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    540 results match your criteria Cancer Genetics [Journal]

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    A neoplasm with FIP1L1-PDGFRA fusion presenting as pediatric T-cell lymphoblastic leukemia/lymphoma without eosinophilia.
    Cancer Genet 2017 Oct 3;216-217:91-99. Epub 2017 Aug 3.
    Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California. Electronic address:
    The 2016 World Health Organization (2016 WHO) classification of hematopoietic malignancies classifies neoplasms with a fusion between the FIP1L1 and PDGFRA genes in 4q12 into a group called "myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1 or with PCM1-JAK2". Neoplasms characterized by this fusion are pluripotent stem cell disorders that can show both myeloid and lymphoid differentiation. They typically occur in adult patients and most are characterized by eosinophilia. Read More

    A novel somatic JAK2 kinase-domain mutation in pediatric acute lymphoblastic leukemia with rapid on-treatment development of LOH.
    Cancer Genet 2017 Oct 31;216-217:86-90. Epub 2017 Jul 31.
    Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia; Australian Genomic Health Alliance, Australia. Electronic address:
    We report a novel somatic mutation in the kinase domain of JAK2 (R938Q) in a high-risk pediatric case of B-cell acute lymphoblastic leukemia (ALL). The patient developed on-therapy relapse at 12 months, and interestingly, the JAK2 locus acquired loss of heterozygosity during treatment resulting in 100% mutation load. Furthermore, we show that primary ALL mononuclear cells harboring the JAK2 R938Q mutation display reduced sensitivity to the JAK1/2 ATP-competitive inhibitor ruxolitinib in vitro, compared to ALL cells that carry a more common JAK2 pseudokinase domain mutation. Read More

    Constitutional mosaicism of a de novo TP53 mutation in a patient with bilateral choroid plexus carcinoma.
    Cancer Genet 2017 Oct 20;216-217:79-85. Epub 2017 Jul 20.
    Department of Oncology, The Children's Memorial Health Institute, 04-730 Warsaw, Poland.
    Choroid plexus tumors (CPT) constitute 2%-5% of all pediatric brain tumors and include high grade choroid plexus carcinoma (CPC). About 40% of CPC patients harbor germline TP53 mutations, associated with diminished survival rates. However, the number of TP53 carriers might be underestimated due to suboptimal ability of Sanger sequencing to identify mosaicism. Read More

    Acute myeloid leukemia with t(14;21) involving RUNX1 and SYNE2: A novel favorable-risk translocation?
    Cancer Genet 2017 Oct 31;216-217:74-78. Epub 2017 Jul 31.
    Division of Hematology/Blood and Marrow Transplantation, Department of Medicine, University of California, San Francisco, CA. Electronic address:
    In acute myeloid leukemia (AML), a translocation between chromosomes 8q22 and 21q22 leads to the RUNX1-RUNXT1 fusion gene which, in the absence of a concomitant KIT mutation, generally portends a more favorable prognosis. Translocations at 21q22, other than those involving 8q22, are uncommon, and the specific prognostic and therapeutic implications are accordingly limited by the small number of reported cases. In this report, we describe the case of a 67-year-old gentleman who presented with AML harboring t(14;21)(q23;q22). Read More

    Upregulation of vascular endothelial growth factor (VEGF), its role in progression and prognosis of non-small cell lung carcinoma.
    Cancer Genet 2017 Oct 29;216-217:67-73. Epub 2017 Jul 29.
    Department of Immunology and Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences, Soura, Srinagar, Kashmir 190011, India. Electronic address:
    Elevated VEGF mRNA (-ΔCT) was significantly associated with adenocarcinoma histology (vs squamous) and advanced NSCLC clinical stages in a univariable analysis; however, this association did not remain significant in the multivariable analysis. Of interest, a Kaplan-Meier analysis showed that NSCLC patients with higher VEGF mRNA (-ΔCT ≥10) had a significantly poorer overall survival and shorter postoperative relapse time in adenocarcinoma and in stage III/IV than those with VEGF mRNA of -ΔCT <10 (P < 0.001). Read More

