734 results match your criteria Cancer Genetics [Journal]


Clinical exome sequencing identified POLB c.C1002A as a possible genetic cause in a family with hereditary cancer-predisposing syndrome.

Cancer Genet 2020 Jun 26;245:49-52. Epub 2020 Jun 26.

Gastro-intestine Surgery Department, Shanghai Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China. Electronic address:

This study recruited a Chinese family with hereditary cancer-predisposing syndrome. To investigate the causative mutations, disease-associated exome sequencing was conducted using peripheral blood of three members with malignant disease. As a result, three variants (PLD2 c. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.06.003DOI Listing

Evolution of histomorphologic, cytogenetic, and genetic abnormalities in an untreated patient with MIRAGE syndrome.

Cancer Genet 2020 Jun 14;245:42-48. Epub 2020 Jun 14.

Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Abramson Research Center, Room 716D, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States. Electronic address:

Gain of function variants in SAMD9 cause MIRAGE syndrome, a rare Mendelian disorder that results in myeloid dysplastic syndrome (MDS), poor immune response, restricted growth, adrenal insufficiency, ambiguous genitalia, feeding difficulties and most often significantly reduced lifespan. In this study, we describe histomorphologic and genetic changes occurring in serial bone marrow measurements in a patient with MIRAGE syndrome and untreated MDS of 9 years. Histomorphological analysis during childhood showed progressive hypocellularity with erythroid and megakaryocytic dysplasia and cytogenetic testing demonstrated monosomy 7. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.06.002DOI Listing

Alcohol consumption and risk of breast and ovarian cancer: A Mendelian randomization study.

Cancer Genet 2020 Jun 12;245:35-41. Epub 2020 Jun 12.

Department of Gynecology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, China. Electronic address:

Background: Alcohol consumption has been found to increase the risk of breast cancer in observation studies, yet it remains unknown if alcohol is related to other hormone-dependent cancers such as ovarian cancer. No Mendelian randomization (MR) studies have been performed to assess a potential causal relationship between alcohol use and risk of breast and ovarian cancer.

Methods: We aim to determine if alcohol consumption is causally associated with the risk of female hormone-dependent cancers, by using summary level genetic data from the hitherto largest genome-wide association studies (GWAS) conducted on alcohol consumption (N=~1. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.06.001DOI Listing

Comprehensive network analysis of the molecular mechanisms associated with sorafenib resistance in hepatocellular carcinoma.

Cancer Genet 2020 May 17;245:27-34. Epub 2020 May 17.

Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Laboratory of South China Structural Heart Disease, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China. Electronic address:

Objective: Hepatocellular carcinoma (HCC) is an intractable disease because patients with HCC frequently develop sorafenib resistance after long-term chemotherapy. Although studies has demonstrated the availability of cumulative information on drug-resistant patients, little is known about the strategies and molecular mechanisms to reverse sorafenib resistance. Here, the present study identified critical mRNAs and transcription factors (TFs) associated with sorafenib resistance of HCC and evaluated the significance correlation between drug-resistant genes and TFs in comprehensive network for HCC xenografts mice. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.04.076DOI Listing

Generation and characterization of the Eµ-Irf8 mouse model.

Cancer Genet 2020 Jun 3;245:6-16. Epub 2020 Jun 3.

Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; South Texas Veterans Health Care System, Audie Murphy VA Hospital, San Antonio, TX 78229, USA. Electronic address:

In mature B-cell malignancies, chromosomal translocations often juxtapose an oncogenic locus to the regulatory regions of the immunoglobulin genes. These genomic rearrangements can associate with specific clinical/pathological sub-entities and inform diagnosis and treatment decisions. Recently, we characterized the t(14;16)(q32;q24) in diffuse large B-cell lymphoma (DLBCL), and showed that it targets the transcription factor IRF8, which is also somatically mutated in ~10% of DLBCLs. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.05.002DOI Listing

High methylation levels of histone H3 lysine 9 associated with activation of hypoxia-inducible factor 1α (HIF-1α) predict patients' worse prognosis in human hepatocellular carcinomas.

Cancer Genet 2020 May 18;245:17-26. Epub 2020 May 18.

Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, P. R. China. Electronic address:

Although it is becoming increasingly apparent that histone methyltransferases and histone demethylases play crucial roles in the cellular response to hypoxia, the impact of hypoxic environments on global patterns of histone methylation is not well demonstrated. In this study, we try to detect the global levels of histone lysine methylation in HCC cases and analyze the correlation between these modifications and the activation of hypoxia-inducible factor 1α (HIF-1α). Immunohistochemistry was used to detect the global levels of histone H3 lysine 9 dimethylation (H3K9me2), histone H3 lysine 9 trimethylation (H3K9me3), histone H3 lysine 27 trimethylation (H3K27me3) and the nuclear expression of HIF-1α in tissue arrays from 111 paraffin-embedded HCC samples. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.04.077DOI Listing

Genetic progression of post-transplant Burkitt-like lymphoma case with 11q-Gain/Loss and MYC amplification.

Cancer Genet 2020 May 18;245:1-5. Epub 2020 May 18.

Cytogenetic Laboratory, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.

"Burkitt-like lymphoma with 11q aberration" is a new provisional entity in the latest revision of lymphoma's World Health Organization classification described as carrying the specific 11q-gain/loss aberration and lacking MYC rearrangement. Morphologically, phenotypically and by gene and microRNA expression profiling these lymphomas resemble Burkitt lymphoma. The 11q-gain/loss was also found in post-transplant patients with molecular Burkitt lymphoma signature without MYC rearrangement. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.05.001DOI Listing
May 2020
2.417 Impact Factor

Twin-to-twin transmission of transient abnormal myelopoiesis without constitutional trisomy 21: A case report.

Cancer Genet 2020 Jun 4;244:62-64. Epub 2020 May 4.

Department of Pediatrics, Baystate Children's Hospital/University of Massachusetts Medical School, Springfield, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cancergen.2020.04.003DOI Listing

Myeloid neoplasm with a novel cryptic PDGFRB rearrangement detected by next-generation sequencing.

Cancer Genet 2020 Jun 3;244:55-59. Epub 2020 May 3.

Division of Hematopathology, Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W 11(th) St, Indianapolis, IN 46202, USA. Electronic address:

Rearrangements of PDGFRB are defining cytogenetic abnormalities seen in "Myeloid/lymphoid neoplasms with eosinophilia and rearrangement of PDGFRB" and are generally evident by common cytogenetic methods. Here we present an unique case in which karyotyping and fluorescence in situ hybridization (FISH) analysis were negative, and the PDGFRB rearrangement was detected by next-generation sequencing (NGS) analysis. The patient presented with approximately one-year history of leukocytosis including neutrophilia, eosinophilia, basophilia and granulocytic left shift. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.03.002DOI Listing

Assessing Genomic Copy Number Alterations as Best Practice for Renal Cell Neoplasia: An Evidence-Based Review from the Cancer Genomics Consortium Workgroup.

Cancer Genet 2020 Jun 1;244:40-54. Epub 2020 May 1.

Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 165 Ashley Avenue, MSC 908, Charleston, SC 29425.

Renal cell neoplasia are heterogeneous with diverse histology, genetic alterations, and clinical behavior that are diagnosed mostly on morphologic features. The Renal Cell Neoplasia Workgroup of the Cancer Genomics Consortium systematically evaluated peer-reviewed literature on genomic studies of renal cell carcinoma (RCC), including clear cell RCC, papillary RCC, chromophobe RCC, and the translocation RCC involving TFE3, TFEB and MITF rearrangements, as well as benign oncocytoma, which together comprise about 95% of all renal cell neoplasia. The Workgroup curated recurrent copy number alterations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), rearrangements, and mutations, found in each subtype and assigned clinical relevance according to established criteria. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.04.004DOI Listing

Familial Cerebral Cavernous Malformation Syndrome with Concomitant Fourth Ventricular Ependymoma: True Association or Mere Coincidence?

Cancer Genet 2020 Jun 3;244:36-39. Epub 2020 May 3.

Department of Neurological Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA. Electronic address:

Familial cerebral cavernous malformation syndromes are most commonly caused by mutations in one of three genes. The overlap of these genetic malformations with other acquired neoplastic lesions and congenital malformations is still under investigation. To the best of our knowledge, the concurrent occurrence of familial cavernous malformations and ependymoma has not been previously reported in the literature. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.04.075DOI Listing

Double mutation of APC and BRCA1 in an Italian family.

Cancer Genet 2020 Jun 28;244:32-35. Epub 2020 Apr 28.

Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.

Familial adenomatous polyposis (FAP) is a rare genetic disorder caused mainly by monoallelic mutations of APC gene. The hereditary breast and ovarian cancer (HBOC) syndrome is an autosomal dominantly inherited disease, which mostly predisposes to breast and ovarian cancers as a result of germline mutations in BRCA1 or BRCA2 genes. In a family, mutations in two cancer susceptibility genes are extremely rare. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.04.074DOI Listing

Evidence-based review of genomic aberrations in B-lymphoblastic leukemia/lymphoma: Report from the cancer genomics consortium working group for lymphoblastic leukemia.

