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Cancer Genetics

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https://www.readbyqxmd.com/read/29778234/egfl7-and-rassf1-promoter-hypermethylation-in-epithelial-ovarian-cancer
#1
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
https://www.readbyqxmd.com/read/29778233/female-specific-association-among-i-j-and-k-mitochondrial-genetic-haplogroups-and-cancer-a-longitudinal-cohort-study
#2
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
https://www.readbyqxmd.com/read/29778232/nuclear-bap1-loss-is-common-in-intrahepatic-cholangiocarcinoma-and-a-subtype-of-hepatocellular-carcinoma-but-rare-in-pancreatic-ductal-adenocarcinoma
#3
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
https://www.readbyqxmd.com/read/29778231/clinical-germline-diagnostic-exome-sequencing-for-hereditary-cancer-findings-within-novel-candidate-genes-are-prevalent
#4
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
https://www.readbyqxmd.com/read/29778230/etv6-runx1-positive-childhood-acute-lymphoblastic-leukemia-all-the-spectrum-of-clonal-heterogeneity-and-its-impact-on-prognosis
#5
Μ Αmpatzidou, S I Papadhimitriou, G Paterakis, D Pavlidis, Κ Tsitsikas, I V Kostopoulos, V Papadakis, G Vassilopoulos, S Polychronopoulou
The prognostic significance of the ETV6/RUNX1-fusion and of the accompanying aberrations is disputable; whether co-existing sub-clones are responsible for delayed MRD-clearance and thus, moderate outcome, remains to be clarified. We studied, in a paediatric cohort of 119 B-ALLs, the relation between the ETV6/RUNX1 aberration and the co-existing subclones with (a) presenting clinical/biological features, (b) early response to treatment(MRD) and (c) long-term outcome over a 12-year period. Patients were homogeneously treated according to BFM-based-protocols...
August 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666008/h2afy-is-a-novel-fusion-partner-of-mecom-in-acute-myeloid-leukemia
#6
Qiaoyan Han, Jiao Lu, Jianjiang Wang, Jinsong Ye, Xin Jiang, Haoyue Chen, Chunhua Liu, Lu Chen, Tong Lin, Suning Chen, Miao Sun, Feng Gao
The MECOM gene encoding a zinc finger protein that functions as a transcription factor, was located on chromosome 3q26, and rearrangements of MECOM often cause its overexpression in acute myeloid leukemia (AML). We identified H2AFY as a novel fusion gene partner of MECOM in an elderly male AML patient with cryptic 3q26 rearrangement using the whole transcriptome sequencing, who carried out abnormal karyotype of 46,XY,t(3;5)(q27;q31),add(14)(p11). We validated the existence of the unreported H2AFY-MECOM fusion gene by RT-PCR and Sanger DNA sequencing, and detected mutations of NRAS and BCOR in this patient...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666007/mutation-analysis-of-therapy-related-myeloid-neoplasms
#7
Takahiro Nishiyama, Yuichi Ishikawa, Naomi Kawashima, Akimi Akashi, Yoshiya Adachi, Hikaru Hattori, Yoko Ushijima, Hitoshi Kiyoi
We analyzed the genetic mutation status of 13 patients with therapy-related myeloid neoplasms (t-MN). Consistent with previous reports, t-MN cells preferentially acquired mutations in TP53 and epigenetic modifying genes, instead of mutations in tyrosine kinase and spliceosome genes. Furthermore, we compared the mutation status of three t-MN cells with each of the initial lymphoid malignant cells, and identified common mutations among t-MN and the initial malignant cells in two patients. In a patient who developed chronic myelomonocytic leukemia (CMML) after follicular lymphoma (FL), TET2 mutation was identified in both CMML and FL cells...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666006/deletion-of-runx1-exons-1-and-2-associated-with-familial-platelet-disorder-with-propensity-to-acute-myeloid-leukemia
#8
Marcela Cavalcante de Andrade Silva, Ana Cristina Victorino Krepischi, Leslie Domenici Kulikowski, Evelin Aline Zanardo, Luciana Nardinelli, Aline Medeiros Leal, Silvia Souza Costa, Nair Hideki Muto, Vanderson Rocha, Elvira Deolinda Rodrigues Pereira Velloso
Familial platelet disorder with propensity to acute myeloid leukemia (FPD/AML) associated with RUNX1 mutations is an autosomal dominant disorder included in the group of the myeloid neoplasms with germ line predisposition. We describe two brothers who were diagnosed with hematological malignancies (one with AML and the other with T-cell lymphoblastic lymphoma). There was a history of leukemia in the paternal family and two of their siblings presented with low platelet counts and no history of significant bleeding...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666005/unexpected-favorable-outcome-in-a-patient-with-high-grade-b-cell-lymphoma-with-abnormalities-of-myc-bcl6-and-bcl2-loci