    RANK and EGFR in invasive breast carcinoma.
    Cancer Genet 2017 Oct 26;216-217:61-66. Epub 2017 Jul 26.
    Clinical and Molecular Oncology Laboratory, Division of Oncology, School of Medicine, University of Patras, 26504, Greece.
    Breast cancer is the most common malignancy, affecting one in eight women in North America and Europe. The human epidermal growth factor receptor (EGFR) protein comprises a major determinant of normal development but also cancer. RANK receptor (Receptor Activator of Nuclear factor-κB) is a tumor necrosis superfamily member and a binding partner for RANKL, which was recently implicated in breast cancer initiation, progression and metastasis. Read More

    First cloned human immortalized adipose derived mesenchymal stem-cell line with chimeric SS18-SSX1 gene (SS-iASC).
    Cancer Genet 2017 Oct 26;216-217:52-60. Epub 2017 Jul 26.
    1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary. Electronic address:
    The SS18-SSX chimeric gene is unique to synovial sarcoma. Multiple model systems including mouse cell lines expressing SS18-SSX, and genetically engineered mouse models of synovial sarcoma have been developed to elucidate the role of the chimeric gene in synovial sarcomagenesis. Although several cell lines stably expressing human SS18-SSX exist, there is an ongoing need for cell culture models enabling researchers to investigate the molecular mechanism of SS18-SSX action in a relevant cellular context. Read More

    Gene expression profiling, pathway analysis and subtype classification reveal molecular heterogeneity in hepatocellular carcinoma and suggest subtype specific therapeutic targets.
    Cancer Genet 2017 Oct 8;216-217:37-51. Epub 2017 Jul 8.
    Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. Electronic address:
    A very low 5-year survival rate among hepatocellular carcinoma (HCC) patients is mainly due to lack of early stage diagnosis, distant metastasis and high risk of postoperative recurrence. Hence ascertaining novel biomarkers for early diagnosis and patient specific therapeutics is crucial and urgent. Here, we have performed a comprehensive analysis of the expression data of 423 HCC patients (373 tumors and 50 controls) downloaded from The Cancer Genome Atlas (TCGA) followed by pathway enrichment by gene ontology annotations, subtype classification and overall survival analysis. Read More

    Prognostic significance of recurrent additional chromosomal abnormalities in adult patients with Philadelphia chromosome-positive acute lymphoblastic leukemia.
    Cancer Genet 2017 Oct 9;216-217:29-36. Epub 2017 Jun 9.
    Department of Laboratory Medicine, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Republic of Korea. Electronic address:
    In Philadelphia (Ph) chromosome-positive acute lymphoblastic leukemia (ALL), additional chromosomal abnormalities (ACAs) are frequently observed. We investigated the cytogenetic characteristics and prognostic significance of ACAs in Ph-positive ALL. We reviewed the clinical data and bone marrow cytogenetic findings of 122 adult Ph-positive ALL patients. Read More

    Significantly mutated genes and regulatory pathways in SCLC-a meta-analysis.
    Cancer Genet 2017 Oct 7;216-217:20-28. Epub 2017 Jun 7.
    Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA; UF Genetics Institute, University of Florida, Gainesville, FL, USA. Electronic address:
    Small cell lung cancer (SCLC) accounts for approximately 15% of all lung cancers and demands effective targeted therapeutic strategies. In this meta-analysis study, we aim to identify significantly mutated genes and regulatory pathways to help us better understand the progression of SCLC and to identify potential biomarkers. Besides ranking genes based on their mutation frequencies, we sought to identify statistically significant mutations in SCLC with the MutSigCV software. Read More

    Identification of a novel CSF3R-SPTAN1 fusion gene in an atypical chronic myeloid leukemia patient with t(1;9)(p34;q34) by RNA-Seq.
    Cancer Genet 2017 Oct 24;216-217:16-19. Epub 2017 May 24.
    Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou 215006, China; Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China. Electronic address:
    Membrane-proximal and truncated mutations of colony-stimulating factor 3 receptor (CSF3R) are frequently found in chronic neutrophilic leukemia (CNL) and atypical chronic myeloid leukemia (aCML). However, rearrangement involving CSF3R in hematological neoplasms has not been reported. Here, we report a case of a 21-year-old female diagnosed as aCML with t(1;9)(p34;q34) who presented a CSF3R rearrangement. Read More