Cancer Genet 2020 May 21;243:52-72. Epub 2020 Mar 21.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.

Clinical management and risk stratification of B-lymphoblastic leukemia/ lymphoma (B-ALL/LBL) depend largely on identification of chromosomal abnormalities obtained using conventional cytogenetics and Fluorescence In Situ Hybridization (FISH) testing. In the last few decades, testing algorithms have been implemented to support an optimal risk-oriented therapy, leading to a large improvement in overall survival. In addition, large scale genomic studies have identified multiple aberrations of prognostic significance that are not routinely tested by existing modalities. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.03.001DOI Listing

Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis.

Cancer Genet 2020 May 17;243:48-51. Epub 2020 Mar 17.

Mayo Clinic, Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Rochester, MN, United States. Electronic address:

Traditional cytogenetic testing methodologies, including conventional chromosome analysis and fluorescence in situ hybridization (FISH), are invaluable for the detection or recurrent genetic abnormalities in various hematologic malignancies. However, technological advances, including a novel next-generation sequencing technique termed mate-pair sequencing (MPseq), continue to revolutionize the field of cytogenetics by enabling the characterization of structural variants at a significantly higher resolution compared to traditional methodologies. To illustrate the power of MPseq, we present a 27-year-old male diagnosed with chronic myeloid leukemia in myeloid blast crisis with multiple chromosomal abnormalities observed in all 20 metaphases from a peripheral blood specimen, including t(9;22)(q34;q11. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.008DOI Listing

Copy number assessment in the genomic analysis of CNS neoplasia: An evidence-based review from the cancer genomics consortium (CGC) working group on primary CNS tumors.

Cancer Genet 2020 May 26;243:19-47. Epub 2020 Feb 26.

Department of Pathology, Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, United States.

The period from the 1990s to the 2010s has witnessed a burgeoning sea change in the practice of surgical neuropathology due to the incorporation of genomic data into the assessment of a range of central nervous system (CNS) neoplasms. This change has since matured into the adoption of genomic information into the definition of several World Health Organization (WHO)-established diagnostic entities. The data needed to accomplish the modern diagnosis of CNS neoplasia includes DNA copy number aberrations that may be assessed through a variety of mechanisms. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.004DOI Listing

Comparison of four next generation sequencing platforms for fusion detection: Oncomine by ThermoFisher, AmpliSeq by illumina, FusionPlex by ArcherDX, and QIAseq by QIAGEN.

Cancer Genet 2020 May 7;243:11-18. Epub 2020 Mar 7.

Cytogenetics Laboratory, Seattle Cancer Care Alliance, United States; Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), 825 Eastlake Ave. E., MS: BL103, Seattle, WA 98109, United States. Electronic address:

As fusion detection NGS techniques are adopted by clinical labs, assay performance comparison is urgently needed. We compared four fusion-detection assay platforms on a pilot cohort of 24 prostate cancer samples: (1) Oncomine Comprehensive panel v3; (2) AmpliSeq comprehensive panel v3; (3) The solid tumor panel of FusionPlex; and (4) The human oncology panel of QIAseq. The assays were compared for the detection of different types of fusion based on whether the partner gene or the breakpoints are known. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.007DOI Listing

Integrating transcriptome-wide association study and copy number variation study identifies candidate genes and pathways for diffuse non-Hodgkin's lymphoma.

Cancer Genet 2020 May 25;243:7-10. Epub 2020 Feb 25.

Department of hematology, The First Affiliated Hospital of Xi'an Jiaotong University, 710061, China. Electronic address:

Background: The genetic basis of diffuse non-Hodgkin's lymphoma (DNHL) is largely unknown now. We conducted a large-scale transcriptome-wide association study (TWAS) of DNHL to identify novel candidates for DNHL.

Methods: The GWAS summary data of DNHL was obtained from the UKBiobank, involving 685 cases and 451,579 controls. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.005DOI Listing
May 2020
2.417 Impact Factor

Novel and recurrent germline mutations in the VHL gene in 5 Arab patients with Von Hippel-Lindau disease.

Cancer Genet 2020 May 6;243:1-6. Epub 2020 Mar 6.

