Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer
Publication date: Available online 6 September 2019Source: Cancer GeneticsAuthor(s): Cihangir Yandım, Gökhan KarakülahABSTRACTLimited studies on breast cancer indicated pathogenic changes in the expressions of some repeat elements. A global analysis was much needed within this context to distinguish the most significant repeats from more than a thousand repeat elements. Utilising a previously presented RNA-seq dataset, we studied expression changes of all repeats in ER+/HER2- human breast tumour samples obtained from 22 patients in comparison to matched normal tissues. 56 repeat subtypes including satellites and...
Source: Cancer Genetics - September 6, 2019 Category: Cancer & Oncology Source Type: research

Burkitt-like Lymphoma in a Pediatric Patient with Familial Adenomatous Polyposis
Publication date: Available online 4 September 2019Source: Cancer GeneticsAuthor(s): Katie M. Strobel, Jacquelyn N. Crane, Kathryn L. Bradford, Yalda Naeini, William A. May, Vivian Y. ChangAbstractFamilial adenomatous polyposis (FAP) is an autosomal dominant condition that predisposes to multiple malignancies, most commonly colorectal carcinoma, but has rarely been associated with lymphoma. We discuss one patient found to have Burkitt-like Lymphoma (BLL) with 11q aberration in the setting of previously undiagnosed FAP. We review the literature of FAP and associated malignancies and the provisional WHO classification of Bur...
Source: Cancer Genetics - September 6, 2019 Category: Cancer & Oncology Source Type: research

A novel BRCA1 germline mutation promotes triple-negative breast cancer cells progression and enhances sensitivity to DNA damage agents
In this study, we conducted whole-exome sequencing to identify the disease-associated genes in a specific pedigree, in which at least eight individuals were diagnosed with cancers, including breast cancer, urothelial cancer, uterine cancer and colorectal cancer. Furthermore, a nonsense mutation BRCA1 p.Trp372X was identified in the proband. The Sanger sequencing data has validated the same nonsense mutation in other 4 cancer patients and 3 normal family members. Additionally, functional experiments detected that this mutation was implicated in TNBC progression, manifesting as increased cell proliferation and migration. Cel...
Source: Cancer Genetics - August 31, 2019 Category: Cancer & Oncology Source Type: research

Potential of epigenetic events in human thyroid cancer
Publication date: Available online 23 August 2019Source: Cancer GeneticsAuthor(s): Abdelkareem A. Ahmed, Mohammed Elmujtba Adam EssaAbstractThyroid cancer remains the highest prevailing endocrine malignancy, and its incidence rate has progressively increased in the previous years. Above 95% of thyroid tumor are follicular cells types of carcinoma in which are considered invasive type of tumor. The pathogenesis and molecular mechanism of thyroid tumors are yet remains elucidated, in spite of activating RET, RAS and BRAF carcinogenesis have been well introduced. Nemours molecular alterations have been defined and have reveal...
Source: Cancer Genetics - August 24, 2019 Category: Cancer & Oncology Source Type: research

A complex and cryptic intrachromosomal rearrangement generating the FIP1L1_PDGFRA in adult acute myeloid leukemia
Publication date: November 2019Source: Cancer Genetics, Volume 239Author(s): Nicoletta Coccaro, Luisa Anelli, Paola Orsini, Antonella Zagaria, Angela Minervini, Luciana Impera, Giuseppina Tota, Crescenzio Francesco Minervini, Cosimo Cumbo, Elisa Parciante, Maria Rosa Coserva, Immacolata Attolico, Giorgina Specchia, Francesco AlbanoAbstractMyeloid neoplasms with eosinophilia and abnormalities of the PDGFRA gene can benefit from therapy with tyrosine kinase inhibitors, therefore revealing the PDGFRA rearrangement is essential to ensure the best choice of treatment. The most common PDGFRA partner is the FIP1L1 gene, generatin...
Source: Cancer Genetics - August 24, 2019 Category: Cancer & Oncology Source Type: research

A loss-of-function heterozygous BRCA1 mutation found in a triple negative breast cancer case with family history of multiple cancers
In this study, we conducted whole-exome sequencing to identify the disease-associated genes in a specific pedigree, in which at least eight individuals were diagnosed with cancers, including breast cancer, urothelial cancer, uterine cancer and colorectal cancer. Furthermore, a nonsense mutation BRCA1 p.Trp372X was identified in the proband. The Sanger sequencing data has validated the same nonsense mutation in other 4 cancer patients and 3 normal family members. Additionally, functional experiments detected that this mutation was implicated in TNBC progression, manifesting as increased cell proliferation and migration. Cel...
Source: Cancer Genetics - August 23, 2019 Category: Cancer & Oncology Source Type: research

Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing
Publication date: Available online 23 August 2019Source: Cancer GeneticsAuthor(s): Chun Hang Au, Dona N. Ho, Beca B.K. Ip, Thomas S.K. Wan, Margaret H.L. Ng, Edmond K.W. Chiu, Tsun Leung Chan, Edmond S.K. MaAbstractDetection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and clinically practical tool, but it depends on expression of RNA transcript from the underlying DNA translocation. Here, we show the clinical utility of nanopore long-read sequencing in rapidly detecting DNA translocation ...
Source: Cancer Genetics - August 23, 2019 Category: Cancer & Oncology Source Type: research

A complex and cryptic intrachromosomal rearrangement generating the fip1l1-pdgfra fusion gene in adult acute myeloid leukemia
Publication date: Available online 21 August 2019Source: Cancer GeneticsAuthor(s): Nicoletta Coccaro, Luisa Anelli, Paola Orsini, Antonella Zagaria, Angela Minervini, Luciana Impera, Giuseppina Tota, Crescenzio Francesco Minervini, Cosimo Cumbo, Elisa Parciante, Maria Rosa Coserva, Immacolata Attolico, Giorgina Specchia, Francesco AlbanoAbstractMyeloid neoplasms with eosinophilia and abnormalities of the PDGFRA gene can benefit from therapy with tyrosine kinase inhibitors, therefore revealing the PDGFRA rearrangement is essential to ensure the best choice of treatment. The most common PDGFRA partner is the FIP1L1 gene, gen...
Source: Cancer Genetics - August 22, 2019 Category: Cancer & Oncology Source Type: research

CONFIRMATION OF DAMAGING EFFECT OF MSH2 c.2634+1G>C MUTATION ON SPLICING, ITS CLASSIFICATION AND IMPLICATIONS FOR COUNSELING
DiscussionMSH2 c.2634+1G>C mutation was not reported previously as LS associated. We confirmed its damaging effect on splicing. in silico tools predict consequent loss of protein domains implicating disrupted protein function. Our results suggest that this mutation should be classified as Pathogenic, and indicate inclusion of bladder cancer in LS cancer spectrum. (Source: Cancer Genetics)
Source: Cancer Genetics - August 15, 2019 Category: Cancer & Oncology Source Type: research

Cytogenomic Characterization of Double Minute Heterogeneity in Therapy Related Acute Myeloid Leukemia
Publication date: Available online 6 August 2019Source: Cancer GeneticsAuthor(s): Prasad Koduru, Weina Chen, Barbara Haley, Kevin Ho, Dwight Oliver, Kathleen WilsonAbstractBreast cancer patients treated with adjuvant chemotherapy regimens containing alkylating agents and anthracyclines are at an increased risk for secondary myeloid malignancies, either acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). Complex genomic changes (karyotypes and/or gene amplification) accompany the development of the secondary neoplasms. Here we present a unique case of a breast cancer patient who developed secondary AML within 18...
Source: Cancer Genetics - August 8, 2019 Category: Cancer & Oncology Source Type: research

Masked hypodiploidy: hypodiploid acute lymphoblastic leukemia (ALL) mimicking hyperdiploid ALL in children: A report from the Children's Oncology Group
Publication date: Available online 30 July 2019Source: Cancer GeneticsAuthor(s): Andrew J Carroll, Mary Shago, Fady M Mikhail, Susana C Raimondi, Betsy A Hirsch, Mignon L Loh, Elizabeth A Raetz, Michael J Borowitz, Brent L Wood, Kelly W Maloney, Leonard A Mattano, Eric C Larsen, Julie Gastier-Foster, Eileen Stonerock, Denise Ell, Samir Kahwash, Meenakshi Devidas, Richard C Harvey, I-Ming L Chen, Cheryl L WillmanAbstractHyperdiploidy with greater than 50 chromosomes is usually associated with favorable prognosis in pediatric acute lymphoblastic leukemia (ALL), whereas hypodiploidy with ≤43 chromosomes is associated with ...
Source: Cancer Genetics - August 1, 2019 Category: Cancer & Oncology Source Type: research

Telomere length measurement in tumor and non‐tumor cells as a valuable prognostic for tumor progression
Publication date: Available online 26 July 2019Source: Cancer GeneticsAuthor(s): Fatma Mehrez, Karim Bougatef, Elisa Delle Monache, Ivan Arisi, Luca Proietti-De-Santis, Giorgio Prantera, Lilia Zouiten, Manuela Caputo, Amel Ben Ammar Elgaaied, Silvia BongiorniAbstractTelomere shortening has been supposed to be implicated in both aging and various human diseases especially carcinogenesis process. This phenomenon can lead to a chromosomal instability, contributing to a cell immortalization and tumor induction. In our study, we analyzed the role of telomere shortening in cancer progression, in Tunisian patients with digestive ...
Source: Cancer Genetics - July 27, 2019 Category: Cancer & Oncology Source Type: research

