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Cancer Genetics

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https://www.readbyqxmd.com/read/28595733/a-novel-cytogenetic-and-molecular-characterization-of-renal-metanephric-adenoma-identification-of-partner-genes-involved-in-translocation-t-9-15-p24-q24
#1
Aida Catic, Amina Kurtovic-Kozaric, Sarah H Johnson, George Vasmatzis, Michael R Pins, Jillene Kogan
Renal metanephric adenoma (MA) is a rare benign tumor frequently misclassified when microscopic features alone are applied. The correct classification of a renal tumor is critical for diagnostic, prognostic, and therapeutic purposes. Despite the advancements in cancer genomics, up until recently relatively few genetic alterations critical to MA development have been recognized. Recent data suggest that 90% of MA have BRAF(V600E) mutations; the genetics of the remaining 10% are unclear. To date, only one case of a chromosomal translocation, t(9;15)(p24;q24) associated with MA has been reported...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28595732/the-novel-double-hit-t-8-22-q24-q11-myc-igl-and-t-14-15-q32-q24-igh-bcl2a1-in-diffuse-large-b-cell-lymphoma
#2
Takashi Akasaka, Chiyuki Kishimori, Katsuhiro Fukutsuka, Miho Nakagawa, Kayo Takeoka, Masahiko Hayashida, Gen Honjo, Hitoshi Ohno
An 82-year-old woman presented with generalized lymphadenopathy and skin involvement. Lymph node biopsy revealed diffuse large B-cell lymphoma with a high proliferation index. G-banding and fluorescence in situ hybridization showed a hypertetraploid karyotype with two copies of t(8;22)(q24;q11), generating the fusion of MYC and the immunoglobulin λ chain gene (IGL), and two copies of the novel immunoglobulin heavy chain gene (IGH) translocation, t(14;15)(q32;q24). A long-distance inverse polymerase chain reaction (PCR) using nested primer combinations designed for each constant gene of IGH showed that Cγ4 was juxtaposed to the downstream sequence of the BCL2A1 (BCL2-related protein A1) gene through the Sγ4 switch region...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28595731/single-nucleotide-polymorphisms-in-an-indian-cohort-and-association-of-cntn4-mmp2-and-sntb1-variants-with-oral-cancer
#3
Subuhi Yete, Sultan Pradhan, Dhananjaya Saranath
Oral cancer is a high incidence cancer in India primarily due to the prevalent tobacco/areca nut chewing habits and hence a major health concern. India constitutes 26% of the global oral cancer burden. Besides the well-established risk factors, the genomic constitution of an individual plays a role in oral cancer. The aim of the current study was to analyse genomic variants represented as single nucleotide polymorphisms (SNPs), analyse their prevalence and investigate risk association of allelotypes/genotypes to oral cancers...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28595730/recurrent-large-genomic-rearrangements-in-brca1-and-brca2-in-an-irish-case-series
#4
Terri P McVeigh, Nuala Cody, Cliona Carroll, Marie Duff, Michael Farrell, Lisa Bradley, David Gallagher, Trudi McDevitt, Andrew J Green
Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Comprehensive mutation testing using these two methods has been facilitated via our centre since 2005...
August 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449811/effects-of-polymorphisms-identified-in-genome-wide-association-studies-of-never-smoking-females-on-the-prognosis-of-non-small-cell-lung-cancer
#5
Seung Soo Yoo, Hyo-Gyoung Kang, Jin Eun Choi, Sook Kyung Do, Won Kee Lee, Sun Ha Choi, So Yeon Lee, Shin Yup Lee, Jaehee Lee, Seung Ick Cha, Chang Ho Kim, Yangki Seok, Eungbae Lee, Moon Soo Kim, Jong Mog Lee, Hyun-Ju Cho, In-Jae Oh, Young-Chul Kim, Sukki Cho, Sanghoon Jheon, Chi Young Jung, Mi-Hyun Kim, Min Ki Lee, Jae Yong Park
A number of genome-wide association studies have reported several variants that influence the risk of lung cancer in never-smoking females. We evaluated the impact of these variants on survival outcome in never-smoking females with non-small cell lung cancer (NSCLC). In total, 510 never-smoking females with NSCLC who underwent curative surgery were enrolled. Eleven variants associated with lung cancer susceptibility in never-smoking females were genotyped and their associations with survival outcome were analyzed...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449810/novel-t-5-11-q32-q13-4-with-numa1-pdgfrb-fusion-in-a-myeloid-neoplasm-with-eosinophilia-with-response-to-imatinib-mesylate
#6
Ying S Zou, Nicole L Hoppman, Zeba N Singh, Sameer Sawhney, Sandy D Kotiah, Maria R Baer
