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Cancer Genetics

Scott C Smith, Lisa M Warren, Linda D Cooley
Chromosome analysis of solid tumors provides valuable information for diagnosis and patient management, yet successfully culturing solid tumors can be challenging. The Children's Mercy (CM) Cytogenetics laboratory has compiled a database of 1371 non-lymphoma solid tumors cultured since 2002. Analysis of the tumor culture data found a culture success rate of 91.6%. Abnormal karyotypes were identified in 47.0% of these tumors. A quality improvement project reviewed the database for methods, cell culture success, yield of clonally abnormal karyotypes, culture failure, tumor diagnostic category, and other...
February 2, 2019: Cancer Genetics
Ivan P Gorlov, Olga Y Gorlova, Christopher I Amos
BACKGROUND: Usually, genes with a higher-than-expected number of somatic mutations in tumor samples are assumed to be cancer related. We identified genes with a fewer-than-expected number of somatic mutations - "untouchable genes". METHODS: To predict the expected number of somatic mutations, we used a linear regression model with the number of mutations in the gene as an outcome, and gene characteristics, including gene size, nucleotide composition, level of evolutionary conservation, expression level and others, as predictors...
February 2019: Cancer Genetics
Jianling Ji, Fariba Navid, Mathew C Hiemenz, Maki Kaneko, Shengmei Zhou, Sulagna C Saitta, Jaclyn A Biegel
Germline pathogenic variants in CBL are associated with an autosomal dominant RASopathy and an increased risk for malignancies, particularly juvenile myelomonocytic leukemia. Herein, we describe a patient with clinical features of a Noonan-spectrum disorder who developed embryonal rhabdomyosarcoma of the bladder at age two years. Tumor analysis using the OncoKids® cancer panel revealed a CBL pathogenic variant: NM_005188.3:c.1100A>C (p.Gln367Pro). Sanger sequencing of peripheral blood DNA confirmed a de novo heterozygous germline variant...
February 2019: Cancer Genetics
Kyung Kim, Su-Hye Choi, Jeeyun Lee, Won-Suk Lee
Colorectal cancer (CRC) is one of the leading causes of cancer-related death. We analyzed genomic of non-familial tubulovillous adenoma (TVA) and two synchronous malignant colorectal adenocarcinomas from a single patient. The number of somatic mutations was higher in the tumor sample (especially, AV 50 cm adenocarcinoma sample) than TVA sample, and also the allele frequency of mutation was higher on colon adenocarcinoma samples than TVA. Although they were very low frequency of sharing same genomic alterations between the three lesions, APC gene mutation was present in all three lesions, which confirm that APC gene mutation was an early event in this patient...
February 2019: Cancer Genetics
Firoz Ahmad, Nagashree Avabhrath, Sripriya Natarajan, Jeenal Parikh, Kamlakar Patole, Bibhu Ranjan Das
Mutations in the BRAF gene have been described to occur in two-third of melanomas. The objective of the study was to establish the frequency of BRAF V600E/K/R mutation in a series of melanomas from Indian origin and to correlate mutation status with clinicopathological features. Seventy melanoma cases were evaluated for BRAF V600 mutation by pyrosequencing. Overall, BRAF mutations were detected in 30% of the patients. All mutations observed were missense type (GTG > GAG) resulting in p.V600E, while none showed V600K/R mutation...
February 2019: Cancer Genetics
Nazanin K Majd, Nicolas R Metrus, Fernando Santos-Pinheiro, Christopher R Trevino, Gregory N Fuller, Jason T Huse, Caroline Chung, Leena Ketonen, Mark D Anderson, Marta Penas-Prado
Astroblastoma is a rare glial neoplasm composed of cells that have broad processes oriented perpendicular to central vessels and often demonstrate vascular sclerosis. The WHO 2016 classification does not specify a grading system for astroblastoma, and categorizes them as well-differentiated or malignant. These broad classification rubrics, however, do not accurately predict clinical outcome. Genetic profiling of astroblastoma has therefore been of particular interest in the recent years. These efforts, although in small number, have revealed heterogeneous molecular findings that may explain astroblastoma's unpredictable clinical outcome...
February 2019: Cancer Genetics
Jedrzej Wykretowicz, Yeohan Song, Brooke McKnight, Sung Won Choi, John Magenau, Radhika Takiar, Paul El Tomb, David Ginsburg, Dale Bixby, Rami Khoriaty
Myelodysplastic syndromes (MDS) are a heterogeneous category of myeloid neoplasms that represent the most common class of acquired bone marrow failure syndromes in adults. MDS is typically associated with a hypoproliferative macrocytic anemia, but atypical findings on initial diagnostic evaluations can raise concern for a distinct pathophysiological process and lead to the investigation of alternative etiologies. Here, we report a case of MDS with a concomitant hypoproliferative microcytic and hypochromic anemia that led to the identification of acquired hemoglobin H due to a novel somatic ATRX mutation...