Clinical implications of clonal chromosomal abnormalities in Philadelphia negative cells in CML patients after treated with tyrosine kinase inhibitors
Publication date: Available online 24 July 2019Source: Cancer GeneticsAuthor(s): Hongyu Ni, Xinlai Sun, Yin Xu, Derek Lyle, Paris Petersen, Xianfeng Zhao, Hong Drum, Bei You, Dongfang Liu, Chen Liu, Jie-Gen JiangABSTRACTEmergence of clonal chromosomal abnormalities in Philadelphia chromosome-negative (CCA/Ph-) cells in chronic myeloid leukemia (CML) patients during the treatment with tyrosine kinase inhibitors (TKIs) is an interesting phenomenon. Although previous studies revealed some potential impact of CCA/Ph- on CML patients’ outcome, clinical significance of CCA/Ph- in CML patients remains to be further elucidat...
Source: Cancer Genetics - July 26, 2019 Category: Cancer & Oncology Source Type: research

RUNX1 Deletion/Amplification in Therapy-Related Acute Myeloid Leukemia: A Case Report and Review of the Literature
We describe here a case of AML with apparent amplification of RUNX1 by cytogenetics and FISH. A 39-year-old female in remission from stage IIIa breast cancer was diagnosed with therapy-related AML (t-AML). The patient's bone marrow was hypocellular for her age (30-40%) with 25% blasts. Cytogenetic analyses revealed a complex karyotype, characterized by rearrangements in chromosomes 1, 5, 17, 20, an additional unidentified marker chromosome, and apparent amplification of chromosome 21. Fluorescence in situ hybridization detected deletions of CKS1B, EGR1, TP53, and apparent amplification of RUNX1 (6-8 signals). Array compara...
Source: Cancer Genetics - July 26, 2019 Category: Cancer & Oncology Source Type: research

Detection of a novel CBFB-MYH11 fusion transcript in acute myeloid leukemia M1 with inv(16)(p13q22)
Publication date: Available online 24 July 2019Source: Cancer GeneticsAuthor(s): Keiji Kurata, Katsuya Yamamoto, Yoko Okazaki, Yoriko Noguchi, Keiji Matsui, Hisayuki Matsumoto, Yumiko Inui, Kimikazu Yakushijin, Mitsuhiro Ito, Yuji Nakamachi, Hiroshi Matsuoka, Jun Saegusa, Hironobu MinamiAbstractAcute myeloid leukemia (AML) with an inv(16)(p13q22) or t(16;16)(p13;q22) chromosomal abnormality represents one of the most common subtypes of de novo cases. These chromosomal rearrangements result in multiple CBFB-MYH11 fusion transcripts, with type-A being the most frequent. We here describe a unique case of de novo AML-M1, with ...
Source: Cancer Genetics - July 26, 2019 Category: Cancer & Oncology Source Type: research

Variants in COL6A3 gene influence susceptibility to esophageal cancer in the Chinese population
In conclusions, our study found that COL6A3 variants were associated with risk of EC in the Chinese population. (Source: Cancer Genetics)
Source: Cancer Genetics - July 14, 2019 Category: Cancer & Oncology Source Type: research

Chronic myelomonocytic leukemia with ETV6-ABL1 rearrangement and SMC1A mutation
We report a patient who had a clinical and morphological presentation consistent with CMML. The genetic work-up showed an ETV6-ABL1 fusion consequent to a 9;12 translocation, and a missense mutation in SMC1A (c.1757G>A, p.Arg586Gln). The SMC1A mutations are recurrent, albeit rare, in myeloid malignancies, without an established clinical significance in CMML. ETV6-ABL1 fusion is a rare but recurrent genetic aberration found in various hematologic malignancies involving both the lymphoid and myeloid lineage, but to the best of our knowledge, CMML is an exceptionally rare presentation of ETV6-ABL1 rearranged neoplasm. ETV6...
Source: Cancer Genetics - July 14, 2019 Category: Cancer & Oncology Source Type: research

ANKRD26-RET - A novel gene fusion involving RET in papillary thyroid carcinoma
ConclusionsANKRD26-RET is a novel rearrangement of the RET gene, associated with RET expression in thyroid tissue. The result is a fusion of the RET tyrosine kinase to prominent protein-protein interaction motifs. Further studies are required to investigate the influence of different RET rearrangements on metastasis and disease-free survival in PTC. (Source: Cancer Genetics)
Source: Cancer Genetics - July 5, 2019 Category: Cancer & Oncology Source Type: research

