peripheral nerve sheath often involving the vestibular cranial nerve (vestibular schwannoma). Histologically, they consist of bipolar spindle cells and show a moderate cellularity. Typically, Antoni A regions with a storiform pattern and loose Antoni B regions are intermingled. Verocay bodies are the pathognomonic palisading structures. Malignant transformation is rare. Merlin (schwannomin), the protein product of NF2, is inactivated by mutations, loss of heterozygosity or methylation...
July 15, 2016: HNO
Pascal D Johann, Volker Hovestadt, Christian Thomas, Astrid Jeibmann, Katharina Heß, Susanne Bens, Florian Oyen, Cynthia Hawkins, Christopher R Pierson, Kenneth Aldape, Sang Pyo Kim, Eva Widing, David Sumerauer, Péter Hauser, Frank van Landeghem, Marina Ryzhova, Andrey Korshunov, David Capper, David T W Jones, Stefan M Pfister, Reinhard Schneppenheim, Reiner Siebert, Werner Paulus, Michael C Frühwald, Marcel Kool, Martin Hasselblatt
Rhabdoid phenotype and loss of SMARCB1 expression in a brain tumor are characteristic features of atypical teratoid/rhabdoid tumors (ATRT). Rare non-rhabdoid brain tumors showing cribriform growth pattern and SMARCB1 loss have been designated cribriform neuroepithelial tumor (CRINET). Small case series suggest that CRINETs may have a relatively favorable prognosis. However, the long-term outcome is unclear and it remains uncertain whether CRINET represents a distinct entity or a variant of ATRT. Therefore, 10 CRINETs were clinically and molecularly characterized and compared with 10 ATRTs of each of three recently described molecular subgroups (i...
July 6, 2016: Brain Pathology
Xiaodong Jiao, Firoz Kabir, Bushra Irum, Arif O Khan, Qiwei Wang, David Li, Asma A Khan, Tayyab Husnain, Javed Akram, Sheikh Riazuddin, J Fielding Hejtmancik, S Amer Riazuddin
PURPOSE: This study was performed to investigate the genetic determinants of autosomal recessive congenital cataracts in large consanguineous families. METHODS: Affected individuals underwent a detailed ophthalmological examination and slit-lamp photographs of the cataractous lenses were obtained. An aliquot of blood was collected from all participating family members and genomic DNA was extracted from white blood cells. Initially, a genome-wide scan was performed with genomic DNAs of family PKCC025 followed by exclusion analysis of our familial cohort of congenital cataracts...
2016: PloS One
Hidehisa Horiguchi, Satoshi Nakata, Sumihito Nobusawa, Shinichi Uyama, Tadashi Miyamoto, Hiromi Ueta, Naomi Fujimoto, Hideaki Yokoo
Atypical teratoid/rhabdoid tumors (AT/RTs) are rare malignant neoplasms of the CNS that preferentially affect young children. We herein report an adult case of AT/RT surviving for more than 5 years with the residual tumor. The patient, a 24-year-old man at onset, presented with a contrast-enhancing mass lesion in the left occipital lobe, and underwent partial tumor resection. Histologically, the tumor was predominantly composed of long spindle cells exhibiting nuclear palisading and perivascular pseudorosettes, which appeared to mimic mesenchymal, ependymal and Schwann cell tumors...
June 14, 2016: Neuropathology: Official Journal of the Japanese Society of Neuropathology
Silvia Stacchiotti, Annalisa Astolfi, Alessandro Gronchi, Andrea Fontana, Maria A Pantaleo, Tiziana Negri, Monica Brenca, Marcella Tazzari, Milena Urbini, Valentina Indio, Chiara Colombo, Stefano Radaelli, Silvia Brich, Angelo P Dei Tos, Paolo G Casali, Chiara Castelli, Gian Paolo Dagrada, Silvana Pilotti, Roberta Maestro
UNLABELLED: Dermatofibrosarcoma protuberans (DFSP) is a rare and indolent cutaneous sarcoma. At times, a fibrosarcomatous transformation marked by a more aggressive clinical behavior may be present. We investigated the natural history and the molecular bases of progression from classic DFSP to the fibrosarcomatous form (FS-DFSP), looking, retrospectively, at the outcome of all patients affected by primary DFSP treated at our institution from 1993 to 2012 and analyzing the molecular profile of 5 DFSPs and 5 FS-DFSPs by an integrated genomics approach (whole transcriptome sequencing, copy number analysis, FISH, qRT-PCR, IHC)...
