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    518 results match your criteria Cancer Genetics [Journal]

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    A novel cytogenetic and molecular characterization of renal metanephric adenoma: Identification of partner genes involved in translocation t(9;15)(p24;q24).
    Cancer Genet 2017 Aug 16;214-215:9-15. Epub 2017 Mar 16.
    Department of Cytogenetics, ACL Laboratories, Rosemont, Illinois, USA; Department of Pathology, Advocate Lutheran General Hospital, Park Ridge, Illinois, USA; Advocate Medical Group Genetics, Park Ridge, Illinois, USA. Electronic address:
    Renal metanephric adenoma (MA) is a rare benign tumor frequently misclassified when microscopic features alone are applied. The correct classification of a renal tumor is critical for diagnostic, prognostic, and therapeutic purposes. Despite the advancements in cancer genomics, up until recently relatively few genetic alterations critical to MA development have been recognized. Read More

    The novel double-hit, t(8;22)(q24;q11)/MYC-IGL and t(14;15)(q32;q24)/IGH-BCL2A1, in diffuse large B-cell lymphoma.
    Cancer Genet 2017 Aug 4;214-215:26-31. Epub 2017 Apr 4.
    Department of Hematology, Tenri Hospital, Japan; Tenri Institute of Medical Research, Japan.
    An 82-year-old woman presented with generalized lymphadenopathy and skin involvement. Lymph node biopsy revealed diffuse large B-cell lymphoma with a high proliferation index. G-banding and fluorescence in situ hybridization showed a hypertetraploid karyotype with two copies of t(8;22)(q24;q11), generating the fusion of MYC and the immunoglobulin λ chain gene (IGL), and two copies of the novel immunoglobulin heavy chain gene (IGH) translocation, t(14;15)(q32;q24). Read More

    Single nucleotide polymorphisms in an Indian cohort and association of CNTN4, MMP2 and SNTB1 variants with oral cancer.
    Cancer Genet 2017 Aug 23;214-215:16-25. Epub 2017 Mar 23.
    Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (deemed-to-be) University, Vile Parle, Mumbai 400056, India. Electronic address:
    Oral cancer is a high incidence cancer in India primarily due to the prevalent tobacco/areca nut chewing habits and hence a major health concern. India constitutes 26% of the global oral cancer burden. Besides the well-established risk factors, the genomic constitution of an individual plays a role in oral cancer. Read More

    Recurrent large genomic rearrangements in BRCA1 and BRCA2 in an Irish case series.
    Cancer Genet 2017 Aug 22;214-215:1-8. Epub 2017 Mar 22.
    Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland.
    Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Read More

    Effects of polymorphisms identified in genome-wide association studies of never-smoking females on the prognosis of non-small cell lung cancer.
    Cancer Genet 2017 Apr 20;212-213:8-12. Epub 2017 Mar 20.
    Departments of Internal Medicine, Kyungpook National University School of Medicine, Daegu, South Korea; Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, South Korea. Electronic address:
    A number of genome-wide association studies have reported several variants that influence the risk of lung cancer in never-smoking females. We evaluated the impact of these variants on survival outcome in never-smoking females with non-small cell lung cancer (NSCLC). In total, 510 never-smoking females with NSCLC who underwent curative surgery were enrolled. Read More

    Novel t(5;11)(q32;q13.4) with NUMA1-PDGFRB fusion in a myeloid neoplasm with eosinophilia with response to imatinib mesylate.
    Cancer Genet 2017 Apr 27;212-213:38-44. Epub 2017 Mar 27.
    University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD. Electronic address:
    We report a NUMA1-PDGFRB fusion in a myeloproliferative neoplasm with eosinophilia in a 61-year old man, with response to imatinib mesylate therapy. A t(5;11) chromosome translocation involving bands 5q32 and 11q13.4 was identified by metaphase chromosome analysis, and rearrangement of the platelet-derived growth factor receptor beta (PDGFRB) gene on 5q32 was demonstrated by FISH using a PDGFRB break-apart probe set. Read More