Homogeneously Staining Region (hsr) on Chromosome 11 Is Highly Specific for KMT2A Amplification in Acute Myeloid Leukemia (AML) and Myelodysplastic syndrome (MDS)
In this study, we correlated hsr(11)(q23) with KMT2A in a large cohort of AML/MDS (n=54) patients. We identified 37 patients with hsr(11)(q23) in the setting of AML (n=27) and MDS (n=10). All patients showed a complex karyotype including 12 cases with monosomy 17. KMT2A FISH analysis was available for 35 patients which showed KMT2A amplification in all patients. Among control cases with hsr involving chromosomes other than 11q [non-11q hsr, n=17], FISH analysis for KMT2A was available in 10 cases and none of these cases showed KMT2A amplification (p=0.0001, Fisher's exact test, two-tailed). Mutational analysis was performe...
Source: Cancer Genetics - July 5, 2019 Category: Cancer & Oncology Source Type: research

Cytogenetic profile of a representative cohort of young adults with de novo Acute Myéloblastic Leukaemia in Morocco
Publication date: Available online 15 June 2019Source: Cancer GeneticsAuthor(s): Nisrine Khoubila, Mounia Bendari, Nezha Hda, Mouna Lamchahab, Meryem Qachouh, Mohamed Rachid, Asmaa QuessarSummaryBackgroundWe analyzed the cytogenetic characteristics of a representative population of young adults with de novo acute myeloblastic leukemia (AML) treated in a single center institution.MethodsPatients with de novo AML included were aged between 20 and 60 years. Cytogenetic analysis was done at diagnosis. Twenty cells were analyzed, although examination of lower numbers of metaphases was also acceptable if an abnormal clone was de...
Source: Cancer Genetics - June 16, 2019 Category: Cancer & Oncology Source Type: research

Prevalence and founder effect of the BRCA1 p.(Val1833Met) variant in the Greek population, with further evidence for pathogenicity and risk modification
ConclusionsAltogether, BRCA1, p.(Val1833Met) variant is a Greek founder and is very likely to predispose for BrCa/OvCa. Therefore, such carriers should be counselled accordingly, with clinical recommendations supporting surveillance and risk-reduction strategies, while providing the option for targeted therapeutic interventions. (Source: Cancer Genetics)
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Characterization of a rarely reported STAT5B/RARA gene fusion in a young adult with newly diagnosed acute promyelocytic leukemia with resistance to ATRA therapy
Publication date: Available online 12 June 2019Source: Cancer GeneticsAuthor(s): Jess F. Peterson, Rui R. He, Hassan Nayer, Raymund S. Cuevo, James B. Smadbeck, George Vasmatzis, Patricia T. Greipp, Rhett P. Ketterling, Nicole L. Hoppman, Linda B. BaughnAbstractThe detection of PML/RARA or variant RARA rearrangements is critical for the diagnosis and treatment of patients with newly diagnosed acute promyelocytic leukemia (APL). While most cases of APL harboring the PML/RARA fusion respond to all-trans retinoic acid (ATRA), some variant RARA rearrangements are ATRA insensitive. Herein, we report a 27-year-old male with newl...
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Inherited cancer syndromes in 220 Italian ovarian cancer patients
ConclusionsSomatic and germline analyses offered to OC patients has proved to be an efficient strategy for the identification of inherited conditions involving OC also in absence of suggestive family histories. The identification of LS and HBOC syndromes through OC patients is an effective tool for OC prevention. (Source: Cancer Genetics)
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Concurrent chromothripsis events in a case of TP53 depleted Acute Myeloid Leukemia with myelodysplasia-related changes
Publication date: Available online 12 June 2019Source: Cancer GeneticsAuthor(s): D. Tolomeo, A. L'Abbate, A. Lonoce, P. D'Addabbo, M.F. Miccoli, C. Lo Cunsolo, P. Iuzzolino, O. Palumbo, M. Carella, V. Racanelli, T. Mazza, E. Ottaviani, G. Martinelli, G. Macchia, C.T. StorlazziAbstractAcute myeloid leukemia with myelodysplasia-related changes (AML-MRC) is a heterogeneous hematological disorder defined by morphological, genetic, and clinical features. Patients with AML-MRC often show cytogenetic changes, which are associated with poor prognosis. Straightforward criteria for AML-MRC diagnosis and a more rigorous characterizat...
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