September 2016: Molecular Cancer Research: MCR
Bing Zhu, Sydney D Finkelstein, Gong Feng, Rajesh N Keswani, Xiaoqi Lin
Although a mucinous nonneoplastic cyst (MNNC) of the pancreas is defined as a benign nonneoplastic lesion with no malignant potential, its histogenesis and etiology are still uncertain. To explore the origin and development of MNNC, we searched for neoplasia-associated mutational change in oncogene and tumor suppressor genes. Specifically, we analyzed KRAS oncogene mutations by polymerase chain reaction/dideoxy DNA (Sanger) sequencing and tumor suppression gene deletion by loss of heterozygosity (LOH) using polymerase chain reaction/capillary gel electrophoresis for a panel of 16 polymorphic microsatellite repeat markers targeting common tumor suppression gene loci at 1p, 3p, 5q, 9p, 10q, 17p, 17q, 18q, 21q, and 22q on DNA isolated from the cystic lining epithelium microdissected from 15 surgically diagnosed MNNCs by microdissection of unstained histologic sections of fixed resection specimens...
September 2016: Human Pathology
Mohamed A M Ali
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm, characterized by the unrestrained expansion of pluripotent hematopoietic stem cells. CML was the first malignancy in which a unique chromosomal abnormality was identified and a pathophysiologic association was suggested. The hallmark of CML is a reciprocal chromosomal translocation between the long arms of chromosomes 9 and 22, t(9; 22)(q34; q11), creating a derivative 9q+ and a shortened 22q-. The latter, known as the Philadelphia (Ph) chromosome, harbors the breakpoint cluster region-abelson (BCR-ABL) fusion gene, encoding the constitutively active BCR-ABL tyrosine kinase that is necessary and sufficient for initiating CML...
August 2016: Molecular Diagnosis & Therapy
P-S Zou, H-F Li, L-S Chen, M Ma, X-H Chen, D Xue, D-H Cao
Partial duplication of the long arm of chromosome 11 and the partial trisomy of 22q are uncommon karyotypic abnormalities. Here, we report the case of a 6-year-old girl who showed partial trisomy of 11q and 22q, as a result of a maternal balanced reciprocal translocation (11;22), and exhibited dysmorphic features, severe intellectual disability, brain malformations, and speech delay related to this unique chromosomal abnormality. Array comparative genomic hybridization (array CGH) revealed a gain in copy number on the long arm of chromosome 11, spanning at least 18...
2016: Genetics and Molecular Research: GMR
Anelisa Gollo Dantas, Adriana Bortolai, Mariana Moysés-Oliveira, Sylvia Takeno Herrero, Adriana Azoubel Antunes, Beatriz Tavares Costa-Carvalho, Vera Ayres Meloni, Maria Isabel Melaragno
We report on a patient conceived via in vitro fertilization (IVF) with a 22q11.2 deletion due to an unusual unbalanced translocation involving chromosomes 6 and 22 in a karyotype with 45 chromosomes. Cytogenomic studies showed that the patient has a 3.3-Mb deletion of chromosome 22q and a 0.4-Mb deletion of chromosome 6p, which resulted in haploinsufficiency of the genes responsible for the 22q11.2 deletion syndrome and also of the IRF4 gene, a member of the interferon regulatory factor family of transcription factors, which is expressed in the immune system cells...
February 2016: Molecular Syndromology
Mileny E S Colovati, Silvia Bragagnolo, Roberta S Guilherme, Anelisa G Dantas, Maria F Soares, Chong A Kim, Ana B A Perez, Maria I Melaragno
The oculo-auriculo-vertebral spectrum (OAVS) is defined as a group of malformations involving the ears, mouth, mandible, eyes, and cervical spine. Establishing an accurate clinical diagnosis of OAVS is a challenge for clinical geneticists, not only because these patients display heterogeneous phenotypes, but also because its etiology encompasses environmental factors, unknown genetic factors and different chromosome aberrations. To date, several chromosomal abnormalities have been associated with the syndrome, most frequently involving chromosome 22...
2015: Cytogenetic and Genome Research
Changkai Deng, Rong Dai, Xuliang Li, Feng Liu
Over the last few decades, numerous biomarkers in Wilms' tumor have been confirmed and shown variations in prevalence. Most of these studies were based on small sample sizes. We carried out a meta-analysis of the research published from 1992 to 2015 to obtain more precise and comprehensive outcomes for genetic tests. In the present study, 70 out of 5175 published reports were eligible for the meta-analysis, which was carried out using Stata 12.0 software. Pooled prevalence for gene mutations WT1, WTX, CTNNB1, TP53, MYCN, DROSHA, and DGCR8 was 0...