#9
Thomas Adams, Deborah Fuchs, Patricia K Shadoan, Laurel Johnstone, Branden M Lau, Lee McGhan, Faiz Anwer, Hussam Al-Kateb
High grade B-cell lymphoma (HGBCL) by WHO 2016 classification requires rearrangements of MYC and BCL2 and/or BCL6, practically covering the so called "double-hit" or "triple hit" lymphomas. We report a case of HGBCL "triple-hit" lymphoma in a 64-year old female. Cytogenetic and fluorescence in situ hybridization (FISH) studies revealed complex karyotype including rearrangement of MYC to a novel, non-IG partner on chromosome 18, and rearrangement of BCL2, BCL6 and IGH as well as ins(3)(q21q27...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666004/biallelic-tp53-gain-of-function-mutations-in-rapidly-progressing-solid-tumors
#10
Christopher M Sande, Brian Chang, Varun Monga, Aaron D Bossler, Deqin Ma
Recent studies are discovering TP53 mutations with gain of function (GOF) properties that promote tumorigenesis via a variety of mechanisms. To our knowledge, all reported compound mutations are allelic. We identified two patients with biallelic GOF TP53 mutations in their tumors and a third with allelic compound variants. The correlation with p53 expression was also examined. Genomic DNA was extracted from formalin-fixed, paraffin-embedded tissue and mutational analysis was performed using Ion AmpliSeq™Cancer HotSpot Panel V2...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666003/long-noncoding-rna-ccat1-polymorphisms-are-associated-with-the-risk-of-colorectal-cancer
#11
Yingjun Li, Fangyuan Jing, Ye Ding, Qingfang He, Yaohong Zhong, Chunhong Fan
Colorectal cancer associated transcript 1 (CCAT1) is a novel long noncoding RNA, whose overexpression is evident in both early phase of tumorigenesis and later disease stages in colorectal cancer (CRC). No study has explored the relationship between CCAT1 polymorphisms and CRC risk. In the present study, a case-control study was conducted to investigate the association between CCAT1 polymorphisms and CRC risk in Chinese population. We identified that CCAT1 rs67085638 polymorphism was associated with an increased risk of CRC (OR = 1...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29666002/clinical-pathologic-cytogenetic-and-molecular-profiling-in-self-identified-black-women-with-uterine-leiomyomata
#12
Mark A Hayden, Zehra Ordulu, C Scott Gallagher, Bradley J Quade, Raymond M Anchan, Nia Robinson Middleton, Serene S Srouji, Elizabeth A Stewart, Cynthia C Morton
Black women are disproportionately affected by uterine leiomyomata (UL), or fibroids, compared to other racial groups, having a greater lifetime risk of developing UL and an earlier age of diagnosis. In order to elucidate molecular and genetic mechanisms responsible for the increased prevalence and morbidity associated with UL in black women, clinical, pathologic, cytogenetic, and select molecular profiling (MED12 mutation analysis) of 75 self-reported black women undergoing surgical treatment for UL was performed...
April 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29625863/circulating-cell-free-dna-for-non-invasive-cancer-management
#13
REVIEW
Caitlin M Stewart, Dana W Y Tsui
Cell-free DNA (cfDNA) was first identified in human plasma in 1948 and is thought to be released from cells throughout the body into the circulatory system. In cancer, a portion of the cfDNA originates from tumour cells, referred to as circulating-tumour DNA (ctDNA), and can contain mutations corresponding to the patient's tumour, for instance specific TP53 alleles. Profiling of cfDNA has recently become an area of increasing clinical relevance in oncology, in particular due to advances in the sensitivity of molecular biology techniques and development of next generation sequencing technologies, as this allows tumour mutations to be identified and tracked non-invasively...
March 11, 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29567030/comparison-of-4-commercial-kits-for-the-extraction-of-circulating-dna-from-plasma
#14
Kristina Warton, Lisa-Jane Graham, Nicole Yuwono, Goli Samimi
The utility of circulating DNA as a source of clinical biomarkers in blood is limited by its low concentration and small fragment size. Effective purification methods can maximize circulating DNA yield and contribute to the success of downstream protocols. We describe the evaluation of 4 commercial DNA purification kits-QIAamp Circulating Nucleic Acids kit, QIAamp DNA Blood Mini kit, QIAamp Ultrasens Virus kit and the QIASymphony DSP Virus kit-for the extraction of high and low molecular weight DNA from blood plasma...