A Unique Case of Complex Variant Translocation of t(6;9;22)(p22;q34;q11.2), der(19) in a Newly Diagnosed Patient with Chronic Myeloid Leukemia
In conclusion, complex translocations in unusual locations of the BCR / ABL gene appear to indicate a poor prognosis. (Source: Cancer Genetics)
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Single-cell cloning of human T-cell lines reveals clonal variation in cell death responses to chemotherapeutics
In this study, we characterize the variation in cell death of fifty clonal cell lines generated from human Jurkat and MOLT-4 T-cells edited by CRISPR-Cas9. We demonstrate a wide distribution of sensitivity to chemotherapeutics between non-edited clonal human leukemia T-cell lines, and also following CRISPR-Cas9 editing at the NLRP1 locus, or following transfection with non-targeting sgRNA controls. The cell death sensitivity profile of clonal cell lines was consistent across experiments and failed to revert to the non-clonal parental phenotype. Whole genome sequencing of two clonal cell lines edited by CRISPR-Cas9 revealed...
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Non-invasive genotyping of metastatic colorectal cancer using circulating cell free DNA
Publication date: Available online 12 June 2019Source: Cancer GeneticsAuthor(s): Xuemei Shi, Dzifa Y. Duose, Meenakshi Mehrotra, Michael A. Harmon, Peter Hu, Ignacio I. Wistuba, Scott Kopetz, Rajyalakshmi LuthraABSTRACTCirculating cell-free DNA (ccfDNA) in plasma provides an easily accessible source of circulating tumor DNA (ctDNA) for detecting actionable genomic alterations that can be used to guide colorectal cancer (CRC) treatment and surveillance. The goal of this study was to test the feasibility of using a traditional amplicon-based next-generation sequencing (NGS) on Ion Torrent platform to detect low-frequency all...
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

Expression deregulation of DNA repair pathway genes in gastric cancer
This study was designed to check correlation of mRNA and protein expression of BER pathway genes(XRCC1, OGG1) and a proliferation marker (Ki-67) in 100 gastric tissue samples and controls (adjacent uninvolved area). The expression was estimated using real time PCR and immunohistochemistry. Genomic instability was also calculated in the same study cohort using 8-OHdG assay, DNA fragmentation assay and comet assay. A significant downregulation of XRCC1 (p
Source: Cancer Genetics - June 13, 2019 Category: Cancer & Oncology Source Type: research

PD-L1 gene copy number and promoter polymorphisms regulate PD-L1 expression in tumor cells of non-small cell lung cancer patients
Publication date: Available online 8 June 2019Source: Cancer GeneticsAuthor(s): Paweł Krawczyk, Anna Grenda, Kamila Wojas-Krawczyk, Marcin Nicoś, Tomasz Kucharczyk, Bożena Jarosz, Katarzyna Reszka, Juliusz Pankowski, Kinga Krukowska, Aleksandra Bożyk, Justyna Szumiło, Marek Sawicki, Tomasz Trojanowski, Janusz MilanowskiAbstractMost drugs targeting PD-1 or PD-L1 are more effective when cancer cells of non-small cell lung cancer (NSCLC) patients express PD-L1 protein. The polymorphisms of PD-L1 gene and PD-L1 gene copy number could be responsible for PD-L1 mRNA and protein expression.We analyzed PD-L1 protein expression...
Source: Cancer Genetics - June 8, 2019 Category: Cancer & Oncology Source Type: research

p53 major hotspot variants are associated with poorer prognostic features in hereditary cancer patients
Publication date: Available online 6 June 2019Source: Cancer GeneticsAuthor(s): Cristina Fortuno, Tina Pesaran, Jill Dolinsky, Amal Yussuf, Kelly McGoldrick, Pik Fang Kho, Paul A. James, Amanda B. SpurdleABSTRACTTP53 pathogenic germline variation is associated with the multi-cancer predisposition Li-Fraumeni syndrome (LFS). Next-generation sequencing and multigene panel testing are highlighting variability in the clinical presentation of patients with TP53 positive results. We aimed to investigate if the p53 variants considered as major hotspots at both germline and somatic levels (p.Arg175His, p.Gly245Asp, p.Gly245Ser, p....
Source: Cancer Genetics - June 7, 2019 Category: Cancer & Oncology Source Type: research

Association of Transcriptional Levels of Folate-Mediated One-Carbon Metabolism-Related Genes in Cancer Cell Lines with Drug Treatment Response
Publication date: Available online 5 June 2019Source: Cancer GeneticsAuthor(s): Dong-Joon Min, Suleyman Vural, Julia KrushkalAbstractFolate-mediated one-carbon metabolism is essential for growth and survival of cancer cells. We investigated whether the response of cancer cells to antitumor treatment may be partially influenced by variation in expression of one-carbon metabolism genes. We used cancer cell line information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources to examine whether variation in pretreatment expression of one-carbon metabolism-related genes was associated...
Source: Cancer Genetics - June 5, 2019 Category: Cancer & Oncology Source Type: research