Genomics, Ontario Institute for Cancer Research, Toronto, Canada. Electronic address:

Inherited germline mutations in the VHL gene cause predisposition to Von Hippel-Lindau (VHL) disease. Patients exhibit benign and cancerous lesions in multiple tissues, including hemangioblastomas, clear cell renal cell carcinoma, cysts in kidneys and pancreas, and pheochromocytomas. Although pathogenic germline mutations in the VHL gene have been widely described in different populations, only a single mutation was previously reported in a family from mixed Arab-Persian ethnicity. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.006DOI Listing

BCL11A gene over-expression in high risk neuroblastoma.

Cancer Genet 2020 Jun 27;244:30-31. Epub 2020 Feb 27.

Department of Cell Therapy & Applied Genomics, King Hussein Cancer Center, 202 Queen Rania Abdullah Street, P.O. Box 1269 Al-Jubaiha, Amman, 11941 Jordan. Electronic address:

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http://dx.doi.org/10.1016/j.cancergen.2020.02.003DOI Listing

LINE-1 retrotransposon encoded ORF1p expression and promoter methylation in oral squamous cell carcinoma: a pilot study.

Cancer Genet 2020 Jun 10;244:21-29. Epub 2020 Feb 10.

Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand, India. Electronic address:

Oral squamous cell carcinoma (OSCC) is highly predominant in India due to excessive use of tobacco. Here we investigated Long INterpersed Element 1 (LINE or L1) retrotransposon activity in OSCC samples in the same population. There are almost 500,000 copies of L1 occupied around 30%  of the human genome. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.01.050DOI Listing

Current concepts in breast cancer genomics: An evidence based review by the CGC breast cancer working group.

Cancer Genet 2020 Jun 8;244:11-20. Epub 2020 Feb 8.

Mayo Clinic, 200 First Street SW, Rochester, MN 55905, United States.

Background: Genomic abnormalities in breast cancer have been described according to diverse conceptual frameworks, including histologic subtypes, clinical molecular subtypes, intrinsic DNA, RNA, and epigenetic profiles, and activated molecular pathways.

Methods: The Cancer Genomics Consortium (CGC) Breast Cancer Workgroup performed an evidence based literature review to summarize current knowledge of clinically significant genomic alterations in breast cancer using CGC levels of evidence. Targetable or disease-defining alterations were prioritized. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.002DOI Listing

Kinetics of DNA damage repair response accompanying initial hepadnavirus-host genomic integration in woodchuck hepatitis virus infection of hepatocyte.

Cancer Genet 2020 Jun 5;244:1-10. Epub 2020 Feb 5.

Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Sciences Centre, Memorial University, St. John's, Newfoundland and Labrador A1B 3V6, Canada. Electronic address:

Mechanism of initial hepatitis B virus (HBV) integrations and kinetics of DNA repair immediately after infection remain essentially unknown impairing understanding of hepadnaviral oncogenesis. WCM260 hepatocytes susceptible to HBV-compatible woodchuck hepatitis virus (WHV) were examined from 15 min to 72 h post-infection (p.i. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.02.001DOI Listing

Enrichment of atypical hyperdiploidy and IKZF1 deletions detected by SNP-microarray in high-risk Australian AIEOP-BFM B-cell acute lymphoblastic leukaemia cohort.

Cancer Genet 2020 Apr 10;242:8-14. Epub 2020 Feb 10.

Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia; Department of Haematology, NSW Health Pathology-Hunter, Newcastle, New South Wales, Australia.

Acute lymphoblastic leukaemia (ALL) is the most common childhood malignancy with the majority of patients being classified as B-cell lineage (B-ALL). The sub-classification of B-ALL is based on genomic architecture. Recent studies have demonstrated the capability of SNP-microarrays to detect genomic changes in B-ALL which cannot be observed by conventional cytogenetic methods. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.01.051DOI Listing
April 2020
2.417 Impact Factor

Identification of gene modules and hub genes in colon adenocarcinoma associated with pathological stage based on WGCNA analysis.

Cancer Genet 2020 Apr 1;242:1-7. Epub 2020 Feb 1.

School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China; Institute of Precision Medicine, Xinxiang Medical University, Xinxiang, China. Electronic address:

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality in the world, in which colon adenocarcinoma (COAD) is the most common histological subtype of CRC. In this study, our aim is to identify gene modules and representative candidate biomarkers for clinical prognosis of patients with COAD, and help to predict prognosis and reveal the mechanisms of cancer progression. Weighted gene co-expression network analysis (WGCNA) was performed to construct a co-expression network and identify gene modules correlated with TNM clinical staging of COAD patients. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.01.052DOI Listing

MYC amplification on double minute chromosomes in plasma cell leukemia with double IGH/CCND1 fusion genes.