    Genomic diagnostics leading to the identification of a TFG-ROS1 fusion in a child with possible atypical meningioma.
    Cancer Genet 2017 Apr 22;212-213:32-37. Epub 2017 Mar 22.
    Department of Paediatrics and Adolescent Medicine, Neuroscience Center, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
    Meningiomas are rare in children. They are highly complex, harboring unique clinical and pathological characteristics, and many occur in patients with neurofibromatosis type 2. Hereby, we present a case of a two-year-old boy presented with a diagnostically challenging intraventricular tumor. Read More

    Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples.
    Cancer Genet 2017 Apr 20;212-213:24-31. Epub 2017 Mar 20.
    Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States. Electronic address:
    Gene copy number changes are important somatic alterations in cancers. A number of high throughput methods, such as next generation sequencing, are capable of detecting copy number aberrations, but their use can be challenging and cost prohibitive for screening a small number of markers. Furthermore, detection of CNAs by high throughput platforms needs confirmation by an orthogonal technique, especially in cases with low level CNAs. Read More

    Cancer in Machado-Joseph disease patients-low frequency as a cause of death.
    Cancer Genet 2017 Apr 30;212-213:19-23. Epub 2017 Mar 30.
    Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Brazil; Laboratório de Identificação Genética, Hospital de Clínicas de Porto Alegre, Brazil; Departamento de Medicina Interna, Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional (INAGEMP), Rio de Janeiro, Brazil. Electronic address:
    Since polyglutamine diseases have been related to a reduced risk of cancer, we aimed to study the 15 years cumulative incidence of cancer (CIC) (arm 1) and the proportion of cancer as a cause of death (arm 2) in symptomatic carriers of spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD). SCA3/MJD and control individuals from our state were invited to participate. A structured interview was performed. Read More

    Gene fusions PAFAH1B1-USP6 and RUNX2-USP6 in aneurysmal bone cysts identified by next generation sequencing.
    Cancer Genet 2017 Apr 24;212-213:13-18. Epub 2017 Mar 24.
    Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH 45229.
    Aneurysmal bone cyst (ABC) is a locally aggressive, expansile, typically multilocular cystic bone tumor. ABC was previously thought to be a non-neoplastic lesion; however, it is now considered to be neoplasm that features recurrent chromosomal translocations resulting in gene fusions between ubiquitin specific peptidase 6 (USP6) and multiple partners, including COL1A1, CDH11, TRAP150, ZNF90 and OMD. Using next generation sequencing (NGS), we uncovered two fusion partners of USP6 in two ABCs: platelet activating factor acetylhydrolase 1b regulatory subunit 1 (PAFAH1B1), which is known to contribute to tumorigenesis in lung cancer, and runt-related transcription factor 2 (RUNX2), which is known to regulate osteoblastic differentiation, osteosarcoma tumorigenesis and its metastasis. Read More

    Spectrum of mismatch repair gene mutations and clinical presentation of Hispanic individuals with Lynch syndrome.
    Cancer Genet 2017 Apr 9;212-213:1-7. Epub 2017 Feb 9.
    Clinical Cancer Genetics, City of Hope National Medical Center, Duarte, CA 91010, USA. Electronic address:
    Lynch syndrome (LS), the most common hereditary colorectal cancer syndrome, is caused by mismatch repair (MMR) gene mutations. However, data about MMR mutations in Hispanics are limited. This study aims to describe the spectrum of MMR mutations in Hispanics with LS and explore ancestral origins. Read More

    Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.
    Cancer Genet 2017 Feb 9;211:9-17. Epub 2017 Jan 9.
    Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Hematology, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Pediatric Hematology, School of Medicine, University of California at Irvine, Orange, CA, USA.
    Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is passed from parent to child. Tumor protein p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Paradoxically, some mutant TP53 carriers remain unaffected, while their children develop cancer within the first few years of life. Read More

    Detection of somatic variants in peripheral blood lymphocytes using a next generation sequencing multigene pan cancer panel.
    Cancer Genet 2017 Feb 16;211:5-8. Epub 2017 Jan 16.
    Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
    Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%. Read More

