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Cancer Genetics

Yu-Liang Jiang, Zi-Ye Zhao, Bai-Rong Li, Hao Wang, En-Da Yu, Shou-Bin Ning
BACKGROUND: The combination of direct sequencing and multiple ligation-dependent probe amplification (MLPA) has resulted in an 80% detection rate of serine/threonine kinase 11 (STK11) gene mutations in Peutz-Jeghers syndrome (PJS); however, this rate varies in different ethnicities. AIMS: To test the efficacy of the combination in Chinese patients with PJS. METHODS: PJS probands visiting our center during one year were enrolled. Sanger sequencing and MLPA were used to detect STK11 mutations...
November 30, 2018: Cancer Genetics
Jess F Peterson, Beth A Pitel, Stephanie A Smoley, James B Smadbeck, Sarah H Johnson, George Vasmatzis, Kathryn E Pearce, Rong He, Katalin Kelemen, Hamid A B Al-Mondhiry, Nicholas E Lamparella, Nicole L Hoppman, Hutton M Kearney, Linda B Baughn, Rhett P Ketterling, Patricia T Greipp
OBJECTIVES: To identify and characterize constitutional chromosomal rearrangements that mimic recurrent genetic abnormalities in acute myeloid leukemia (AML). METHODS: Bone marrow and blood chromosome studies were reviewed to identify constitutional rearrangements that resemble those designated by the 2017 revised World Health Organization (WHO) "AML with recurrent genetic abnormalities". Mate-pair sequencing (MPseq) was performed on cases with constitutional chromosome mimics of recurrent AML abnormalities to further define the rearrangement breakpoints...
November 20, 2018: Cancer Genetics
Jennelle C Hodge, David Bosler, Lauren Rubinstein, Navid Sadri, Shashirekha Shetty
The inv(3)(q21q26.2) altering a single chromosome 3 homolog is an established myeloid malignancy-associated entity. Comparatively, double inv(3) cases involving both homologs are exceedingly rare with 13 reports across AML, CML and MDS. This scarcity was confirmed by finding only 2 new cases out of 34,898 bone marrows collected during a 55 year period at a large medical center (0.0005%). The double inv(3) was detected by karyotype and confirmed by FISH on both homologs in a 41 year old female and a 72 year old male with AML...
November 16, 2018: Cancer Genetics
Hu Zhuhong, Bai Zhenyu, Chen Xiangyuan, Xu Tingzhen, Song Libin
Last decades have witnessed the great progress in exploration of tumor transcriptome. However, most researches were restricted in gene-level expression. mRNA isoforms, especially tumor-specific isoforms have not been fully explored in tumor. Here, by analyzing RNA-seq data derived from hundreds of samples in TCGA projects, we comprehensively characterized the expression variations of mRNA isoforms in adenocarcinoma of lung (LUAD), which is one of leading causes of cancer-related death. Our analysis found that a variety of mRNA isoforms showed differential expression in LUAD tumor samples...
November 13, 2018: Cancer Genetics
Gabriela Molinari Roberto, Gabriela Maciel Vieira, Lara Elis Alberici Delsin, Marcela de Oliveira Silva, Rodrigo Guedes Hakime, Edgard Eduard Engel, Carlos Alberto Scrideli, Luiz Gonzaga Tone, María Sol Brassesco
BACKGROUND: Overall survival of Ewing sarcoma (EWS) remains poor and less than 30% of patients with metastatic or recurrent disease survive despite current treatments. Thus, there is a constant search for new biomarkers for diagnosis, prognosis and prediction of therapy. Numerous studies have reported the abnormal expression of miR-708-5p in tumors of different origins. However, its role in EWS remains unclear. PROCEDURE: qRT-PCR was performed in nineteen consecutive EWS samples and twelve non-tumor bone samples from age-matched controls...
November 13, 2018: Cancer Genetics
Julia Isabelle Staubitz, Arno Schad, Erik Springer, Krishnaraj Rajalingam, Hauke Lang, Wilfried Roth, Nils Hartmann, Thomas Johannes Musholt
BACKGROUND: In the field of gene fusions driving tumorigenesis in papillary thyroid carcinoma (PTC), rearrangement of the proto-oncogene RET is the most frequent alteration. Apart from the most common rearrangement of RET to CCDC6, more than 15 partner genes are yet reported. The landscape of RET rearrangements in PTC ("RET-PTC") can notably be enlarged by modern targeted next-generation sequencing, indicating similarities between oncogenic pathways in other cancer types with identical genetic alterations...