Cancer Genet 2020 Apr 27;242:35-40. Epub 2020 Jan 27.

Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.

In multiple myeloma (MM), MYC rearrangements that result in increased MYC expression are associated with an aggressive form of MM and adverse outcome. However, the consequences of MYC amplification in MM remain unclear. Here, we describe an unusual case of plasma cell leukemia (PCL) harboring MYC amplification on double minute chromosomes (dmin). Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.01.049DOI Listing

Molecular profiling of gynecologic cancers for treatment and management of disease - demonstrating clinical significance using the AMP/ASCO/CAP guidelines for interpretation and reporting of somatic variants.

Cancer Genet 2020 Apr 14;242:25-34. Epub 2020 Jan 14.

The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States. Electronic address:

Molecular features of gynecologic cancers have been investigated in comprehensive studies, but correlation of these molecular signatures with clinical significance for precision medicine is yet to be established. Towards this end, we evaluated 95 gynecologic cancer cases submitted for testing using The JAX ActionSeq™ NGS panel. Molecular profiles were studied and compared to TCGA datasets to identify similarities and distinguishing features among subtypes. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.008DOI Listing

The combination of WGS and RNA-Seq is superior to conventional diagnostic tests in multiple myeloma: Ready for prime time?

Cancer Genet 2020 Apr 11;242:15-24. Epub 2020 Jan 11.

MLL Munich Leukemia Laboratory, Munich, Germany. Electronic address:

The diagnosis and risk stratification of multiple myeloma (MM) is based on clinical and cytogenetic tests. Magnetic CD138 enrichment followed by interphase FISH (fluorescence in situ hybridisation) is the gold standard to identify prognostic translocations and copy number alterations (CNA). Although clinical implications of gene expression profiling (GEP) or panel based sequencing results are evident, those tests have not yet reached routine clinical application. Read More

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http://dx.doi.org/10.1016/j.cancergen.2020.01.001DOI Listing

LncRNA HRCEG, regulated by HDAC1, inhibits cells proliferation and epithelial-mesenchymal-transition in gastric cancer.

Cancer Genet 2020 Feb 8;241:25-33. Epub 2020 Jan 8.

Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan, 528316, China. Electronic address:

Recently, a number of long noncoding RNAs (lncRNAs) have been reported to play significant roles in human tumorigenesis. However, only few gastric cancer related lncRNAs have been well characterized. Here, we identified one lncRNA HRCEG, whose expression was decreased in the gastric cancer tissues compared with adjacent normal tissues. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.007DOI Listing
February 2020

hsa_circ_0062389 promotes the progression of non-small cell lung cancer by sponging miR-103a-3p to mediate CCNE1 expression.

Cancer Genet 2020 Feb 18;241:12-19. Epub 2019 Dec 18.

Anhui Provincial Center for Clinical Laboratories, No. 17 Lujiang Road, Hefei, Anhui 230001, China. Electronic address:

Recently, increasing evidence showed that circular RNAs (circRNAs) play critical roles in tumor progression. However, the roles of hsa_circ_0062389 in non-small cell lung cancer (NSCLC) development remain unclear. In the present study, hsa_circ_0062389 expression was significantly increased in NSCLC tissues and cell lines. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.004DOI Listing
February 2020

BRCA1-BRCA2 mutation analysis results in 910 individuals: Mutation distribution and 8 novel mutations.

Cancer Genet 2020 Feb 2;241:20-24. Epub 2020 Jan 2.

Ege University Faculty of Medicine, Department of Medical Genetic, 35100 Bornova, Izmir, Turkey.

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http://dx.doi.org/10.1016/j.cancergen.2019.12.008DOI Listing
February 2020

Long Interspersed Nuclear Elements 1 (LINE1): The chimeric transcript L1-MET and its involvement in cancer.

Cancer Genet 2020 Feb 21;241:1-11. Epub 2019 Nov 21.

Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX 06720, México; Laboratorio de RNAs no codificantes, Unidad de Investigación Médica en Genética Humana del Hospital de Pediatría "Silvestre Frenk Freund", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), Mexico. Electronic address:

Long interspersed nuclear elements 1 (LINE1) are non-LTR retrotransposons that represent the greatest remodeling force of the human genome during evolution. Genomically, LINE1 are constituted by a 5´ untranslated region (UTR), where the promoter regions are located, three open reading frames (ORF0, ORF1, and ORF2) and one 3´UTR, which has a poly(A) tail that harbors the short interspersed nuclear elements (SINEs) Alu and SVA. Although the intrinsic nature of LINE1 is to be copied and inserted into the genome, an increase in their mobility produces genomic instability. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.004DOI Listing
February 2020
2.417 Impact Factor

Rapid progressive lung cancers harbouring multiple clonal driver mutations with big bang evolution model.