    FAS c.-671A>G polymorphism and cervical cancer risk: a case-control study and meta-analysis.
    Cancer Genet 2017 Feb 26;211:18-25. Epub 2017 Jan 26.
    Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia. Electronic address:
    This study aimed to investigate the association between FAS c.-671A>G polymorphism and cervical cancer risk in a case-control setting, followed by a meta-analysis of the published literatures. The case-control study involved genotyping of the polymorphism in 185 histopathologically confirmed cervical cancer patients and 209 cancer-free female controls utilizing PCR-RFLP technique, followed by logistic regression analyses. Read More

    TAF15-ZNF384 fusion gene in childhood mixed phenotype acute leukemia.
    Cancer Genet 2017 Feb 10;211:1-4. Epub 2017 Jan 10.
    Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, the First Affiliated Hospital of Soochow University, Suzhou, China; Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China. Electronic address:

    Chromosomal instability analysis and regional tumor heterogeneity in colon cancer.
    Cancer Genet 2017 Jan 22;210:9-21. Epub 2016 Nov 22.
    Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Italy; Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Italy. Electronic address:
    Chromosomal instability (CIN) is classically defined as an increase in the rate at which numerical or structural chromosomal aberrations are acquired in a cancer cell. The number of somatic copy number abnormalities (CNAs) revealed by high resolution genomic array can be considered as a surrogate marker for CIN, but several points, related to sample processing and data analysis, need to be standardized. In this work we analyzed 51 CRC samples and matched normal mucosae by whole genome SNP arrays and compared different bioinformatics tools in order to identify broad (>25% of a chromosomal arm) and focal somatic copy number abnormalities (BCNAs and FCNAs respectively). Read More

    Next-generation repeat-free FISH probes for DNA amplification in glioblastoma in vivo: Improving patient selection to MDM2-targeted inhibitors.
    Cancer Genet 2017 Jan 1;210:28-33. Epub 2016 Dec 1.
    Department of Diagnostics and Public Health, Anatomic Pathology, AOUI Hospital Trust of Verona, Italy.
    A next-generation FISH probe mapping to the MDM2 locus-specific region has recently been designed. The level of MDM2 gene amplification (high versus low) may allow selection of patients for cancer treatment with MDM2 inhibitors and may predict their responsiveness. We investigated the spectrum of MDM2 gene alterations using the new probes in vivo after visualizing single neoplastic cells in situ from a series of glioblastomas. Read More

    Prevalence of BRCA1 and BRCA2 large genomic rearrangements in Tunisian high risk breast/ovarian cancer families: Implications for genetic testing.
    Cancer Genet 2017 Jan 18;210:22-27. Epub 2016 Nov 18.
    Faculté de Médecine de Tunis, Laboratoire Génétique Humaine, University Tunis El manar, Tunis, Tunisia.
    Germline mutations in the BRCA tumor suppressor genes account for a substantial proportion of hereditary breast/ovarian cancer. However, this contribution is lower than expected. This underestimation can partly be explained by the BRCA alterations missed by using Sanger sequencing methods. Read More

    Clonal evolution as detected by interphase fluorescence in situ hybridization is associated with worse overall survival in a population-based analysis of patients with chronic lymphocytic leukemia in British Columbia, Canada.
    Cancer Genet 2017 Jan 3;210:1-8. Epub 2016 Nov 3.
    Division of Hematology, Vancouver General Hospital, University of British Columbia, Vancouver, BC, Canada; Leukemia/BMT Program of BC, Vancouver General Hospital and British Columbia Cancer Agency, University of British Columbia, Vancouver, BC, Canada. Electronic address:
    This study evaluates prognostic markers as predictors of clonal evolution (CE) and assesses the impact of CE on overall survival (OS) in a population-based cohort of 159 consecutive eligible patients with chronic lymphocytic leukemia (CLL) obtained from the British Columbia Provincial CLL Database. CE was detected by interphase fluorescence in situ hybridization (FISH) in 34/159 patients (21%) with 65% of CE patients acquiring deletion 17p or 11q. CD38 positive status (≥30%) on flow cytometry predicted 2. Read More

