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Cancer Genetics

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https://www.readbyqxmd.com/read/29625863/circulating-cell-free-dna-for-non-invasive-cancer-management
#1
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
#2
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
#3
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/29666008/h2afy-is-a-novel-fusion-partner-of-mecom-in-acute-myeloid-leukemia
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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/29405996/familial-esophageal-squamous-cell-carcinoma-with-damaging-rare-germline-mutations-in-kcnj12-kcnj18-and-gprin2-genes
#11
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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/29405991/svatools-for-junction-detection-of-genome-wide-chromosomal-rearrangements-by-mate-pair-sequencing-mpseq
#16
Sarah H Johnson, James B Smadbeck, Stephanie A Smoley, Athanasios Gaitatzes, Stephen J Murphy, Faye R Harris, Travis M Drucker, Roman M Zenka, Beth A Pitel, Ross A Rowsey, Nicole L Hoppman, Umut Aypar, William R Sukov, Robert B Jenkins, Andrew L Feldman, Hutton M Kearney, George Vasmatzis
Mate-pair sequencing (MPseq), using long-insert, paired-end genomic libraries, is a powerful next-generation sequencing-based approach for the detection of genomic structural variants. SVAtools is a set of algorithms to detect both chromosomal rearrangements and large (>10 kb) copy number variants (CNVs) in genome-wide MPseq data. SVAtools can also predict gene disruptions and gene fusions, and characterize the genomic structure of complex rearrangements. To illustrate the power of SVAtools' junction detection methods to provide comprehensive molecular karyotypes, MPseq data were compared against a set of samples previously characterized by traditional cytogenetic methods...
February 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29310839/decoding-colorectal-cancer-epigenomics
#17
REVIEW
Khalid El Bairi, Kanwal Tariq, Imane Himri, Abdeslam Jaafari, Wiam Smaili, Abdul Hafeez Kandhro, Adel Gouri, Bouchra Ghazi
Colorectal cancer (CRC) is very heterogeneous and presents different types of epigenetic alterations including DNA methylation, histone modifications and microRNAs. These changes are considered as characteristics of various observed clinical phenotypes. Undoubtedly, the discovery of epigenetic pathways with novel epigenetic-related mechanisms constitutes a promising advance in cancer biomarker discovery. In this review, we provide an evidence-based discussing of the current understanding of CRC epigenomics and its role in initiation, epithelial-to-mesenchymal transition and metastasis...
January 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29310838/a-leukemic-double-hit-follicular-lymphoma-associated-with-a-complex-variant-translocation-t-8-14-18-q24-q32-q21-involving-bcl2-myc-and-igh
#18
Daisuke Minakata, Kazuya Sato, Takashi Ikeda, Yumiko Toda, Shoko Ito, Kiyomi Mashima, Kento Umino, Hirofumi Nakano, Ryoko Yamasaki, Kaoru Morita, Yasufumi Kawasaki, Miyuki Sugimoto, Chihiro Yamamoto, Masahiro Ashizawa, Kaoru Hatano, Iekuni Oh, Shin-Ichiro Fujiwara, Ken Ohmine, Hirotoshi Kawata, Kazuo Muroi, Ikuo Miura, Yoshinobu Kanda
Double-hit lymphoma (DHL) is defined as lymphoma with concurrent BCL2 and MYC translocations. While the most common histological subtype of DHL is diffuse large B-cell lymphoma, the present patient had leukemic follicular lymphoma (FL). A 52-year-old man was admitted to our hospital due to general fatigue and cervical and inguinal lymph node swelling. The patient was leukemic and the pathological diagnosis of the inguinal lymph node was FL grade 1. Chromosomal analysis revealed a complex karyotype including a rare three-way translocation t(8;14;18)(q24;q32;q21) involving the BCL2, MYC, and IGH genes...
January 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29310837/assessment-of-a-fbxw8-frameshift-mutation-c-1312_1313delgt-in-breast-cancer-patients-and-controls-from-central-europe
#19
Jing Wang, Natalia Bogdanova, Peter Schürmann, Tjoung-Won Park-Simon, Robert Geffers, Thilo Dörk
F-box proteins participate in multiple cellular processes through ubiquitylation and subsequent degradation of target proteins, such as cyclin D1 as target of FBXW8. To investigate the spectrum of FBXW8 germ-line mutations in patients with breast cancer and healthy controls, we analyzed the whole FBXW8 coding region and flanking untranslated portions in germ-line DNA samples of 91 breast cancer patients and 277 healthy controls using next-generation amplicon sequencing. Five missense variants, one splice site variant, one frameshift variant, one synonymous variant, and one variant in the 3'-UTR were identified...
January 2018: Cancer Genetics
https://www.readbyqxmd.com/read/29310836/circulating-long-non-coding-rna-malat1-expression-as-molecular-biomarker-in-egyptian-patients-with-breast-cancer
#20
Haidy E Zidan, Rehab A Karam, Omnia S El-Seifi, Tamer M Abd Elrahman
The abnormal contribution of long non-coding RNA (lncRNAs) expression to human tumorigenesis is still a matter of debate. Breast cancer is the most common cancer in females; it represents a terrible problem in our country. The aim of this research was to assess the role of MALAT1, as one of lncRNAs, as a potential biomarker in breast cancer. This study comprised 80 patients with breast cancer and 80 controls. MALAT1 expression was measured by RT-quantitative polymerase chain reaction (qPCR). CA15-3 was estimated using chemiluminescence immunoassay (CLIA)...
January 2018: Cancer Genetics
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