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Genes, Chromosomes & Cancer

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https://www.readbyqxmd.com/read/29761599/analysis-of-the-exome-aggregation-consortium-exac-database-suggests-that-the-bap1-tumor-predisposition-syndrome-is-underreported-in-cancer-patients
#1
James B Massengill, Klarke M Sample, Robert Pilarski, Joseph McElroy, Frederick H Davidorf, Colleen M Cebulla, Mohamed H Abdel-Rahman
The BAP1-tumor predisposition syndrome (BAP1-TPDS) has been recently identified to predispose patients to a variety of cancers and preneoplastic lesions. About 130 unrelated probands have been identified worldwide; however, the impact of the syndrome is suspected to be much larger given the diversity of the cancer phenotype. To evaluate the frequency of germline BAP1 mutations in the general and cancer populations, we analyzed the Exome Aggregation Consortium (ExAC), a database that contains 53105 exomes of unrelated individuals unaffected by cancer (general population) and exomes of 7601 unrelated individuals affected by cancer provided by the Cancer Genome Atlas (TCGA, cancer subjects)...
May 15, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29726617/copy-number-variant-analysis-using-genome-wide-mate-pair-sequencing
#2
James B Smadbeck, Sarah H Johnson, Stephanie A Smoley, Athanasios Gaitatzes, Travis M Drucker, Roman M Zenka, Farhad Kosari, Stephen J Murphy, Nicole Hoppman, Umut Aypar, William R Sukov, Robert B Jenkins, Hutton M Kearney, Andrew L Feldman, George Vasmatzis
Copy number variation (CNV) is a common form of structural variation detected in human genomes, occurring as both constitutional and somatic events. Cytogenetic techniques like chromosomal microarray (CMA) are widely used in analyzing CNVs. However, CMA techniques cannot resolve the full nature of these structural variations (i.e. the orientation and location of associated breakpoint junctions) and must be combined with other cytogenetic techniques, such as karyotyping or FISH, to do so. This makes the development of a next-generation sequencing (NGS) approach capable of resolving both CNVs and breakpoint junctions desirable...
May 4, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29726589/chromosomal-rearrangements-in-uveal-melanoma-chromothripsis
#3
Natasha M van Poppelen, Serdar Yavuzyigitoglu, Kyra N Smit, Jolanda Vaarwater, Bert Eussen, Tom Brands, Dion Paridaens, Emine Kiliç, Annelies de Klein
Uveal melanoma (UM) is the most common primary intraocular malignancy in the Western world. Recurrent mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, EIF1AX and SF3B1 are described as well as non-random chromosomal aberrations. Chromothripsis is a rare event in which chromosomes are shattered and rearranged and has been reported in a variety of cancers including UM. SNP arrays of 249 UM from patients who underwent enucleation, biopsy or endoresection were reviewed for the presence of chromothripsis. Chromothripsis was defined as ten or more breakpoints per chromosome involved...
May 4, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29726059/two-novel-fusion-genes-aif1l-etv6-and-abl1-aif1l-result-together-with-etv6-abl1-from-a-single-chromosomal-rearrangement-in-acute-lymphoblastic-leukemia-with-prenatal-origin
#4
Julius Lukes, Eliska Potuckova, Lucie Sramkova, Jan Stary, Julia Starkova, Jan Trka, Felix Votava, Jan Zuna, Marketa Zaliova
Fusion genes resulting from chromosomal rearrangements represent a hallmark of childhood acute lymphoblastic leukemia (ALL). Unlike more common fusion genes generated via simple reciprocal chromosomal translocations, formation of the ETV6-ABL1 fusion gene requires 3 DNA breaks and usually results from an interchromosomal insertion. We report a child with ALL in which a single interchromosomal insertion led to the formation of ETV6-ABL1 and two novel fusion genes: AIF1L-ETV6 and ABL1-AIF1L. We demonstrate the prenatal origin of this complex chromosomal rearrangement, which apparently initiated the leukemogenic process, by successful backtracking of the ETV6-ABL1 fusion into the patient's archived neonatal blood...