    Molecular profiles in foregut oncology.
    Cancer Genet 2016 Dec 29;209(12):537-553. Epub 2016 Oct 29.
    Florida Hospital Tampa, 3000 Medical Park Drive Suite 310, Tampa, FL 33613, USA. Electronic address:
    Oncology is and will continue to evolve resulting from a better understanding of the biology and intrinsic genetic profile of each cancer. Tumor biomarkers and targeted therapies are the new face of precision medicine, so it is essential for all physicians caring for cancer patients to understand and assist patients in understanding the role and importance of such markers and strategies to target them. This review was initiated in an attempt to identify, characterize, and discuss literature supporting clinically relevant molecular markers and interventions. Read More

    Differences in global DNA methylation of testicular seminoma are not associated with changes in histone modifications, clinical prognosis, BRAF mutations or gene expression.
    Cancer Genet 2016 Nov 31;209(11):506-514. Epub 2016 Oct 31.
    Dept. of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Denmark; International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Denmark. Electronic address:
    Testicular germ cell tumours of young adults are comprised of a heterogeneous group of non-seminomas and a homogeneous group of seminomas. While the majority of seminomas retain a hypo-methylated genome, a small fraction displays a highly methylated genome, resembling hyper-methylated non-seminomas. It is well established from e. Read More

    Chromosomal rearrangements in myoepithelial carcinoma of the breast that presented as metachronic double cancer with invasive ductal carcinoma in the ipsilateral breast.
    Cancer Genet 2016 Nov 29;209(11):501-505. Epub 2016 Oct 29.
    Division of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
    Myoepithelial carcinoma of the breast is an extremely rare tumor composed entirely of malignant spindle cells with myoepithelial differentiation. The majority of previously reported cases have mainly described the clinicopathological features of the disease, and few have presented cytogenetic data. We herein present the case of a 48-year-old woman who was admitted with a left-sided breast lump in the inner upper quadrant that was initially diagnosed as a myoepithelioma with potentially malignant disorder. Read More

    Pathogenic germline MCM9 variants are rare in Australian Lynch-like syndrome patients.
    Cancer Genet 2016 Nov 11;209(11):497-500. Epub 2016 Oct 11.
    Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia. Electronic address:
    Lynch syndrome is a hereditary cancer syndrome caused by the autosomal dominant inheritance of loss-of-function mutations in DNA mismatch repair (MMR) genes. Approximately one quarter of clinically suspected cases have no identifiable germline mutation in any MMR gene, a condition known as Lynch-like syndrome (LLS). MCM9 was recently identified as the DNA helicase in the mammalian MMR complex and loss of helicase activity results in microsatellite instability. Read More

    Pri-miR-34b/c rs4938723 polymorphism is associated with the risk of childhood acute lymphoblastic leukemia.
    Cancer Genet 2016 Nov 30;209(11):493-496. Epub 2016 Sep 30.
    Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.
    MicroRNAs (miRNAs), small noncoding regulatory RNAs, are key regulators of gene expression. The impact of Pri-miR-34b/c rs4938723 variant on development of various cancers is still controversial. In the present study, we examined whether a rs4938723 variant located at the promoter region of Pri-miR-34b/c is associated with childhood ALL. Read More

    In silico, in vitro and case-control analyses as an effective combination for analyzing BRCA1 and BRCA2 unclassified variants in a population-based sample.
    Cancer Genet 2016 Nov 20;209(11):487-492. Epub 2016 Sep 20.
    Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain. Electronic address:
    Ascertaining the clinical consequences of BRCA1 and BRCA2 variants of uncertain significance (VUS) is currently indispensable for providing effective genetic counseling and preventive actions for families with hereditary breast and ovarian cancer (HBOC). To this end, we conducted a combination of in silico prediction and cDNA splicing analyses of 13 BRCA1 and 10 BRCA2 VUS identified in our cohort as well as a case-control analysis in a population-based sample of 10 recurrent VUS. We observed consistent results between the in silico predictions and sequencing analyses for all analyzed VUS. Read More