March 6, 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29572011/analysis-of-circulating-tumor-dna-in-breast-cancer-as-a-diagnostic-and-prognostic-biomarker
#15
REVIEW
Mersedeh Rohanizadegan
Despite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic utility is still under investigation...
February 24, 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29405996/familial-esophageal-squamous-cell-carcinoma-with-damaging-rare-germline-mutations-in-kcnj12-kcnj18-and-gprin2-genes
#16
Narjes Khalilipour, Ancha Baranova, Amir Jebelli, Alireza Heravi-Moussavi, Sergey Bruskin, Mohammad Reza Abbaszadegan
In Iran, esophageal cancer is the fourth common cancers in women and sixth common cancers in men. Here we evaluated the importance of familial risk factors and the role of genetic predisposition in Esophageal Squamous Cell Carcinoma (ESCC) using Whole-Exome Sequencing (WES). Germline damaging mutations were identified in WES data from 9 probands of 9 unrelated ESCC pedigrees. Mutations were confirmed with Sanger sequencing and evaluated amplification-refractory mutation system-Polymerase Chain Reaction (ARMS-PCR) in 50 non-related ethnically matched samples and in complete genomics database...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29405995/survey-of-gynecological-carcinosarcomas-in-families-with-breast-and-ovarian-cancer-predisposition
#17
Carla B Ripamonti, Siranoush Manoukian, Bernard Peissel, Jacopo Azzollini, Maria Luisa Carcangiu, Paolo Radice
Carcinosarcomas (CSs) are biphasic neoplasms composed of high grade, malignant, epithelial and mesenchymal elements. The incidence of gynecological CSs (GCSs) is 0.4/100,000 women per year. Patients affected with GCSs have been occasionally reported in Hereditary Breast Ovarian Cancer (HBOC) families, including a few cases with pathogenic variants in BRCA1/BRCA2 genes. The prevalence and the association of GCSs in HBOC families have not been systematically investigated. Thus, we searched for families with GCSs in the HBOC registry of the National Cancer Institute of Milan...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29405994/alk-tpm3-rearrangement-in-adult-renal-cell-carcinoma-report-of-a-new-case-showing-loss-of-chromosome-3-and-literature-review
#18
Yohan Bodokh, Damien Ambrosetti, Valérie Kubiniek, Branwel Tibi, Matthieu Durand, Jean Amiel, Morgane Pertuit, Anne Barlier, Florence Pedeutour
Seven cases of translocation-associated renal cell carcinoma involving ALK (ALK-tRCC) were referenced in the last World Health Organization's classification (2016), in a group of emerging/provisional RCC. The first three cases were pediatric, medullary-based, associated with sickle-cell trait and showed a fusion of ALK with VCL. Thirteen cases have been further described. They displayed clinical, morphological and genomic heterogeneity. Most of them occurred in adults. None of the patients was affected by sickle-cell disease...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29405993/molecular-approaches-identify-a-cryptic-mecom-rearrangement-in-a-child-with-a-rapidly-progressive-myeloid-neoplasm
#19
Roberto R Capela de Matos, Moneeb A K Othman, Gerson M Ferreira, Elaine S Costa, Joana B Melo, Isabel M Carreira, Mariana T de Souza, Bruno A Lopes, Mariana Emerenciano, Marcelo G P Land, Thomas Liehr, Raul C Ribeiro, Maria Luiza M Silva
Myeloid neoplasms are a heterogeneous group of hematologic disorders with divergent patterns of cell differentiation and proliferation, as well as divergent clinical courses. Rare recurrent genetic abnormalities related to this group of cancers are associated with poor outcomes. One such abnormality is the MECOM gene rearrangement that typically occurs in cases with chromosome 7 abnormalities. MECOM encodes a transcription factor that plays an essential role in cell proliferation and maintenance and also in epigenetic regulation...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29405992/characterization-of-novel-large-duplications-in-the-msh2-gene-of-three-unrelated-lynch-syndrome-patients
#20
Raffaella Liccardo, Marina De Rosa, Giovanni Battista Rossi, Gabriele Rigler, Paola Izzo, Francesca Duraturo
Lynch syndrome (LS) is associated with germ-line mutations in the DNA mismatch repair (MMR) genes, mainly MLH1, MSH2, MSH6, and PMS2. Most of genetic variants in the MMR genes predisposing to LS are point mutations, small deletions and insertions but large genomic rearrangements in the MMR genes also predisposing to Lynch syndrome. In this study, we report a novel, large rearrangement of the MSH2 gene, manifested by a duplication spanning a 14,846-bps region from intron 7 through intron 9. The breakpoints of this rearrangement were characterized by sequencing...
February 2018: Cancer Genetics
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