May 4, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29700887/cic-nutm1-fusion-a-case-which-expands-the-spectrum-of-nut-rearranged-epithelioid-malignancies
#5
Inga-Marie Schaefer, Paola Dal Cin, Christopher D M Fletcher, Glenn J Hanna, Christopher A French
NUT carcinoma (NC) shows very aggressive clinical behavior, occurs predominantly in the thorax and head and neck region of children and adults, and is defined by the presence of NUT (aka NUTM1) rearrangement, mostly BRD4-NUTM1 fusion resulting from t(15;19)(q13, p13.1). So-called "NUT variants" harbor alternate fusions between NUTM1 and BRD3, NSD3, ZNF532, or unknown partners. Rare cases of pediatric tumors with CIC-NUTM1 fusion were recently reported in somatic soft tissue, brain, and kidney. However, such cases have not been identified in adult patients and the presence of a fusion between CIC, characteristic of CIC-rearranged sarcoma, and NUTM1, a defining feature of NC - poses a diagnostic challenge...
April 26, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29700881/elucidation-of-the-developmental-mechanism-of-ovarian-mature-cystic-teratomas-using-b-allele-frequency-plots-of-single-nucleotide-polymorphism-array-data
#6
Hirokazu Usui, Kazuhiko Nakabayashi, Hiroshi Kaku, Kayoko Maehara, Kenichiro Hata, Makio Shozu
Ovarian mature cystic teratomas (MCTs) originate from post-meiotic germ cells. Conventional methods such as karyotyping or short tandem repeat-polymorphism analysis may be used to better classify MCTs, although such data would be insufficient. The aim of this study was to elucidate the origin of ovarian MCTs using B allele-frequency (BAF) plots of single nucleotide polymorphism array data. MCTs can be classified in terms of the zygosity of the centromeres and distal chromosome regions. We evaluated the zygosity of all chromosomes from 38 MCT specimens using BAF plot data...
April 26, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29696703/mcl1-gene-co-expression-module-stratifies-multiple-myeloma-and-predicts-response-to-proteasome-inhibitor-based-therapy
#7
Ayaz Ali Samo, Jiuyi Li, Min Zhou, Yingyu Sun, Yang Yuan, Yunqiu Zhang, Li Jing, Mark van Duin, Xuzhang Lu, Xiaolong Fan
Multiple myeloma (MM) is the second most common hematologic cancer, characterized by abnormal accumulation of plasma cells in the bone marrow. The extensive biological and clinical heterogeneity of MM hinders effective treatment and etiology research. Several molecular classification systems of prognostic impact have been proposed, but they do not predict the response to treatment nor do they correlate to plasma cell development pathways. Here we describe the classification of MM into two distinct subtypes based on the expression levels of a gene module co-expressed with MCL1 (MCL1-M), a regulator of plasma cell survival...
April 26, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29689622/prognostic-value-of-chromosomal-imbalances-gene-mutations-and-bap1-expression-in-uveal-melanoma
#8
Serena Patrone, Irena Maric, Mariangela Rutigliani, Francesco Lanza, Matteo Puntoni, Barbara Banelli, Silvia Rancati, Giovanna Angelini, Adriana Amaro, Paolo Ligorio, Carlotta Defferrari, Mauro Castagnetta, Roberto Bandelloni, Carlo Mosci, Andrea DeCensi, Massimo Romani, Urlich Pfeffer, Silvia Viaggi, Domenico A Coviello
Uveal melanoma (UM) exhibits recurring chromosomal abnormalities and gene driver mutations, which are related to tumor evolution/progression. Almost half of the patients with UM develop distant metastases, predominantly to the liver, and so far there are no effective adjuvant therapies. An accurate UM genetic profile could assess the individual patient's metastatic risk, and provide the basis to determine an individualized targeted therapeutic strategy for each UM patient. To investigate the presence of specific chromosomal and gene alterations, BAP1 protein expression, and their relationship with distant progression free survival (DPFS), we analyzed tumor samples from 63 UM patients (40 men and 23 women, with a median age of 64 years), who underwent eye enucleation by a single cancer ophthalmologist from December 2005 to June 2016...