    Polymorphisms and haplotypes of the CYP2B6 detoxification gene in the predisposition of Acute Myeloid Leukemia (AML) and induction of its cytogenetic abnormalities.
    Cancer Genet 2016 Nov 28;209(11):525-533. Epub 2016 Oct 28.
    Laboratory of Health Physics, Radiobiology & Cytogenetics, National Centre for Scientific Research (NCSR) "Demokritos", Athens, Greece. Electronic address:
    CYP2B6 is a polymorphic detoxification gene which plays a vital role in the degradation of genotoxic compounds. In this study we hypothesized that inadequate detoxification due to CYP2B6 polymorphisms may contribute to AML. To evaluate the potential impact of CYP2B6 polymorphisms on AML development and induction of its specific chromosomal abnormalities we studied C(777)A and A(785)G polymorphisms for the first time in AML. Read More

    Six generations of epidermolytic palmoplantar keratoderma, associated with a KRT9 R163W mutation.
    Cancer Genet 2016 Nov 29;209(11):515-524. Epub 2016 Oct 29.
    People's Hospital of Xinjiang Uygur Autonomous Region, China.
    Epidermolytic palmoplantar keratoderma (EPPK) is a rare autosomal dominant skin disorder characterized by diffuse hyperkeratosis on the palms and soles. Whole-exome sequencing (WES) has become a powerful tool for the detection of rare causal variants of Mendelian disorders. However, no causal gene for EPPK in the Uygur population has been identified until now, and no treatment exists than can address the underlying pathology. Read More

    Chronic myelogenous leukemia with acquired t(11;14)(q13;q32) CCND1-IGH: A case report and literature review.
    Cancer Genet 2016 Oct 21;209(10):481-485. Epub 2016 Sep 21.
    Department of Pathology, University of New Mexico, Albuquerque, NM, USA. Electronic address:
    Approximately 5-10% of chronic myeloid leukemia (CML) patients are found to have structural or numerical additional chromosomal abnormality (ACAs) in addition to the characteristic t(9;22)(q34;q11.2) BCR/ABL1 at the time of diagnosis. The prognostic significance of such additional chromosomal abnormalities has been controversial. Read More

    Genotyping and differential expression analysis of inflammasome genes in sporadic malignant melanoma reveal novel contribution of CARD8, IL1B and IL18 in melanoma susceptibility and progression.
    Cancer Genet 2016 Oct 16;209(10):474-480. Epub 2016 Sep 16.
    Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Avenida Prof. Lineu Prestes 1730, 05508-000 Cidade Universitaria, Sao Paulo, Brazil.
    Sporadic melanoma malignancy is correlated with constitutive secretion of IL-1β in transformed melanocytes suggesting the involvement of inflammasome in melanoma. Common variants in inflammasome genes are known to affect IL-1β expression. To investigate the contribution of inflammasome genetics in melanoma development and progression and to identify a potential prognostic marker, the distribution of selected inflammasome SNPs was analysed in a Brazilian case/control cohort of sporadic malignant melanoma (SMM) and then the expression of inflammasome components was evaluated in melanoma biopsies. Read More

    Co-localized genomic regulation of miRNA and mRNA via DNA methylation affects survival in multiple tumor types.
    Cancer Genet 2016 Oct 12;209(10):463-473. Epub 2016 Sep 12.
    Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA.
    Aberrant gene expression in cancer is due in part to irregular patterns of DNA methylation and miRNA target gene down regulation. Using data from The Cancer Genome Atlas (TGCA), we investigated co-localized mRNA, miRNA and DNA methylation data across 15 cancer types, focusing on cases where evidence for direct regulation was strong. Restricting attention to regions where miRNA markers co-localize within a corresponding mRNA transcript, we checked expression data from 2839 samples for 354 mRNAs, 389 miRNAs and 13,809 DNA methylation probes for correlations greater than an absolute 0. Read More