We report a NUMA1-PDGFRB fusion in a myeloproliferative neoplasm with eosinophilia in a 61-year old man, with response to imatinib mesylate therapy. A t(5;11) chromosome translocation involving bands 5q32 and 11q13.4 was identified by metaphase chromosome analysis, and rearrangement of the platelet-derived growth factor receptor beta (PDGFRB) gene on 5q32 was demonstrated by FISH using a PDGFRB break-apart probe set. Bacterial artificial chromosome (BAC) FISH mapping of the PDGFRB fusion partner gene narrowed the breakpoint at 11q13...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449809/genomic-diagnostics-leading-to-the-identification-of-a-tfg-ros1-fusion-in-a-child-with-possible-atypical-meningioma
#7
Maria Rossing, Christina Westmose Yde, Astrid Sehested, Olga Østrup, David Scheie, Volodia Dangouloff-Ros, Birgit Geoerger, Gilles Vassal, Karsten Nysom
Meningiomas are rare in children. They are highly complex, harboring unique clinical and pathological characteristics, and many occur in patients with neurofibromatosis type 2. Hereby, we present a case of a two-year-old boy presented with a diagnostically challenging intraventricular tumor. It was incompletely resected 6 times over 14 months but kept progressing and was ultimately deemed unresectable. Histologically, the tumor was initially classified as schwannoma, but extensive international review concluded it was most likely an atypical meningioma, WHO grade II...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449808/validation-of-quantitative-pcr-based-assays-for-detection-of-gene-copy-number-aberrations-in-formalin-fixed-paraffin-embedded-solid-tumor-samples
#8
Meenakshi Mehrotra, Rajyalakshmi Luthra, Ronald Abraham, Bal Mukund Mishra, Shumaila Virani, Hui Chen, Mark J Routbort, Keyur P Patel, L Jeffrey Medeiros, Rajesh R Singh
Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Here, we have validated TaqMan based quantitative PCR (qPCR) assays to detect CNAs in genes of high clinical importance in formalin-fixed, paraffin-embedded (FFPE) samples...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449807/cancer-in-machado-joseph-disease-patients-low-frequency-as-a-cause-of-death
#9
Gabriele Nunes Souza, Nathália Kersting, Thomaz Abramsson Gonçalves, Daphne Louise Oliveira Pacheco, Maria-Luiza Saraiva-Pereira, Suzi Alves Camey, Jonas Alex Morales Saute, Laura Bannach Jardim
Since polyglutamine diseases have been related to a reduced risk of cancer, we aimed to study the 15 years cumulative incidence of cancer (CIC) (arm 1) and the proportion of cancer as a cause of death (arm 2) in symptomatic carriers of spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD). SCA3/MJD and control individuals from our state were invited to participate. A structured interview was performed. CIC as published by the Brazilian National Institute of Cancer, was used as populational control...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449806/gene-fusions-pafah1b1-usp6-and-runx2-usp6-in-aneurysmal-bone-cysts-identified-by-next-generation-sequencing
#10
Mikako Warren, Dongbin Xu, Xia Li
Aneurysmal bone cyst (ABC) is a locally aggressive, expansile, typically multilocular cystic bone tumor. ABC was previously thought to be a non-neoplastic lesion; however, it is now considered to be neoplasm that features recurrent chromosomal translocations resulting in gene fusions between ubiquitin specific peptidase 6 (USP6) and multiple partners, including COL1A1, CDH11, TRAP150, ZNF90 and OMD. Using next generation sequencing (NGS), we uncovered two fusion partners of USP6 in two ABCs: platelet activating factor acetylhydrolase 1b regulatory subunit 1 (PAFAH1B1), which is known to contribute to tumorigenesis in lung cancer, and runt-related transcription factor 2 (RUNX2), which is known to regulate osteoblastic differentiation, osteosarcoma tumorigenesis and its metastasis...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28449805/spectrum-of-mismatch-repair-gene-mutations-and-clinical-presentation-of-hispanic-individuals-with-lynch-syndrome
#11
Annette Y Sunga, Charité Ricker, Carin R Espenschied, Danielle Castillo, Marilena Melas, Josef Herzog, Sarah Bannon, Marcia Cruz-Correa, Patrick Lynch, Ilana Solomon, Stephen B Gruber, Jeffrey N Weitzel
Lynch syndrome (LS), the most common hereditary colorectal cancer syndrome, is caused by mismatch repair (MMR) gene mutations. However, data about MMR mutations in Hispanics are limited. This study aims to describe the spectrum of MMR mutations in Hispanics with LS and explore ancestral origins. This case series involved an IRB-approved retrospective chart review of self-identified Hispanic patients (n = 397) seen for genetic cancer risk assessment at four collaborating academic institutions in California, Texas, and Puerto Rico who were evaluated by MMR genotyping and/or tumor analysis...