April 24, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29664232/correlation-of-tet2-snp-rs2454206-with-improved-survival-in-children-with-acute-myeloid-leukemia-featuring-intermediate-risk-cytogenetics
#9
Xingjuan Wang, Xi Chen, Zhenzhen Yang, Hu Dou, Ling Lu, Junqin Bi, Lin Zou, Jie Yu, Liming Bao
Single nucleotide polymorphisms (SNPs) may influence the disease course and outcome of hematologic neoplasms. SNP rs2454206 is common in the TET2 gene, which plays a role in epigenetic regulation of myelopoiesis. Few investigations examined the role of TET2 SNP rs2454206 in acute myeloid leukemia (AML) and none of those studies was performed in Chinese populations. Here, we report the prevalence and clinical relevance of TET2 SNP rs2454206 in 254 Chinese patients with childhood AML. Our data demonstrate that TET2 SNP rs2454206AG/GG is associated with improved overall survival and event-free survival in AML patients with intermediate-risk cytogenetics features...
April 17, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29663558/usefulness-of-bcor-gene-mutation-as-a-prognostic-factor-in-acute-myeloid-leukemia-with-intermediate-cytogenetic-prognosis
#10
Kazuki Terada, Hiroki Yamaguchi, Toshimitsu Ueki, Kensuke Usuki, Yutaka Kobayashi, Kenji Tajika, Seiji Gomi, Saiko Kurosawa, Riho Saito, Yutaka Furuta, Keiki Miyadera, Taichiro Tokura, Atushi Marumo, Ikuko Omori, Masahiro Sakaguchi, Yusuke Fujiwara, Shunsuke Yui, Takeshi Ryotokuji, Kunihito Arai, Tomoaki Kitano, Satoshi Wakita, Takahiro Fukuda, Koiti Inokuchi
BCOR gene is a transcription regulatory factor that plays an essential role in normal hematopoiesis. The wider introduction of next-generation sequencing technology has led to reports in recent years of mutations in the BCOR gene in acute myeloid leukemia (AML), but the related clinical characteristics and prognosis are not sufficiently understood. We investigated the clinical characteristics and prognosis of 377 de novo AML cases with BCOR or BCORL1 mutation. BCOR or BCORL1 gene mutations were found in 28 cases (7...
April 16, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29575536/mutation-analysis-of-adenomas-and-carcinomas-of-the-colon-early-and-late-drivers
#11
Roger K Wolff, Michael D Hoffman, Erica C Wolff, Jennifer S Herrick, Lori C Sakoda, Wade Samowitz, Martha L Slattery
Colorectal cancer (CRC) accounts for about 8% of all new cancer cases diagnosed in the US. We used whole exome sequence data from triplet samples (colon carcinoma, colon adenoma, and colon normal tissue) from 18 individuals to assess gene mutation rates. Of the 2204 genes that were mutated, APC, TTN, TP53, KRAS, OBSCN, SOX9, PCDH17, SIGLEC10, MYH6, and BRD9 were consistent with genes being an early driver of carcinogenesis, in that they were mutated in multiple adenomas and multiple carcinomas. Fifty-two genes were mutated in ≥12...