Cancer Genet 2020 Feb 25;241:51-56. Epub 2019 Dec 25.

Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; The University of Tokyo, Tokyo, Japan.

Introduction: Next-generation sequencing (NGS) of multiple metastases in an advanced cancer patient reveals the evolutional history of the tumor. The evolutionary model is clinically valuable because it reflects the future course of the tumorigenic process and prognosis of the patient.

Materials And Methods: We experienced two lung cancer patients whose clinical courses were abruptly deteriorating resulting in very poor prognosis. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.006DOI Listing
February 2020

Secondary acquisition of BCR-ABL1 fusion in de novo GATA2-MECOM positive acute myeloid leukemia with subsequent emergence of a rare KMT2A-ASXL2 fusion.

Cancer Genet 2020 Feb 26;241:67-71. Epub 2019 Dec 26.

Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA. Electronic address:

Secondary acquisition of t(9;22)(q34;q11.2)/BCR-ABL1 fusion in the context of de novo acute myeloid leukemia (AML) with inv(3)(q21q26)/GATA2-MECOM rearrangement has been rarely reported. Furthermore, t(2;11)(p23;q23)/KMT2A-ASXL2 fusion has been rarely described with only a single case reported to date. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.005DOI Listing
February 2020

Pediatric gastrointestinal stromal tumor: Report of two novel patients harboring germline variants in SDHB and SDHC genes.

Cancer Genet 2020 Feb 16;241:61-65. Epub 2019 Dec 16.

Laboratory of Medical Genetics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and rarely occur in pediatric patients. 85% of pediatric GISTs and 15% of adult GISTs lack of KIT or PDGFRA mutations. 40% of these "wild-type" GISTs present loss of function mutations in genes encoding for the subunits of the succinate dehydrogenase (SDH) complex. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.002DOI Listing
February 2020

Low ALK FISH positive metastatic non-small cell lung cancer (NSCLC) patients have shorter progression-free survival after treatment with ALK inhibitors.

Cancer Genet 2020 Feb 13;241:57-60. Epub 2019 Dec 13.

Section of Clinical Cytogenetics, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, United States.

ALK FISH assay guides clinical decision to initiate therapy with ALK inhibitors in patients with stage IV non-small cells lung cancer (NSCLC). In this single institution retrospective study, we investigated the association between the strength of ALK positivity and progression-free survival (PFS) We screened 4,829 patients tested for ALK rearrangement by FISH from 01/06/2012 to 06/30/2018 and included 66 stage IV NSCLC ALK positive patients, who were ALK inhibitor naïve, received an ALK inhibitor, and been followed at least 10 months to the study. The median PFS for cases high positive cases [≥=50% positive nuclei; n = 49] and low positive cases [16-49% positive nuclei; n = 17] is 16 months and 4 months respectively, and the hazard ratio is 2. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.003DOI Listing
February 2020

Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.

Cancer Genet 2020 Feb 10;241:34-41. Epub 2019 Dec 10.

Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden.

The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.12.001DOI Listing
February 2020

Utility of copy number variants in the classification of intracranial ependymoma.

Cancer Genet 2020 Jan 18;240:66-72. Epub 2019 Nov 18.

Department of Pathology and Immunology, Washington University School of Medicine, 660 S. Euclid Avenue, St Louis, MO 63110, USA. Electronic address:

Ependymomas are neuroepithelial tumors that differentiate along the ependymal cell lineage, a lining of the ventricles of the brain and the central canal of the spinal cord. They are rare in adults, but account for around 9% of brain tumors in children, where they usually have an aggressive course. Efficient stratification could lead to improved care but remains a challenge even in the genomic era. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.003DOI Listing
January 2020

Longitudinal whole-genome sequencing reveals the evolution of MPAL.

Cancer Genet 2020 Jan 22;240:59-65. Epub 2019 Nov 22.

The Second Hospital of Dalian Medical University, Dalian, Liaoning, China. Electronic address:

Purpose: Mixed phenotype acute leukemia (MPAL) is a rare subtype of acute leukemia and its progressive genomic basis over time remains unclear. We aimed to investigate the longitudinal genomic evolution of MPAL from diagnosis to relapse.