    Identification of pathogenic retrotransposon insertions in cancer predisposition genes.
    Cancer Genet 2017 Oct 24;216-217:159-169. Epub 2017 Aug 24.
    Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA. Electronic address:
    Cancer risks have been previously reported for some retrotransposon element (RE) insertions; however, detection of these insertions is technically challenging and very few oncogenic RE insertions have been reported. Here we evaluate RE insertions identified during hereditary cancer genetic testing using a comprehensive testing strategy. Individuals who had single-syndrome or pan-cancer hereditary cancer genetic testing from February 2004 to March 2017 were included. Read More

    Potential circulating miRNA signature for early detection of NSCLC.
    Cancer Genet 2017 Oct 7;216-217:150-158. Epub 2017 Aug 7.
    Lung Transplantation Research Center, NRITLD, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
    Circulating microRNAs (c-miRNAs) are promising biomarkers for screening, early detection and prognosis of cancer. The purpose of this investigation was to identify a panel of c-miRNAs in plasma that could contribute to early detection of non-small cell lung cancer (NSCLC). We profiled the expression of 44 unique plasma miRNAs in training set of 34 NSCLC patients and 20 matched healthy individuals by miRCURY LNA™ Universal RT microRNA PCR Panel and calculated dysregulation fold changes using the 2-ΔΔCt equation. Read More

    Trisomy 12 assessment by conventional fluorescence in-situ hybridization (FISH), FISH in suspension (FISH-IS) and laser scanning cytometry (LSC) in chronic lymphocytic leukemia.
    Cancer Genet 2017 Oct 4;216-217:142-149. Epub 2017 Aug 4.
    College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia; Hematology, Molecular Medicine and Pathology, Bedford Park, SA Australia. Electronic address:
    Chronic lymphocytic leukemia (CLL) has an extremely heterogeneous clinical course, and prognostication is based on common genetic abnormalities which are detected by standard cytogenetic methods. However, current methods are restricted by the low number of cells able to be analyzed, resulting in the potential to miss clinically relevant sub-clonal populations of cells. A novel high throughput methodology called fluorescence in situ hybridization in suspension (FISH-IS) incorporates a flow cytometry-based imaging approach with automated analysis of thousands of cells. Read More

    Addition of chromosomal microarray and next generation sequencing to FISH and classical cytogenetics enhances genomic profiling of myeloid malignancies.
    Cancer Genet 2017 Oct 14;216-217:128-141. Epub 2017 Aug 14.
    PathGroup, Nashville, TN.
    Comprehensive genetic profiling is increasingly important for the clinical workup of hematologic tumors, as specific alterations are now linked to diagnostic characterization, prognostic stratification and therapy selection. To characterize relevant genetic and genomic alterations in myeloid malignancies maximally, we utilized a comprehensive strategy spanning fluorescence in situ hybridization (FISH), classical karyotyping, Chromosomal Microarray (CMA) for detection of copy number variants (CNVs) and Next generation Sequencing (NGS) analysis. In our cohort of 569 patients spanning the myeloid spectrum, NGS and CMA testing frequently identified mutations and copy number changes in the majority of genes with important clinical associations, such as TP53, TET2, RUNX1, SRSF2, APC and ATM. Read More

    Prognostic classification of MDS is improved by the inclusion of FISH panel testing with conventional cytogenetics.
    Cancer Genet 2017 Oct 16;216-217:120-127. Epub 2017 Aug 16.
    Cytogenetics division, SRL Diagnostic Ltd., Prime Square Building, Gaiwadi Industrial Estate, S.V.Road, Goregaon, Mumbai 400 062, India. Electronic address:
    Cytogenetics is a critical independent prognostic factor in myelodysplastic syndromes (MDS). Conventional cytogenetics (CC) and Fluorescence in situ hybridization (FISH) Panel Testing are extensively used for the prognostic stratification of MDS, although the FISH test is not yet a bona fide component of the International Prognostic Scoring System (IPSS). The present study compares the utility of CC and FISH to detect chromosomal anomalies and in prognostic categorization. Read More