May 2016: Cancer Science
Alain C Borczuk, Jianming Pei, Robert N Taub, Brynn Levy, Odelia Nahum, Jinli Chen, Katherine Chen, Joseph R Testa
Malignant mesothelioma (MM) is an aggressive tumor arising from mesothelial linings of the serosal cavities. Pleural space is the most common site, accounting for about 80% of cases, while peritoneum makes up the majority of the remaining 20%. While histologically similar, tumors from these sites are epidemiologically and clinically distinct and their attribution to asbestos exposure differs. We compared DNA array-based findings from 48 epithelioid peritoneal MMs and 41 epithelioid pleural MMs to identify similarities and differences in copy number alterations (CNAs)...
2016: Cancer Biology & Therapy
Miika Mehine, Eevi Kaasinen, Hanna-Riikka Heinonen, Netta Mäkinen, Kati Kämpjärvi, Nanna Sarvilinna, Mervi Aavikko, Anna Vähärautio, Annukka Pasanen, Ralf Bützow, Oskari Heikinheimo, Jari Sjöberg, Esa Pitkänen, Pia Vahteristo, Lauri A Aaltonen
Uterine leiomyomas are common benign smooth muscle tumors that impose a major burden on women's health. Recent sequencing studies have revealed recurrent and mutually exclusive mutations in leiomyomas, suggesting the involvement of molecularly distinct pathways. In this study, we explored transcriptional differences among leiomyomas harboring different genetic drivers, including high mobility group AT-hook 2 (HMGA2) rearrangements, mediator complex subunit 12 (MED12) mutations, biallelic inactivation of fumarate hydratase (FH), and collagen, type IV, alpha 5 and collagen, type IV, alpha 6 (COL4A5-COL4A6) deletions...
February 2, 2016: Proceedings of the National Academy of Sciences of the United States of America
Florian Böhrnsen, Christina Enders, Hans-Christoph Ludwig, Wolfgang Brück, Laszlo Füzesi, Angelika Gutenberg
Tumors of the pineal region (PR) are rare and can be subdivided into four main histomorphological groups: Pineal-parenchymal tumors (PPT), germ cell tumors (GCT), glial tumors and miscellaneous tumors. The appropriate pathological classification and grading of these malignancies is essential for determining the clinical management and prognosis. However, an early diagnosis is often delayed due to unspecific clinical symptoms, and histological support is not always decisive to identify the diversity of tumors of the PR...
September 2015: Oncology Letters
Timothy Ito, Jianming Pei, Essel Dulaimi, Craig Menges, Philip H Abbosh, Marc C Smaldone, David Y T Chen, Richard E Greenberg, Alexander Kutikov, Rosalia Viterbo, Robert G Uzzo, Joseph R Testa
PURPOSE: Sarcomatoid changes in renal cell carcinoma are associated with a poor prognosis. The identification of genetic alterations that drive this aggressive phenotype could aid in the development of more effective targeted therapies. In this study we aimed to pinpoint unique copy number alterations in sarcomatoid renal cell carcinoma compared to classical renal cell carcinoma subtypes. MATERIALS AND METHODS: Genomic copy number analysis was performed using single nucleotide polymorphism based microarrays on tissue extracted from the tumors of 81 patients who underwent renal mass excision, including 17 with sarcomatoid renal cell carcinoma...
April 2016: Journal of Urology
Nakul Singh, Arun D Singh, Winston Hide
PURPOSE: The purpose of this study is to study the genomic evolution of primary uveal melanoma. METHODS: Primary uveal melanoma genomic DNA was assayed on the Illumina Human660W-Quad v1.0 DNA Analysis BeadChip. Raw signal intensity data were quantile normalized to estimate copy number aberration with the Genome Alteration Print algorithm. Distance between samples was calculated as the Manhattan distance between the copy number profiles of the tumors. From the distance matrix, a phylogenetic network (evolutionary relationship inference) was estimated using SplitsTree4...
October 2015: Investigative Ophthalmology & Visual Science
Assunta De Rienzo, Michael A Archer, Beow Y Yeap, Nhien Dao, Daniele Sciaranghella, Antonios C Sideris, Yifan Zheng, Alexander G Holman, Yaoyu E Wang, Paola S Dal Cin, Jonathan A Fletcher, Renee Rubio, Larry Croft, John Quackenbush, Peter E Sugarbaker, Kiara J Munir, Jesse R Battilana, Corinne E Gustafson, Lucian R Chirieac, Soo Meng Ching, James Wong, Liang Chung Tay, Stephen Rudd, Robert Hercus, David J Sugarbaker, William G Richards, Raphael Bueno
Malignant pleural mesothelioma (MPM) is an aggressive cancer that occurs more frequently in men, but is associated with longer survival in women. Insight into the survival advantage of female patients may advance the molecular understanding of MPM and identify therapeutic interventions that will improve the prognosis for all MPM patients. In this study, we performed whole-genome sequencing of tumor specimens from 10 MPM patients and matched control samples to identify potential driver mutations underlying MPM...
January 15, 2016: Cancer Research
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