Methods: We performed whole genome sequencing (WGS) on bone marrow (BM) samples obtained at the four stages of this disease in a male patient with Philadelphia chromosome positive (Ph+) MPAL, including primary, complete cytogenetic remission (CCR), complete molecular remission (CMR), and relapse stage during the 3 year follow-up period. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.007DOI Listing
January 2020

Stem cell factor receptor gene mutation: Achalasia, mastocytosis and gastrointestinal stromal tumors.

Cancer Genet 2020 Feb 20;241:66. Epub 2019 Nov 20.

Department of Gastroenterology. Digestive Surgery Division,University of São Paulo, Av. Dr. Eneas de Carvalho Aguiar 255, São Paulo, SP, CEP 05403-000, Brazil.

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http://dx.doi.org/10.1016/j.cancergen.2019.11.006DOI Listing
February 2020

MIR605 rs2043556 is associated with the occurrence of multiple primary tumors in TP53 p.(Arg337His) mutation carriers.

Cancer Genet 2020 Jan 20;240:54-58. Epub 2019 Nov 20.

Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil; Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil; Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil; Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil.

Li-Fraumeni and Li-Fraumeni-like (LFS/LFL) Syndrome are cancer predisposition syndromes caused by germline pathogenic variants in TP53 and are associated with an increased risk of multiple early-onset cancers. In Southern and Southeastern Brazil, a germline founder variant with partial penetrance located in the oligomerization domain of TP53, c.1010G>A p. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.005DOI Listing
January 2020
2.417 Impact Factor

c.1227_1228dupGG (p.Glu410Glyfs), a frequent variant in Tunisian patients with MUTYH associated polyposis.

Cancer Genet 2020 Jan 4;240:45-53. Epub 2019 Nov 4.

Cytogenetic, Molecular Genetics and Human Reproduction Biology - FARHAT HACHED University Hospital, Sousse, Tunisia.

Introduction: Familial adenomatous polyposis (FAP) is an autosomal dominant-inherited disease caused by germline variants in the APC gene. It is characterized by the development of hundreds to thousands of adenomatous polyps in colon and rectum. Recently, biallelic germline variants in the base excision repair (BER) gene: MUTYH have been identified in patients with attenuated FAP and/or negative APC result. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.007DOI Listing
January 2020

Molecular and phenotypic characterization of an early T-cell precursor acute lymphoblastic lymphoma harboring PICALM-MLLT10 fusion with aberrant expression of B-cell antigens.

Cancer Genet 2020 Jan 9;240:40-44. Epub 2019 Nov 9.

Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL, United States.

T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is usually diagnosed based on the presence of immature lymphoid marker terminal deoxynucleotidyl transferase (TdT), and T-cell specific markers, specifically CD3, by immunohistochemistry (IHC) staining on bone marrow and/or extramedullary tissue. We present a novel, TdT and CD3 negative, aggressive early T-cell precursor LBL (ETP-LBL) initially misdiagnosed as a high grade B-cell lymphoma due to expression of CD79a and the erroneous detection of BCL2/IGH fusion. The patient was eventually evaluated using molecular diagnostic techniques, including fluorescence in situ hybridization (FISH) and next generation sequencing (NGS) assays that demonstrated PICALM-MLLT10 fusion and a NOTCH1 mutation in the absence of BCL2/IGH fusion. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.002DOI Listing
January 2020

Circ-SLC7A5, a potential prognostic circulating biomarker for detection of ESCC.

Cancer Genet 2020 Jan 5;240:33-39. Epub 2019 Nov 5.

Department of Oncology Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China. Electronic address:

Circular RNAs (circRNAs), resulting from the non-canonical splicing of linear pre-mRNAs, have permanently altered our perspectives toward cancer recently, especially in carcinogenesis and cancer progression. However, the roles of circRNAs in esophageal squamous cell carcinoma (ESCC) remain largely unknown. In the current study, circRNAs expression profiles are screened in ESCC, using plasma samples from 10 ESCC patients, including different TNM stages and 5 normal controls. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.11.001DOI Listing
January 2020
2.417 Impact Factor

Clinicopathologic features and genetic characteristics of the BRCA1/2 mutation in Turkish breast cancer patients.

Cancer Genet 2020 Jan 16;240:23-32. Epub 2019 Oct 16.

Department of General Surgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey.