March 25, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29569294/aml-with-t-7-12-q36-p13-is-associated-with-infancy-and-trisomy-19-data-from-nopho-aml-and-review-of-the-literature
#12
Anne Dorte Lerche Espersen, Ulrika Noren-Nyström, Jonas Abrahamsson, Shau-Yin Ha, Cornelis Jan Pronk, Kirsi Jahnukainen, Ólafur G Jónsson, Birgitte Lausen, Josefine Palle, Bernward Zeller, Lars Palmqvist, Henrik Hasle
The t(7;12)(q36;p13) (MNX1/ETV6) is not included in the WHO classification but has been described in up to 30% of acute myeloid leukemia (AML) in children <2 years and associated with a poor prognosis. We present the clinical and cytogenetics characteristics of AML cases with t(7;12)(p36;p13). A literature review identified 35 patients with this translocation, published between 2000 and 2015. Outcome data were available in 22 cases. The NOPHO-AML (Nordic Society for Pediatric Hematology and Oncology) database contained 651 patients with AML from 1993 to 2014 and seven (1...
March 22, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29532557/a-prolonged-response-to-platinum-based-therapy-in-a-patient-with-metastatic-urothelial-carcinoma-harboring-a-single-rearranged-and-truncated-nf2-gene
#13
Tala Achkar, Siraj M Ali, Allison Welsh, Rajiv Dhir, Susanne M Gollin, Rahul A Parikh
Tumor genome sequencing has become an invaluable resource in determining targets for new therapies. In this report, we describe the case of a patient with metastatic urothelial carcinoma with sarcomatoid features. Sarcomatoid differentiation is a rare histologic subtype that confers a more aggressive course. The first-line treatment for patients with urothelial carcinoma is platinum-based chemotherapy. Next generation tumor sequencing performed using the FoundationOne assay revealed loss of one NF2 allele and an unbalanced der(22)t(10;22)(p11...
March 13, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29520894/evaluation-of-mlh1-variants-of-unclear-significance
#14
Nicole Köger, Lea Paulsen, Francisco López-Kostner, Adriana Della Valle, Carlos Alberto Vaccaro, Edenir Inêz Palmero, Karin Alvarez, Carlos Sarroca, Florencia Neffa, Pablo German Kalfayan, Maria Laura Gonzalez, Benedito Mauro Rossi, Rui Manuel Reis, Angela Brieger, Stefan Zeuzem, Inga Hinrichsen, Mev Dominguez-Valentin, Guido Plotz
Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in silico predictions on structure and conservation...
July 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29516567/investigating-piwi-interacting-rna-regulome-in-human-neuroblastoma
#15
Jyoti Roy, Bibekanand Mallick
Remarkable attempts have been exercised in recent years using high-throughput technologies to identify and decipher the functions of piRNAs in various abnormalities like cancer. However, piRNAs in the oncogenesis of neuroblastoma (NB) has not been reported yet even after their illustrated roles in neurological processes. Therefore, we investigated the piRNA transcriptome in IMR-32 and SH-SY-5Y NB cell lines by employing high-throughput next-generation sequencing after confirming the expression of three associated PIWILs both at mRNAs and protein level by qRT-PCR and immunofluroscence, respectively...
July 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29460398/centralization-errors-in-comparative-genomic-hybridization-array-analysis-of-pituitary-tumor-samples
#16
Hélène Lasolle, Eudeline Alix, Clément Bonnefille, Mad-Hélénie Elsensohn, Jessica Michel, Damien Sanlaville, Pascal Roy, Gérald Raverot, Claire Bardel
Reliable interpretation of comparative genomic hybridization array (aCGH) results requires centralization and normalization of the data. We evaluated the reliability of aCGH centralization by comparing aCGH results (with classical centralization-normalization steps) to fluorescence in situ hybridization (FISH) results. In addition, we propose a method to correct centralization bias. Sixty-six pituitary tumors were analyzed (Agilent aCGH + SNP 4 × 180K microarray). For each tumor, the FISH-based log2 (ratios) of a subset of chromosomes were compared with the corresponding aCGH raw log2 (ratios)...