Down-regulation of STIP1 regulate apoptosis and invasion of glioma cells via TRAP1/AKT signaling pathway
ConclusionsSTIP1 is highly expressed in glioblastoma compared to normal brain tissues. Downregulation of STIP1 in glioma cells reduces cell proliferation rate and invasion and increases cell apoptosis. (Source: Cancer Genetics)
Source: Cancer Genetics - June 4, 2019 Category: Cancer & Oncology Source Type: research

Classic bladder exstrophy and adenocarcinoma of the bladder: methylome analysis provide no evidence for underlying disease-mechanisms of this association
Publication date: Available online 31 May 2019Source: Cancer GeneticsAuthor(s): Amit Sharma, Holger Fröhlich, Rong Zhang, Anne-Karoline Ebert, Wolfgang Rösch, Henning Reis, Glen Kristiansen, Jörg Ellinger, Heiko ReutterAbstractThe bladder exstrophy-epispadias complex (BEEC) represents the severe end of uro-rectal malformation spectrum involving aberrant embryonic morphogenesis of the cloacal membrane and the urorectal septum. The most common form of BEEC is isolated classic bladder exstrophy (CBE). Long-term complications in CBE are malignancies of the bladder with 95% of them being adenocarcinomas. Since CB...
Source: Cancer Genetics - June 1, 2019 Category: Cancer & Oncology Source Type: research

A novel CHEK2 variant identified by next generation sequencing in an Indian family with hereditary breast cancer syndrome
We report a BRCA negative family with multiple affected women having breast cancer, with a novel, missense, likely pathogenic variant in the CHEK2 gene (c.1376T>G; p.Ile459Ser) that segregated with subjects with breast cancer. This case provides insight into the role of the CHEK2 gene in causing breast cancer susceptibility in families and supports the use of multigene panel testing in cases with hereditary predisposition to breast cancer. (Source: Cancer Genetics)
Source: Cancer Genetics - June 1, 2019 Category: Cancer & Oncology Source Type: research

Acute lymphoblastic leukemia in a nine-year-old girl with isodicentric chromosome 15 syndrome
Publication date: Available online 18 May 2019Source: Cancer GeneticsAuthor(s): Roberto Antonucci, Nadia Vacca, Elisa Ghisu, Gloria Acquaviva, Carlo Cosmi, Anna Maria Marinaro, Cristian Locci, Claudio FozzaAbstractIsodicentric chromosome 15, also called idic(15), is a rare chromosomal abnormality resulting from inverted duplication of proximal 15q. It is associated with specific clinical findings such as early central hypotonia, developmental delay, cognitive dysfunction, autism spectrum disorders, and seizure. Herein we describe a case of a girl with idic(15) syndrome who developed acute lymphoblastic leukemia (ALL) at th...
Source: Cancer Genetics - May 20, 2019 Category: Cancer & Oncology Source Type: research

Editorial Board
Publication date: April 2019Source: Cancer Genetics, Volumes 233–234Author(s): (Source: Cancer Genetics)
Source: Cancer Genetics - May 18, 2019 Category: Cancer & Oncology Source Type: research

FANCM, RAD1, CHEK1 and TP53I3 act as BRCA-like tumor suppressors and are mutated in hereditary ovarian cancer
Publication date: Available online 9 May 2019Source: Cancer GeneticsAuthor(s): Jaime L. Lopes, Sophia Chaudhry, Guilherme S. Lopes, Nancy K. Levin, Michael A. TainskyAbstractAlthough 25% of ovarian cancer cases are due to inherited factors, most of the genetic risk remains unexplained. We previously identified candidate genes through germline whole exome sequencing of BRCA1/BRCA2 negative ovarian cancer patients with familial risk. Here, we performed functional assessment to determine whether they act as BRCA-like tumor suppressors.Seven candidate risk genes were targeted by siRNA for mRNA depletion followed by functional ...
Source: Cancer Genetics - May 11, 2019 Category: Cancer & Oncology Source Type: research

Somatic Mutation Panels: Time to clear their names
Publication date: Available online 26 April 2019Source: Cancer GeneticsAuthor(s): Amy M. Trottier, Marcela Cavalcante de Andrade Silva, Zejuan Li, Lucy A. GodleyAbstractWith improvements in DNA sequencing technologies and the consequent reduction in costs, next generation sequencing is being utilized increasingly in panel-based testing to perform molecular profiling of tumors. Such tumor-based panels are often referred to as ‘somatic’ panels, but this term is misleading and should not be used, since not all DNA variants within a tumor are somatic in nature. Every cell in a person's body contains that person's g...
Source: Cancer Genetics - April 27, 2019 Category: Cancer & Oncology Source Type: research