The aim of this study was to identify the frequency and spectrum of germline BRCA1/2 pathogenic alterations in a cohort of patients with breast carcinoma. In this study, a total of 603 breast cancer subjects from Turkey were screened for BRCA1/BRCA2 mutations using HDA and Sanger sequencing. In the present study, 21 BRCA1 and BRCA2 pathogenic variants were detected in 30 patients and BRCA1/2 mutations were significantly associated with a family history of breast/ovarian cancer. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.004DOI Listing
January 2020

Cytogenetic and molecular genetic characterization of KMT2A-PTD positive acute myeloid leukemia in comparison to KMT2A-Rearranged acute myeloid leukemia.

Cancer Genet 2020 Jan 1;240:15-22. Epub 2019 Nov 1.

MLL Munich Leukemia Laboratory, Munich, Germany. Electronic address:

To define the biological differences in acute myeloid leukaemia (AML) with KMT2A gene involvements and their prognostic impact, we compared 190 de novo AML patients at diagnosis, 95 harbouring KMT2A-rearrangement (KMT2Ar) and 95 KMT2A-PTD by performing cytogenetic and molecular genetic analyses. Both AML subtypes had an unfavourable outcome, particularly in patients > 60 years. Patients with KMT2Ar were younger compared to patients with KMT2A-PTD (mean 52 vs 65 years, p < 0. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.006DOI Listing
January 2020

High-resolution copy number analysis of clear cell endometrial carcinoma.

Cancer Genet 2020 Jan 21;240:5-14. Epub 2019 Oct 21.

Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

Uterine cancer is the 6th leading cause of cancer death amongst American women. Most uterine cancers are endometrial carcinomas (ECs), which are classified into histological subtypes including endometrioid, serous, and clear cell ECs. Somatic copy number alterations (SCNAs) are frequent in serous EC, infrequent in endometrioid ECs, and poorly defined in clear cell ECs. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911624PMC
January 2020
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ATM whole gene deletion in an Italian family with hereditary pancreatic cancer: Challenges to cancer risk prediction associated with an 11q22.3 microdeletion.

Cancer Genet 2020 Jan 12;240:1-4. Epub 2019 Oct 12.

McMaster University, Department of Pathology and Molecular Medicine, 1280 Main Street West, L8S 4L8, Hamilton, ON, Canada; Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, 1200 Main Street West, L8S 4J9, Hamilton, ON, Canada. Electronic address:

Hereditary pancreatic cancer has been attributed to variants of several cancer predisposition genes including ATM. While heterozygous pathogenic variants in the ATM gene are implicated as a cause of familial breast and pancreatic cancers to our knowledge ATM whole gene deletions have not been previously reported. We describe a contiguous gene deletion of the ATM locus in a multi-generation family of Italian descent with a strong family history of pancreatic cancer. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.003DOI Listing
January 2020

Aberrant epigenetic inactivation of RASSF1A and MGMT gene and genetic mutations of KRAS, cKIT and BRAF in Indian testicular germ cell tumours.

Cancer Genet 2020 Feb 13;241:42-50. Epub 2019 Oct 13.

Research and Development Division, SRL Ltd, Plot no. 1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, India. Electronic address:

Testicular germ cell tumor (TGCT) development may involve a series of modification at epigenetic and genetic level which may act synergistically and transform the primordial gonocyte. This study evaluated the frequency and distribution pattern of RASSF1A/MGMT gene methylation and KRAS, BRAF and cKIT gene mutation in Indian TGCT patient, and their correlation with clinicopathological features. Forty-one TGCT tumors were used to investigate hypermethylation of RASSF1A and MGMT gene and mutations of KRAS codon 12/13, BRAF V600E and cKIT exon 17 mutations. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.002DOI Listing
February 2020
2.417 Impact Factor

Progress in quantitative technique of circulating cell free DNA and its role in cancer diagnosis and prognosis.

Cancer Genet 2019 11 11;239:75-84. Epub 2019 Oct 11.

Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Shanghai 200032, China; Department of Surgery, Minhang Hospital, Fudan University, Shanghai 201199, China. Electronic address:

The interest in the potential application value of circulating cell free DNA (ccfDNA) has increased rapidly in recent years, as numerous researchers have demonstrated that the change of its level in the blood is associated with many diseases. Its potential role in cancer management is of particular concern. In comparison with traditional invasive tissue biopsy, quantitative analysis of ccfDNA level for the detection of cancer is advantageous due to the non-invasiveness of blood collection. Read More

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http://dx.doi.org/10.1016/j.cancergen.2019.10.001DOI Listing
November 2019