February 2019: Cancer Genetics
El-Khoury Riyad, Hajj Mirnab Jinan Khraibani, Audi Emma, Monsef Carla, Farra Chantal
BRCA1 and BRCA2 associated pathogenic variants are the major cause of familial cases of early onset breast and ovarian cancers. Here we report two novel heterozygous pathogenic variants in exons 18 and 11 of the BRCA2 gene in two Lebanese families. The double nucleotide insertion c.8052_8053dupAA was identified in a 38-year-old Lebanese woman diagnosed with a breast cancer. The patient had a family history of affected first degree relatives. The double nucleotide deletion c.4342_4343delAA was identified in a 67-year-old woman with ovarian cancer...
February 2019: Cancer Genetics
Young Ran Park, Soo Teik Lee, Se Lim Kim, Shi Mao Zhu, Min Ro Lee, Seong Hun Kim, In Hee Kim, Seung Ok Lee, Seung Young Seo, Sang Wook Kim
MicroRNA-9 (miR-9) has been reported to play a suppressive or promoting role according to cancer type. In this study, we investigated the effects of anoctamin-1 (ANO1) and miR-9 on colorectal cancer (CRC) cell proliferation, migration, and invasion and determined the underlying molecular mechanisms. Thirty-two paired CRC tissues and adjacent normal tissues were analyzed for ANO1 expression using quantitative real-time PCR (qRT-PCR). HCT116 cells were transiently transfected with miR-9 mimic, miR-9 inhibitor, or si-ANO1...
February 2019: Cancer Genetics
Shahid M Baba, Zafar A Shah, Arshad A Pandith, Dil-Afroze, Aleem Jan, Khurshid A Mir, Sheikh A Aziz, Zahoor Ahmad
AIMS: Distinct types of PML-RARα hybrid transcripts viz bcr-1, bcr-2 and bcr-3 result from translocation between chromosomes 15 and 17 t(15;17) in Acute Promyelocytic Leukemia patients. We aimed to determine the frequencies of the PML-RARα transcripts and FLT3-ITD mutations in APL patients to evaluate their prognostic implications and also to analyze their impact on disease outcome. MAIN METHOD: RT-PCR and Rq-PCR were adopted for transcript typing and quantitation of PML-RARα transcripts while FLT3-ITD was detected by PCR in APL patients...
February 2019: Cancer Genetics
Peter Papenhausen, Carla A Kelly, Zhenxi Zhang, James Tepperberg, Rachel D Burnside, Stuart Schwartz
T-cell acute lymphoblastic leukemia (T-ALL) is not as frequently reported as the B-cell counterpart (B-ALL), only occurring in about 15% of pediatric cases with a typically heterogeneous etiology. Approximately 8% of childhood T-ALL cases have rearrangements involving the ABL1 tyrosine kinase gene at 9q34.12; although a t(9;22), resulting in a fusion of ABL1 with the BCR gene at 22q11.23 is a common occurrence in B-ALL, it is not a typical finding in T-ALL. A subset of 10 of 40 documented cases of T-ALL analyzed over a 5-year period is presented, each having gene rearrangements within band 9q34 that resulted in fusions other than BCR/ABL1...
February 2019: Cancer Genetics
Reham Abo Elwafa, Marwa Gamaleldin, Omar Ghallab
OBJECTIVES: The marked heterogeneity of acute myeloid leukemia (AML) renders precisely predicting patient prognosis extremely difficult. Genetic alterations, fusions and mutations, may result in misexpression of key genes in AML. We aimed to investigate the expression patterns of 4 novel genes; FIS1, SPI1, PDCD7 and Ang2 to determine their potential prognostic role in AML patients. METHODS: Bone marrow mononuclear cells were analyzed for of FIS1, SPI1, PDCD7 and Ang2 expression levels by real-time quantitative PCR as well as of FLT3/ITD and NPM1 mutations in 100 newly diagnosed cytogenetically normal (CN-AML) patients, and 100 non-malignant controls...
December 7, 2018: Cancer Genetics
Kathy Chun, Gail D Wenger, Alka Chaubey, D P Dash, Rashmi Kanagal-Shamanna, Sibel Kantarci, Ravindra Kolhe, Daniel L Van Dyke, Lu Wang, Daynna J Wolff, Patricia M Miron
The prognostic role of cytogenetic analysis is well-established in B-cell chronic lymphocytic leukemia (CLL). Approximately 80% of patients have a cytogenetic aberration. Interphase FISH panels have been the gold standard for cytogenetic evaluation, but conventional cytogenetics allows detection of additional abnormalities, including translocations, complex karyotypes and multiple clones. Whole genome copy number assessment, currently performed by chromosomal microarray analysis (CMA), is particularly relevant in CLL for the following reasons: (1) copy number alterations (CNAs) represent key events with biologic and prognostic significance; (2) DNA from fresh samples is generally available; and (3) the tumor burden tends to be relatively high in peripheral blood...
December 2018: Cancer Genetics
C B Ripamonti, S Manoukian, B Peissel, J Azzollini, M L Carcangiu, P Radice
No abstract text is available yet for this article.