November 13, 2018: Cancer Genetics
Chinmay Satish Rahane, Arne Kutzner, Klaus Heese
Adrenocortical carcinoma (ACC) is a rare and aggressive tumor whose molecular signaling pathways are not fully understood. Using an in-silico clinical data analysis approach we retrieved human gene mutation data from the highly reputed Cancer Genome Atlas (TCGA). ACC-specific gene mutations were correlated with proliferation marker FAM72 expression and Mutsig along with the algorithmic implementation of the 20/20 rule were used to validate their oncogenic potential. The newly identified oncogenic driver gene set (ZFPM1, LRIG1, CRIPAK, ZNF517, GARS and DGKZ), specifically and most repeatedly mutated in ACC, is involved in tumor suppression and cellular proliferation and thus could be useful for the prognosis and development of therapeutic approaches for the treatment of ACC...
November 9, 2018: Cancer Genetics
Eveline E Vietsch, Garrett T Graham, Justine N McCutcheon, Aamir Javaid, Giuseppe Giaccone, John L Marshall, Anton Wellstein
Cancer is a heterogeneous disease harboring diverse subclonal populations that can be discriminated by their DNA mutations. Environmental pressure selects subclones that ultimately drive disease progression and tumor relapse. Circulating cell-free DNA (ccfDNA) can be used to approximate the mutational makeup of cancer lesions and can serve as a marker for monitoring disease progression at the molecular level without the need for invasively acquired samples from primary or metastatic lesions. This potential for molecular analysis makes ccfDNA attractive for the study of clonal evolution and for uncovering emerging therapeutic resistance or sensitivity...
November 9, 2018: Cancer Genetics
Rashmi Kanagal-Shamanna, Jennelle C Hodge, Tracy Tucker, Shashi Shetty, Ashwini Yenamandra, Amanda Dixon-McIver, Christine Bryke, Emma Huxley, Patrick A Lennon, Gordana Raca, Xinjie Xu, Sally Jeffries, Fabiola Quintero-Rivera, Patricia T Greipp, Marilyn L Slovak, M Anwar Iqbal, Min Fang
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS)...
October 10, 2018: Cancer Genetics
Xinjie Xu, Christine Bryke, Madina Sukhanova, Emma Huxley, D P Dash, Amanda Dixon-Mciver, Min Fang, Patricia T Griepp, Jennelle C Hodge, Anwar Iqbal, Sally Jeffries, Rashmi Kanagal-Shamanna, Fabiola Quintero-Rivera, Shashi Shetty, Marilyn L Slovak, Ashwini Yenamandra, Patrick A Lennon, Gordana Raca
Structural genomic abnormalities, including balanced chromosomal rearrangements, copy number gains and losses and copy-neutral loss-of-heterozygosity (CN-LOH) represent an important category of diagnostic, prognostic and therapeutic markers in acute myeloid leukemia (AML). Genome-wide evaluation for copy number abnormalities (CNAs) is at present performed by karyotype analysis which has low resolution and is unobtainable in a subset of cases. Furthermore, examination for possible CN-LOH in leukemia cells is at present not routinely performed in the clinical setting...
October 6, 2018: Cancer Genetics
Trevor J Pugh, James M Fink, Xinyan Lu, Susan Mathew, Joyce Murata-Collins, Pascale Willem, Min Fang
BACKGROUND: Plasma cell neoplasms (PCNs) encompass a spectrum of disorders including monoclonal gammopathy of undetermined significance, smoldering myeloma, plasma cell myeloma, and plasma cell leukemia. Molecular subtypes have been defined by recurrent cytogenetic abnormalities and somatic mutations that are prognostic and predictive. Karyotype and fluorescence in situ hybridization (FISH) have historically been used to guide management; however, new technologies and markers raise the need to reassess current testing algorithms...
October 5, 2018: Cancer Genetics
L B Baughn, M M Meredith, L Oseth, T A Smolarek, B Hirsch
Acute lymphoblastic leukemia (ALL) represents the most common childhood malignancy. Although survival for pediatric B-ALL has approached 90%, variability in outcome among and within cytogenetically defined subgroups persists. While G-banding and fluorescence in situ hybridization (FISH) have been used to characterize leukemic clones, there is added value of chromosomal microarray and next generation sequencing in screening genome-wide for copy number aberrations, copy neutral loss of heterozygosity and nucleotide variations...
October 2018: Cancer Genetics
Mei Shao, Wenyun Liu, Yu Wang
Glioblastoma (GBM) is the most common and aggressive brain tumor with the poor clinical outcome. LncRNAs (Long non-coding RNAs) play an important role in the occurrence and development of glioblastoma. We aimed to explore the role that lncRNAs play in regulating glioblastoma and the pathways they are enriched in. The expression data of a total of 516 GBM samples were downloaded from TCGA (The Cancer Genome Atlas). We identified the differentially expressed lncRNAs between cancer and normal tissues and performed annotation of differentially expressed lncRNAs to figure out the functions and pathways they were enriched in...