    Genetic Gastric Cancer Susceptibility in the International Clinical Cancer Genomics Community Research Network.
    Cancer Genet 2017 Oct 17;216-217:111-119. Epub 2017 Aug 17.
    Division of Clinical Cancer Genomics, City of Hope National Medical Center, 1500 E. Duarte Rd., Bldg 173, Duarte, CA 91010; Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010.
    Few susceptibility genes for gastric cancer have been identified. We sought to identify germline susceptibility genes from participants with gastric cancer from an international hereditary cancer research network. Adults with gastric cancer of any histology, and with a germline DNA sample (n = 51), were retrospectively selected. Read More

    Regulatory mechanisms of long noncoding RNAs on gene expression in cancers.
    Cancer Genet 2017 Oct 9;216-217:105-110. Epub 2017 Aug 9.
    Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, PR China. Electronic address:
    Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. Read More

    A rare case of pediatric lipoma with t(9;12)(p22;q14) and evidence of HMGA2-NFIB gene fusion.
    Cancer Genet 2017 Oct 9;216-217:100-104. Epub 2017 Aug 9.
    Genetics Department, Children's Hospital of Eastern Ontario, Ottawa, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Canada. Electronic address:
    Lipoma is a benign tumor, typically of adulthood, with characteristic cytogenetic findings, including rearrangement of 12q13-15; these rearrangements often lead to the fusion of the HMGA2 gene at this locus to the transcriptional regulatory domain of its fusion partner, resulting in neomorphic activity that presumably facilitates the neoplastic process. Herein, we report a rare case of pediatric lipoma with t(9;12)(p22;q14) and evidence of HMGA2-NFIB gene fusion in a 9 year-old boy. This case provides further evidence of the link between NFIB rearrangement and early-onset, deep-seated lipomatous tumors. Read More

    A novel TRIP11-FLT3 fusion in a patient with a myeloid/lymphoid neoplasm with eosinophilia.
    Cancer Genet 2017 Oct 10;216-217:10-15. Epub 2017 May 10.
    Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:
    FLT3 fusions are associated with myeloid and lymphoid neoplasms with eosinophilia. We describe a patient presenting with clinicopathologic features of both chronic eosinophilic leukemia, not otherwise specified (CEL, NOS) and systemic mastocytosis (SM). The bone marrow demonstrated a myeloproliferative neoplasm with eosinophilia and aggregates of atypical mast cells. Read More

    Clonal chromosomal aberrations in Philadelphia negative cells such as monosomy 7 and trisomy 8 may persist for years with no impact on the long term outcome in patients with chronic myeloid leukemia.
    Cancer Genet 2017 Oct 28;216-217:1-9. Epub 2017 Apr 28.
    Department of Clinical Genetics, Medical University of Bialystok, 13 Waszyngtona Street, 15-089 Białystok, Poland.
    The appearance of clonal chromosomal aberrations in Philadelphia negative cells (CCA/Ph-) during the treatment of chronic myeloid leukemia (CML) was recently confirmed. Importance of these findings has not been clearly defined. We present data on the time of appearance, persistence, size of the CCA/Ph- clone in terms of drugs used and hematological, cytogenetic and molecular response rates. Read More

    Clinical utility of emerging liquid biomarkers in advanced prostate cancer.
    Cancer Genet 2017 Aug 25. Epub 2017 Aug 25.
    Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia, Canada V6H 3Z6. Electronic address:
    The therapeutic landscape of advanced prostate cancer (PCa) has rapidly expanded in recent years. Despite significant improvements in patient overall survival, it remains challenging to determine the optimal therapy and sequence of therapies for individual patients. The development of molecular biomarkers will be key for patient stratification, and for monitoring response and resistance to therapy. Read More

    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 02 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

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