    Clinical and molecular cytogenetic studies in ten patients with hematological malignancies characterized by t(20;21)(q11;q11) resulted from del(20q).
    Cancer Genet 2016 Oct 19;209(10):456-462. Epub 2016 Sep 19.
    Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, China. Electronic address:
    This study reports 10 patients with hematological malignances with t(20;21)(q11;q11) resulting from del(20q) (for example, der(20)del(20)(q11q13)t(20;21)(q11;q11) and der(21)t(20;21)(q11;q11)) and described their clinical features and the possible prognostic significance of this abnormality. The t(20;21)(q11;q11) was a rare but recurrent abnormality secondary to del(20q) besides i(20q-). The frequency of der(20)del(20)(q11q13)t(20;21)(q11;q11) among our patients with del(20q) was 2. Read More

    The emerging role of long non-coding RNAs in endometrial cancer.
    Cancer Genet 2016 Oct 13;209(10):445-455. Epub 2016 Sep 13.
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia. Electronic address:
    The human genome is pervasively transcribed and approximately 98% of the genome is non-coding. Long non-coding RNAs (lncRNAs) are a heterogeneous group of RNA transcripts that are >200 nucleotides in length with minimal to no protein-coding potential. Similar to proteins, lncRNAs have important biological functions in both normal cells and disease states including many types of cancer. Read More

    A new NFIA:RAF1 fusion activating the MAPK pathway in pilocytic astrocytoma.
    Cancer Genet 2016 Oct 16;209(10):440-444. Epub 2016 Sep 16.
    Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark. Electronic address:
    Pilocytic astrocytoma (PA) is one of the most common brain cancers among children and activation of the Mitogen-Activated Protein Kinase (MAPK) pathway is considered the hallmark. In the majority of cases, oncogenic BRAF fusions or BRAF V600E mutations are observed, while RAF1 or NF1 alterations are more rarely found. However, in some cases, no apparent cancer driver events can be identified. Read More

    MYC rearranged B-cell neoplasms: Impact of genetics on classification.
    Cancer Genet 2016 Oct 14;209(10):431-439. Epub 2016 Sep 14.
    MLL Munich Leukemia Laboratory, Munich, Germany. Electronic address:
    A cohort comprising 156 patients with B-cell neoplasms harboring an MYC rearrangement was analyzed with respect to phenotypic presentation, molecular markers (TP53, MYC and ID3) and additional cytogenetic abnormalities (concomitantly occurring BCL2, BCL6 and/or CCND1 rearrangements; double, triple or quadruple hit lymphomas = multiple hit lymphomas). MYC translocations occurred as single hit (only MYC rearranged, 63%) or multiple hit lymphoma (37%) and presented as acute leukemia (AL) (14%), Burkitt lymphoma (30%), chronic lymphocytic leukemia (CLL) (21%) or other mature B-cell neoplasms (35%). Multiple hit lymphomas more frequently showed a complex karyotype compared to single hit lymphomas (62% vs. Read More

    Karyotypic abnormalities associated with Epstein-Barr virus status in classical Hodgkin lymphoma.
    Cancer Genet 2016 Sep 15;209(9):408-416. Epub 2016 Aug 15.
    Department of Pathology and Laboratory Medicine, The University of North Carolina School of Medicine, Chapel Hill, NC, USA.
    Classical Hodgkin lymphoma (CHL) is morphologically characterized by scattered malignant Hodgkin/Reed-Sternberg (HRS) cells that are far outnumbered by surrounding reactive hematolymphoid cells. Approximately half of all cases of CHL are associated with infection by Epstein-Barr virus (EBV), an oncogenic herpesvirus that expresses a number of proteins thought to contribute to transformation. While a small number of published studies have attempted to identify recurrent cytogenetic abnormalities in CHL, no large case series have explored karyotypic differences between EBV-positive and EBV-negative tumors. Read More