Outcomes of Disease-Specific Next-Generation Sequencing Gene Panel Testing in Adolescents and Young Adults with Colorectal Cancer
ConclusionHereditary syndromes were identified in 29.4% of patients. Panel testing in patients without a phenotype did not increase diagnostic yield, but identified variants in one-third. Disease-specific panel testing is of low yield in young patients without a suggestive personal/family history. Testing broader panels may increase the yield of mutation pick-up in this population, although at the expense of identifying variants. (Source: Cancer Genetics)
Source: Cancer Genetics - April 27, 2019 Category: Cancer & Oncology Source Type: research

Retrotransposon Elements among Initial Sites of Hepatitis B Virus Integration into Human Genome in the HepG2-NTCP Cell Infection Model
We examined the time-frame and host sites at which HBV integrates in HepG2 cells overexpressing sodium taurocholate co-transporting polypeptide (NTCP) receptor mediating HBV entry. HepG2-NTCP cells were analyzed from 15 min to 13 days post-infection (p.i.). The results showed that except for 15 min p.i., HBV-host integrations were detected at all time points thereafter. At 30 min p.i., virus junctions with retrotransposon SINE and with neuroblastoma breakpoint family member 1 gene were detected. At one-hour p.i., HBV integration with retrotransposon THE-1B-LTR was identified, while virus insertions into proline-rich protei...
Source: Cancer Genetics - April 26, 2019 Category: Cancer & Oncology Source Type: research

Uptake of genetic testing for germline BRCA1/2 pathogenic variants in a predominantly Hispanic population
Publication date: Available online 24 April 2019Source: Cancer GeneticsAuthor(s): Julia E. McGuinness, Meghna S. Trivedi, Thomas Silverman, Awilda Marte, Jennie Mata, Rita Kukafka, Katherine D. CrewAbstractBackgroundGenetic counseling is under-utilized in women who meet family history criteria for BRCA1 and BRCA2 (BRCA1/2) testing, particularly among racial/ethnic minorities. We evaluated the uptake of BRCA1/2 genetic testing among women presenting for screening mammography in a predominantly Hispanic, low-income population of Washington Heights in New York City.MethodsWe administered the Six-Point Scale (SPS) to women pre...
Source: Cancer Genetics - April 26, 2019 Category: Cancer & Oncology Source Type: research

Circulating cell-free DNA integrity as a diagnostic and prognostic marker for breast and prostate cancers
ConclusionALU species 115 and 247 levels in serum were elevated in breast and prostate cancer patients compared to their counterpart healthy controls. DNA integrity was higher in prostate cancer patients than the control but in breast cancer patients was lower compared to their controls. In prostate but not in breast cancers, DNA integrity increased with disease severity and higher staging. (Source: Cancer Genetics)
Source: Cancer Genetics - April 23, 2019 Category: Cancer & Oncology Source Type: research

Aberrant methylation status of SPG20 promoter in Hepatocellular Carcinoma: a potential tumor metastasis biomarker
Publication date: Available online 12 April 2019Source: Cancer GeneticsAuthor(s): Lifeng He, Xiaoxiao Fan, Yirun Li, Bin Cui, Zhaoqi Shi, Daizhan Zhou, Hui LinAbstractPurposeThe aim of this study is to analyze the methylation levels of SPG20 promotor region and explore the association between the methylation levels and clinical features in hepatocellular carcinoma (HCC).Materials and methodsWe collected paired of HCC and adjacent non-cancerous tissues (ANT) from 160 HCC patients and analyze the methylation levels through MassARRAY Analyzer 4. The statistical calculations were performed using SPSS version 22.0. Real-time-qu...
Source: Cancer Genetics - April 13, 2019 Category: Cancer & Oncology Source Type: research

A comparison of survival analysis methods for cancer gene expression RNA-Sequencing data
Publication date: Available online 12 April 2019Source: Cancer GeneticsAuthor(s): Pichai Raman, Samuel Zimmerman, Komal S. Rathi, Laurence de Torrenté, Mahdi Sarmady, Chao Wu, Jeremy Leipzig, Deanne M. Taylor, Aydin Tozeren, Jessica C. MarAbstractIdentifying genetic biomarkers of patient survival remains a major goal of large-scale cancer profiling studies. Using gene expression data to predict the outcome of a patient's tumor makes biomarker discovery a compelling tool for improving patient care. As genomic technologies expand, multiple data types may serve as informative biomarkers, and bioinformatic strategies ha...
Source: Cancer Genetics - April 13, 2019 Category: Cancer & Oncology Source Type: research