June 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29427526/nup98-bptf-gene-fusion-identified-in-primary-refractory-acute-megakaryoblastic-leukemia-of-infancy
#17
Mathieu Roussy, Mélanie Bilodeau, Loubna Jouan, Pauline Tibout, Louise Laramée, Emmanuelle Lemyre, France Léveillé, Frédérique Tihy, Sophie Cardin, Camille Sauvageau, Françoise Couture, Isabelle Louis, Aurélien Choblet, Natalie Patey, Patrick Gendron, Michel Duval, Pierre Teira, Josée Hébert, Brian T Wilhelm, John K Choi, Tanja A Gruber, Henrique Bittencourt, Sonia Cellot
The advent of large scale genomic sequencing technologies significantly improved the molecular classification of acute megakaryoblastic leukaemia (AMKL). AMKL represents a subset (∼10%) of high fatality pediatric acute myeloid leukemia (AML). Recurrent and mutually exclusive chimeric gene fusions associated with pediatric AMKL are found in 60%-70% of cases and include RBM15-MKL1, CBFA2T3-GLIS2, NUP98-KDM5A and MLL rearrangements. In addition, another 4% of AMKL harbor NUP98 rearrangements (NUP98r), with yet undetermined fusion partners...
June 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29383790/xpnpep3-is-a-novel-transcriptional-target-of-canonical-wnt-%C3%AE-catenin-signaling
#18
Raju Kumar, Viswakalyan Kotapalli, Ashmala Naz, Swarnalata Gowrishankar, Satish Rao, Jonathan R Pollack, Murali Dharan Bashyam
Canonical Wnt/β-catenin signaling plays important roles in embryonic development and adult tissue regeneration while aberrant Wnt activation is the major driver of sporadic colorectal cancer (CRC). Thus, it is important to characterize the complete β-catenin target transcriptome. We previously performed microarray-based mRNA profiling of rectal cancer samples stratified for Wnt status. In addition to AXIN2 and EPHB2, XPNPEP3 transcripts were significantly elevated in tumors exhibiting activated Wnt/β-catenin signaling, validated by Q-PCR...
June 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29377495/cancer-etiology-variation-in-cancer-risk-among-tissues-is-poorly-explained-by-the-number-of-gene-mutations
#19
Miguel López-Lázaro
Recent evidence indicates that the risk of being diagnosed with cancer in a tissue is strongly correlated (0.80) with the number of stem cell divisions accumulated by the tissue. Since cell division can generate random mutations during DNA replication, this correlation has been used to propose that cancer is largely caused by the accumulation of unavoidable mutations in driver genes. However, no correlation between the number of gene mutations and cancer risk across tissues has been reported. Because many somatic mutations in cancers originate prior to tumor initiation and the number of cell divisions occurring during tumor growth is similar among tissues, I use whole genome sequencing information from 22 086 cancer samples and incidence data from the largest cancer registry in each continent to study the relationship between the number of gene mutations and the risk of cancer across 33 tissue types...
June 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29359367/truncating-mutations-of-tp53aip1-gene-predispose-to-cutaneous-melanoma
#20
Meriem Benfodda, Steven Gazal, Vincent Descamps, Nicole Basset-Seguin, Lydia Deschamps, Luc Thomas, Celeste Lebbe, Philippe Saiag, Roberto Zanetti, Lidia Sacchetto, Giovanna Chiorino, Maria Scatolini, Bernard Grandchamp, Armand Bensussan, Nadem Soufir
Genetic predisposition to cutaneous malignant melanoma (CMM) involves highly penetrant predisposing genes and low and intermediate penetrant predisposing alleles. However, the missing heritability in (CMM) is still high. For such and in order to identify new genetic factors for CMM, we conducted an exome sequencing study in high-risk CMM patients. Two rounds of exome sequencing were successively performed in 33 and 27 high-risk patients. We focused on genes carrying rare nonsense, frameshift, and splice variants (allelic frequency <1%) that were present in both series of exomes...
June 2018: Genes, Chromosomes & Cancer
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