October 2018: Cancer Genetics
Hui Chen, Rajyalakshmi Luthra, Keyur P Patel, Mark Routbort, Asif Rashid, Sinchita Roy-Chowdhuri, Alexander Lazar, Russell Broaddus, Jawad Manekia, Rajesh R Singh, Anna Yemelyanova
Analysis of somatic mutations in solid tumors and hematologic malignancies using targeted next generation sequencing (NGS)-based assays has become part of routine oncology practice as well as clinical trials. The use of paired tumor-normal DNA samples increases confidence of somatic calls. NGS assays that utilize unique patient identifiers (SNP IDs) allow further comparison of samples within a run or paired tumor/normal samples. The sources of germline DNA include peripheral blood (PB) and formalin-fixed paraffin-embedded tissue (FFPE)...
October 2018: Cancer Genetics
Wenbin Mo, Xiaoxue Wang, Yue Wang, Yan Li, Rui Zhang
Sweet's syndrome (SS), also known as acute febrile neutrophilic dermatosis is often associated with a hematological malignancy, especially acute myeloid leukemia (AML) and myeloid dysplasia syndrome. Histopathologically, SS is characterized by diffuse infiltrates in the upper dermis, predominantly consisting of mature neutrophils. The origin of neutrophils invading the skin remains unknown. Herein, we report a patient with concurrent acute monoblastic leukemia and SS who initially presented with discrete erythematous papules and nodules on the neck...
October 2018: Cancer Genetics
Dekel Shlomi, Nir Peled, Yehuda A Schwarz, Guy W Soo Hoo, Raj K Batra, Gershon Fink, Tal Kaplan, Lahav Cohen, Scott Mollan, William R Burfeind
BACKGROUND: Early detection decreases lung cancer mortality. The Target-FISH Lung Cancer Detection (LCD) Test is a non-invasive test designed to detect chromosomal changes (deletion or amplification) via Fluorescence in situ Hybridization (FISH) in sputum specimens from persons suspected of having lung cancer. We evaluated the performance of the LCD test in patients with highly suspicious pulmonary nodules who were scheduled for a biopsy procedure. METHODS: Induced sputum was collected from patients who were scheduled for biopsy of a solitary pulmonary nodule (0...
October 2018: Cancer Genetics
Yanisa Rattanapan, Veerawat Korkiatsakul, Adcharee Kongruang, Takol Chareonsirisuthigul, Budsaba Rerkamnuaychoke, Anna Wongkularb, Sarikapan Wilailak
DNA methylation is one of the epigenetic mechanisms associated with gene expression and plays a key role as in activation and deactivation of oncogenes and tumor suppressor genes, respectively. This study employed DNA methylation array to identify methylated genes which are highly correlated with various phenotypes of epithelial ovarian cancer (EOC) in Thai patients and to quantify promoter CpG-island methylation of candidate genes. Tissues from patients with serous and non-serous EOC showed significantly higher promoter methylation of EGFL7 and RASSF1 compared to benign cases...
August 2018: Cancer Genetics
Claudio Luchini, Alessia Nottegar, Alberto Vaona, Brendon Stubbs, Jacopo Demurtas, Stefania Maggi, Nicola Veronese
Recent studies highlighted the role of mitochondrial dysregulation in cancer, suggesting that the different mitochondrial haplogroups might play a role in tumorigenesis and risk of cancer development. Our aim is to investigate whether any mitochondrial haplogroups carried a significant higher risk of cancer development in a large prospective cohort of North American people. The haplogroup assignment was performed by a combination of sequencing and PCR-RFLP techniques. Our specific outcome of interest was the incidence of any cancer during follow-up period...
August 2018: Cancer Genetics
Asmaa Mosbeh, Khalil Halfawy, Wael S Abdel-Mageed, Dina Sweed, Mohamed H Abdel-Rahman
Deletion in the 3p21 region, the chromosomal location of BAP1, has been reported in a subset of hepatocellular carcinoma (HCC), biliary and pancreatic cancers. This suggests that BAP1 could play a role in the pathogenesis of these tumors. We assessed the frequency of BAP1 loss by immunohistochemistry in 103 hepatic, biliary and pancreatic cancers. We also assessed chromosomal alterations in the BAP1 region in the same tumors by genotyping. We identified high frequency 4/8 (50%) of BAP1 loss in intrahepatic cholangicarcinoma (ICC)...
August 2018: Cancer Genetics
Zöe Powis, Carin R Espenschied, Holly LaDuca, Kelly D Hagman, Tripti Paudyal, Shuwei Li, Hiroto Inaba, Ann Mauer, Katherine L Nathanson, James Knost, Elizabeth C Chao, Sha Tang
Clinical diagnostic exome sequencing (DES) has been effective in diagnosing individuals with suspected genetic conditions; nevertheless little has been described regarding its clinical utility in individuals with a personal and family history of cancer. This study aimed to assess diagnostic yield and clinical characteristics of pediatric and adult patients undergoing germline DES for hereditary cancer. We retrospectively reviewed 2171 patients referred for DES; cases with a personal and/or family history of cancer were further studied...
August 2018: Cancer Genetics
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