December 2018: Cancer Genetics
Megan L Sierant, Scott K Davey
The human RAD9A protein is required for successful execution of the G2/M DNA damage checkpoint. Along with RAD1 and HUS1, RAD9A exists in a heterotrimeric ring-shaped complex which is necessary for activation of the CHK1 checkpoint kinase. RAD9A is also required for proper localization of both TopBP1 and the Claspin adaptor protein during the DNA damage response. We have shown large, RAD9A-dense nuclear foci containing several members of the homologous recombination pathway as well as BRCA1 and the DNA damage marker γH2AX...
December 2018: Cancer Genetics
Paula Silva Felicio, Barbara Alemar, Aline Silva Coelho, Gustavo Noriz Berardinelli, Matias Eliseo Melendez, André Van Helvoort Lengert, Rodrigo Depieri Miche Lli, Rui M Reis, Gabriela Carvalho Fernandes, Ingrid Petroni Ewald, Camila Matzenbacher Bittar, Cristina Brinckmann Oliveira Netto, Osvaldo Artigalas, Ana Peixoto, Manuela Pinheiro, Manuel R Teixeira, Fernando Regla Vargas, Anna Cláudia Evangelista Dos Santos, Miguel Angelo Martins Moreira, Patricia Ashton-Prolla, Edenir Inêz Palmero
Portuguese immigration to Brazil occurred in several waves and greatly contributed to the genetic composition of current Brazilian population. In this study, we evaluated the frequency of a Portuguese founder Alu insertion in BRCA2 exon 3 (c.156_157insAlu) among individuals fulfilling Hereditary Breast and Ovarian Cancer (HBOC) syndrome criteria in 1,380 unrelated families originated from three distinct Brazilian States. We identified the c.156_157insAlu BRCA2 mutation in nine (9/1,380; 0.65%) probands analised...
December 2018: Cancer Genetics
Abeer A Bahnasy, Raghda Shehab El-Din, Nagwa Ali Sabri, Chahd A Abdel-Rahman, Ahmed El Bastawisy
BACKGROUND: Malignant Pleural Mesothelioma (MPM) is a lethal cancer with few therapeutic options. Patients with MPM have a poor prognosis, with estimated 1 year median survival and currently no treatment is curative. The BRCA associated protein 1 (BAP1) has the highest prevalence of protein-altering mutations identified in MPM. AIMS: Assessment of the frequency and pattern of BAP1 gene mutations in Egyptian patients with advanced sporadic MPM in relation to disease progression and survival rates in order to identify a novel therapeutic target for MPM...
December 2018: Cancer Genetics
Hyewon Seo, Deuk Kju Jung, Hyo-Gyoung Kang, Ji Yun Jeong, Shin Yup Lee, Jin Eun Choi, Mi Jeong Hong, Sook Kyung Do, Jang Hyuck Lee, Won Kee Lee, Kyung Min Shin, Seung Soo Yoo, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Jae Yong Park
BACKGROUND: We conducted this study to identify regulatory variants in cancer-related pathway genes which can predict clinical outcomes of chemotherapy in advanced NSCLC, using a comprehensive list of regulatory SNPs prioritized by RegulomeDB. METHODS: A total of 509 potentially functional SNPs in cancer-related pathway genes were evaluated. The SNPs were analyzed in a discovery set (n = 198), and an independent validation set (n = 181). The associations of the SNPs with chemotherapy response and overall survival (OS) were analyzed...
December 2018: Cancer Genetics
Abeer A Bahnassy, Thanaa El-A Helal, Ibrahim Mh El-Ghazawy, Gamal F Samaan, Moataz M Galal El-Din, Mona S Abdellateif, Eman Desouky, Abdel-Rahman N Zekri
BACKGROUND: We assessed the role of E-cadherin (CDH1), runt-related transcription factor 3, p21waf and p27 promoter methylation (PM) and protein expression in Helicobacter pylori (HP)-associated gastric carcinomas (GCs) and adjacent non-neoplastic tissues (ANNTs). PATIENTS AND METHODS: 192 cases were assessed for PM and protein expression of CDH1, RUNX3, p21waf and p27 by methylation-specific PCR (MSP) and immunohistochemistry. The CagA gene was also assessed. RESULTS: In GCs, 66 (34...
December 2018: Cancer Genetics
Robyn T Sussman, Sydney Shaffer, Elizabeth M Azzato, Daniel DeSloover, Midhat S Farooqi, Anders Meyer, David B Lieberman, Ashkan Bigdeli, Carmela Paolillo, Karthik Ganapathy, Shrey Sukhadia, Jason N Rosenbaum, Robert D Daber, Jennifer J D Morrissette
One caveat of next-generation sequencing (NGS)-based clinical oncology testing is the high amount of input DNA required. We sought to develop a focused NGS panel that could capture hotspot regions in relevant genes requiring 0.5-10 ng input DNA. The resulting Penn Precision Panel (PPP) targeted 20 genes containing clinically significant variants relevant to many cancers. One hundred twenty-three samples were analyzed, including 83 solid tumor specimens derived from FFPE. Various input quantities of DNA (0...
December 2018: Cancer Genetics
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