Prevalence and characteristics of likely-somatic variants in cancer susceptibility genes among individuals who had hereditary pan-cancer panel testing
Publication date: Available online 13 April 2019Source: Cancer GeneticsAuthor(s): Thomas P. Slavin, Bradford Coffee, Ryan Bernhisel, Jennifer Logan, Hannah C. Cox, Guido Marcucci, Jeffrey Weitzel, Susan L. Neuhausen, Debora Mancini-DiNardoABSTRACTNext-generation sequencing (NGS) hereditary pan-cancer panel testing can identify somatic variants, which exhibit lower allele frequencies than do germline variants and may confound hereditary cancer predisposition testing. This analysis examined the prevalence and characteristics of likely-somatic variants among 348,543 individuals tested using a clinical NGS hereditary pan-cance...
Source: Cancer Genetics - April 13, 2019 Category: Cancer & Oncology Source Type: research

PIP4K2A and PIP4K2C transcript levels are associated with cytogenetic risk and survival outcomes in acute myeloid leukemia
Publication date: Available online 11 April 2019Source: Cancer GeneticsAuthor(s): Keli Lima, Juan Luiz Coelho-Silva, Gabriela Sarti Kinker, Diego Antonio Pereira-Martins, Fabiola Traina, Pedro Augusto Carlos Magno Fernandes, Regina Pekelmann Markus, Antonio Roberto Lucena-Araujo, João Agostinho Machado-NetoAbstractPhosphoinositide signaling pathway orchestrates primordial molecular and cellular functions in both healthy and pathologic conditions. Phosphatidylinositol-5-phosphate 4-kinase type 2 lipid kinase (PIP4K2) family, which compromises PIP4K2A, PIP4K2B and PIP4K2C, has drawn the attention in human cancers. Par...
Source: Cancer Genetics - April 12, 2019 Category: Cancer & Oncology Source Type: research

Prognostic significance of CDC25C in lung adenocarcinoma: an analysis of TCGA data
Publication date: Available online 9 April 2019Source: Cancer GeneticsAuthor(s): Zengfei Xia, Wen Ou-yang, Ting Hu, Ketao DuAbstractObjectiveCell division cycle 25C (CDC25C) is involved in the regulation of the G2/M phase transition and is associated with various cancers, including non-small cell lung cancer. We evaluated its prognostic value in lung adenocarcinoma (LUAD) based on data from The Cancer Genome Atlas (TCGA).MethodsThe Kruskal–Wallis test, Wilcoxon signed-rank test, and logistic regression were used to evaluate relationships between clinical-pathologic features and CDC25C expression. Cox regression analy...
Source: Cancer Genetics - April 10, 2019 Category: Cancer & Oncology Source Type: research

PTPRD copy number variants and Ewing's sarcoma: Strengthening the association and therapeutic implications
Publication date: Available online 26 March 2019Source: Cancer GeneticsAuthor(s): Avi Saskin, Kimberly Seath, Frederique Tihy, Emmanuelle Lemyre, Jeffrey Davis, Fahed Halal, Linlea ArmstrongAbstractEwing sarcoma (ES), a common pediatric primary bone neoplasm, has a well-defined genomic landscape with various predisposing genomic elements including TP53, PMS2 and RET. Additionally, germline and somatic variants in protein tyrosine phosphatase delta (PTPRD), a tumor suppressor gene, have been identified in a limited number of ES patients. Here we present an ES patient, remarkable in terms of his young age and extent at prese...
Source: Cancer Genetics - March 28, 2019 Category: Cancer & Oncology Source Type: research

The Benefits of A Model of Interval Comprehensive Assessments (MICA) in Hereditary Cancer Syndromes: Hereditary Diffuse Gastric Cancer (HDGC) as an Example
Publication date: Available online 25 March 2019Source: Cancer GeneticsAuthor(s): Henry T. Lynch, Rosemary Nustas, Thamer Kassim, Carrie Snyder, Trudy Shaw, Osama DiabAbstractA high percentage of individuals at risk for hereditary cancer syndromes are unaware of their risk. This is especially detrimental in syndromes such as hereditary diffuse gastric cancer due to a CDH1 germline mutation, for which lifesaving prevention is possible. Surveillance for diffuse gastric cancer in the syndrome is limited, hence the recommendation for prophylactic total gastrectomy for mutation carriers. Genetic counseling and testing is crucia...
Source: Cancer Genetics - March 26, 2019 Category: Cancer & Oncology Source Type: research

Corrigendum to “The cancer COMPASS: Navigating the functions of MLL complexes in cancer” [Cancer Genetics 208 (2015) pp. 178–191]
Publication date: Available online 21 March 2019Source: Cancer GeneticsAuthor(s): David J. Ford, Andrew K. Dingwall (Source: Cancer Genetics)
Source: Cancer Genetics - March 22, 2019 Category: Cancer & Oncology Source Type: research