April 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28279309/allele-specific-wild-type-tp53-expression-in-the-unaffected-carrier-parent-of-children-with-li-fraumeni-syndrome
#12
Jeffrey S Buzby, Shirley A Williams, Lana Schaffer, Steven R Head, Diane J Nugent
Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is passed from parent to child. Tumor protein p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Paradoxically, some mutant TP53 carriers remain unaffected, while their children develop cancer within the first few years of life. To address this paradox, response to UV stress was compared in dermal fibroblasts (dFb) from an affected LFS patient vs. their unaffected carrier parent...
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28279308/detection-of-somatic-variants-in-peripheral-blood-lymphocytes-using-a-next-generation-sequencing-multigene-pan-cancer-panel
#13
Bradford Coffee, Hannah C Cox, John Kidd, Scott Sizemore, Krystal Brown, Susan Manley, Debora Mancini-DiNardo
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%...
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28279307/fas-c-671a-g-polymorphism-and-cervical-cancer-risk-a-case-control-study-and-meta-analysis
#14
Shing Cheng Tan, Mohd Pazudin Ismail, Daniel Roza Duski, Nor Hayati Othman, Ravindran Ankathil
This study aimed to investigate the association between FAS c.-671A>G polymorphism and cervical cancer risk in a case-control setting, followed by a meta-analysis of the published literatures. The case-control study involved genotyping of the polymorphism in 185 histopathologically confirmed cervical cancer patients and 209 cancer-free female controls utilizing PCR-RFLP technique, followed by logistic regression analyses. Meta-analysis was then conducted under homozygous, heterozygous, dominant, recessive and allele contrast models to combine data from 12 studies which consisted of 2798 cases and 3039 controls...
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28279306/taf15-znf384-fusion-gene-in-childhood-mixed-phenotype-acute-leukemia
#15
LETTER
Li Yao, Jiannong Cen, Jinlan Pan, Dandan Liu, Yong Wang, Zixing Chen, Changgeng Ruan, Suning Chen
No abstract text is available yet for this article.
February 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212810/chromosomal-instability-analysis-and-regional-tumor-heterogeneity-in-colon-cancer
#16
Vincenza Barresi, Sergio Castorina, Nicolò Musso, Carmela Capizzi, Tonia Luca, Giovanna Privitera, Daniele Filippo Condorelli
Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively)...
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212809/inactivating-frameshift-mutation-of-putative-tumor-suppressor-genes-pla2r1-and-srpk1-in-gastric-and-colorectal-cancers
#17
LETTER
Ju Hwa Lee, Yun Sol Jo, Min Sung Kim, Nam Jin Yoo, Sug Hyung Lee
No abstract text is available yet for this article.
January 2017: Cancer Genetics
https://www.readbyqxmd.com/read/28212808/next-generation-repeat-free-fish-probes-for-dna-amplification-in-glioblastoma-in-vivo-improving-patient-selection-to-mdm2-targeted-inhibitors
#18
Matteo Brunelli, Albino Eccher, Luca Cima, Tobia Trippini, Serena Pedron, Marco Chilosi, Mattia Barbareschi, Aldo Scarpa, Giampietro Pinna, Giulio Cabrini, Sara Pilotto, Luisa Carbognin, Emilio Bria, Giampaolo Tortora, Adele Fioravanzo, Nicola Schiavo, Mario Meglio, Teodoro Sava, Laura Belli, Guido Martignoni, Claudio Ghimenton
A next-generation FISH probe mapping to the MDM2 locus-specific region has recently been designed. The level of MDM2 gene amplification (high versus low) may allow selection of patients for cancer treatment with MDM2 inhibitors and may predict their responsiveness. We investigated the spectrum of MDM2 gene alterations using the new probes in vivo after visualizing single neoplastic cells in situ from a series of glioblastomas. Signals from next-generation repeat-free FISH interphase probes were identified in tissue microarrays that included 3 spots for each of the 48 cases...
January 2017: Cancer Genetics
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
#19
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/28212806/clonal-evolution-as-detected-by-interphase-fluorescence-in-situ-hybridization-is-associated-with-worse-overall-survival-in-a-population-based-analysis-of-patients-with-chronic-lymphocytic-leukemia-in-british-columbia-canada
#20
Steven J Huang, Krystal Bergin, Adam C Smith, Alina S Gerrie, Helene Bruyere, Chinmay B Dalal, Daniele K Sugioka, Monica Hrynchak, Khaled M Ramadan, Aly Karsan, Tanya L Gillan, Cynthia L Toze
This study evaluates prognostic markers as predictors of clonal evolution (CE) and assesses the impact of CE on overall survival (OS) in a population-based cohort of 159 consecutive eligible patients with chronic lymphocytic leukemia (CLL) obtained from the British Columbia Provincial CLL Database. CE was detected by interphase fluorescence in situ hybridization (FISH) in 34/159 patients (21%) with 65% of CE patients acquiring deletion 17p or 11q. CD38 positive status (≥30%) on flow cytometry predicted 2...
January 2017: Cancer Genetics
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