    Breast cancer risk is similar for CHEK2 founder and non-founder mutation carriers.
    Cancer Genet 2016 Sep 15;209(9):403-407. Epub 2016 Aug 15.
    Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA; Department of Pediatrics, Division of Genetics and Genomic Medicine, University of California, 2054 E. Hewitt Hall, Irvine, CA 92697, USA.
    CHEK2 mutations are associated with increased cancer risks, including breast; however, published risk estimates are limited to those conferred by CHEK2 founder mutations, presenting uncertainty in risk assessment for carriers of other CHEK2 mutations. This study aimed to assess phenotypes and molecular characteristics of CHEK2 mutation carriers (CHEK2 + s) from a multi-gene panel testing (MGPT) cohort, focusing on comparing phenotypes of founder and non-founder CHEK2 + s. Clinical histories and molecular results were reviewed from 45,879 patients who underwent MGPT including CHEK2 at a commercial laboratory. Read More

    Jumping translocations in myelodysplastic syndromes.
    Cancer Genet 2016 Sep 8;209(9):395-402. Epub 2016 Aug 8.
    Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview ave N, Seattle, WA 98109, USA; Department of Pathology, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA; Department of Laboratory Medicine, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA.
    Jumping translocations (JT) have been identified in numerous malignancies, including leukemia, but infrequently in patients with myelodysplastic syndromes (MDS). The responsible genetic region has been mapped to the JTB gene at 1q21, but breakpoints involving other chromosomal loci, such as 3q and 11q, have been described as well. We have characterized the pathological and mutational landscape, and the clinical course of 6 new MDS patients with jumping mutations using chromosome genomic array testing (CGAT) and target gene panel next generation sequencing. Read More

    Association between microRNA-27a rs895819 polymorphism and risk of colorectal cancer: A meta-analysis.
    Cancer Genet 2016 Sep 10;209(9):388-394. Epub 2016 Aug 10.
    Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, No. 115 Donghu Road, Wuhan 430071, China; Global Health Institute, Wuhan University, No. 115 Donghu Road, Wuhan 430071, China. Electronic address:
    Colorectal cancer (CRC) is the most common malignancy in the human digestive system. Previous results regarding the association between microRNA-27a rs895819 polymorphisms and CRC risk are controversial. We therefore performed a meta-analysis of seven studies totaling 2230 cases and 2775 controls to systematically evaluate this association. Read More

    Mesothelioma families without inheritance of a BAP1 predisposing mutation.
    Cancer Genet 2016 Sep 18;209(9):381-387. Epub 2016 Jul 18.
    Department of Oncology, San Luigi Hospital, University of Turin, Regione Gonzole, 10-10043 Orbassano, Italy.
    Familial malignant mesothelioma clusters are ideal candidates to explore BAP1 genomic status as a predisposing risk factor. We report data on BAP1 analysis in four families with multiple mesothelioma cases to investigate possible BAP1 alterations associated with an inherited cancer syndrome. We also recorded family history of cancer and assessed asbestos exposure. Read More

    Mutant TP53 disrupts age-related accumulation patterns of somatic mutations in multiple cancer types.
    Cancer Genet 2016 Sep 9;209(9):376-380. Epub 2016 Jul 9.
    Department of Computer Science, Xavier University of Louisiana, New Orleans, LA, USA. Electronic address:
    Most cancers are driven by somatic mutations in proto-oncogenes and tumor suppressor genes. Genetic changes in a tumor may accumulate in the tissue self-renewal phase prior to neoplasm. The risk of sporadic mutations increases with age. Read More

    Association of programmed death-1 polymorphisms with the risk and prognosis of esophageal squamous cell carcinoma.
    Cancer Genet 2016 Sep 5;209(9):365-375. Epub 2016 Jul 5.
    Hebei Provincial Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China. Electronic address:
    Programmed death-1 (PD-1) is an immunoinhibitory receptor belonging to the CD28 family. This study was designed to investigate the association of PD-1 rs36084323:A>G, rs2227981:C>T, rs2227982:C>T and rs10204525:A>G single nucleotide polymorphisms (SNPs) with the risk and prognosis of esophageal squamous cell carcinoma (ESCC) in a high-incidence population from Northern China. These four SNPs were genotyped by polymerase chain reaction ligase detection reaction (PCR-LDR) method in 584 ESCC patients and 585 healthy controls. Read More

    Prevalence of Hispanic BRCA1 and BRCA2 mutations among hereditary breast and ovarian cancer patients from Brazil reveals differences among Latin American populations.
    Cancer Genet 2016 Sep 20;209(9):417-422. Epub 2016 Jun 20.
    Department of Population Sciences, Division of Clinical Cancer Genetics, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
    Germline mutations in BRCA1 or BRCA2 (BRCA) are responsible for 5-15% of breast (BC) and ovarian cancers (OC), predisposing to the development of early onset and often multiple primary tumors. Since mutation carriers can benefit from risk-reducing interventions, the identification of individuals with hereditary breast and ovarian cancer (HBOC) syndrome has a significant clinical impact. We assessed whether a panel assay for recurrent Hispanic BRCA mutations (HISPANEL) has an adequate breadth of coverage to be suitable as a cost effective screening tool for HBOC in a cohort of patients from Southern Brazil. Read More

    Monosomal karyotype of chromosome 5/7 was an independent poor prognostic factor for Chinese myelodysplastic syndrome patients.
    Cancer Genet 2016 Sep 23;209(9):423-429. Epub 2016 Jun 23.
    Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China. Electronic address:
    Monosomal karyotype (MK) was defined as the presence of at least 2 autosomal monosomies or of a single monosomy associated with at least one additional structural abnormality. 6.4-16. Read More

    The pathways of genetic transformation in cholangiocarcinogenesis.
    Cancer Genet 2016 Dec 16;209(12):554-558. Epub 2016 Aug 16.
    SUNY Downstate Medical Center, Brooklyn, NY 11203, United States.
    Cholangiocarcinoma (CCA) is an aggressive malignancy that originates from the epithelial cells of the biliary duct system. Depending on the anatomical location, CCA can be considered extrahepatic (eCCA) or intrahepatic (iCCA) (1). Two thirds of CCAs involve the extrahepatic biliary system, whereas the rest are confined within the liver parenchyma, beyond the secondary biliary radicals (2). Read More

    Molecular targeted therapy for pancreatic adenocarcinoma: A review of completed and ongoing late phase clinical trials.
    Cancer Genet 2016 Dec 2;209(12):567-581. Epub 2016 Aug 2.
    Division of Surgical Oncology, Brody School of Medicine, East Carolina University, Greenville, NC, USA. Electronic address:
    Molecular targeted therapy is widely utilized and effective in a number of solid tumors. In pancreatic adenocarcinoma, targeted therapy has been extensively evaluated; however, survival improvement of this aggressive disease using a targeted strategy has been minimal. The purpose of this study is to review therapeutic molecular targets in completed and ongoing later phase (II and III) clinical trials to have a better understanding of the rationale and progress towards targeted molecular therapies for pancreatic cancer. Read More

    Available technologies and clinical applications of targeted chemotherapy in pancreatic cancer.
    Cancer Genet 2016 Dec 5;209(12):582-591. Epub 2016 Aug 5.
    Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA.
    The incidence of pancreatic cancer, the fourth leading cause of cancer death in United States, is increasing worldwide. Even though the cure rate has doubled in 40 years, it is abysmally poor at 6-7%. As surgical resection remains the only curative treatment and less than 20% of the newly diagnosed cancers are resectable, the major burden of disease management lies in early diagnosis, good prognostication, and proper neo-adjuvant and/or adjuvant therapy. Read More

    A practical approach to liver metastasis from unknown primary cancer: What surgeons need to know.
    Cancer Genet 2016 Dec 15;209(12):559-566. Epub 2016 Aug 15.
    Florida Hospital Tampa, Southeastern Center for Digestive Disorders and Pancreatic Cancer, Tampa, FL, USA.
    The liver is a site of metastasis in 25% of metastatic cancers (Abbruzzese et al., 1995). In Western countries, metastases are the most common type of malignant neoplasms in the liver. Read More

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