Molecular and Pathologic Characterization of AML with Double Inv(3)(q21q26.2)
Publication date: Available online 16 November 2018Source: Cancer GeneticsAuthor(s): Jennelle C. Hodge, David Bosler, Lauren Rubinstein, Navid Sadri, Shashirekha ShettyAbstractThe inv(3)(q21q26.2) altering a single chromosome 3 homolog is an established myeloid malignancy-associated entity. Comparatively, double inv(3) cases involving both homologs are exceedingly rare with 13 reports across AML, CML and MDS. This scarcity was confirmed by finding only 2 new cases out of 34,898 bone marrows collected during a 55 year period at a large medical center (0.0005%). The double inv(3) was detected by karyotype and confirmed by FI...
Source: Cancer Genetics - November 16, 2018 Category: Cancer & Oncology Source Type: research

Reprint of: Circulating cell-free DNA mutation patterns in early and late stage colon and pancreatic cancer
Publication date: Available online 9 November 2018Source: Cancer GeneticsAuthor(s): Eveline E. Vietsch, Garrett T. Graham, Justine N. McCutcheon, Aamir Javaid, Giuseppe Giaccone, John L. Marshall, Anton WellsteinCancer is a heterogeneous disease harboring diverse subclonal populations that can be discriminated by their DNA mutations. Environmental pressure selects subclones that ultimately drive disease progression and tumor relapse. Circulating cell-free DNA (ccfDNA) can be used to approximate the mutational makeup of cancer lesions and can serve as a marker for monitoring disease progression at the molecular level withou...
Source: Cancer Genetics - November 15, 2018 Category: Cancer & Oncology Source Type: research

Genome-wide isoform-level analysis reveals tumor-specific isoforms for lung adenocarcinoma diagnosis and prognosis: Tumor-specific mRNA isoforms for lung cancer diagnosis and prognosis
Publication date: Available online 13 November 2018Source: Cancer GeneticsAuthor(s): Hu Zhuhong, Bai Zhenyu, Chen Xiangyuan, Xu Tingzhen, Song LibinAbstractLast decades have witnessed the great progress in exploration of tumor transcriptome. However, most researches were restricted in gene-level expression. mRNA isoforms, especially tumor-specific isoforms have not been fully explored in tumor. Here, by analyzing RNA-seq data derived from hundreds of samples in TCGA projects, we comprehensively characterized the expression variations of mRNA isoforms in adenocarcinoma of lung (LUAD), which is one of leading causes of cance...
Source: Cancer Genetics - November 14, 2018 Category: Cancer & Oncology Source Type: research

MiR-708-5p is inversely associated with EWS/FLI1 Ewing sarcoma but does not represent a prognostic predictor
ConclusionsTaken together, our results suggest that despite downregulated in EWS samples, this miRNA might represent a secondary genetic alteration derived from the pleiotropic cellular effects of the abnormal EWS/FLI1 transcription factor that does not affect tumor growth but instead, is related with the promotion of tumor invasion, not being suitable for future therapeutic intervention. (Source: Cancer Genetics)
Source: Cancer Genetics - November 14, 2018 Category: Cancer & Oncology Source Type: research

Novel rearrangements involving the RET gene in papillary thyroid carcinoma
ConclusionsRUFY2-RET and KIAA1468-RET are novel RET/PTC rearrangements. The fusions were previously described in non–small cell lung cancer. The rearrangement results in a fusion of the RET tyrosine kinase to regulatory domains of RUFY2 and KIAA1468. (Source: Cancer Genetics)
Source: Cancer Genetics - November 14, 2018 Category: Cancer & Oncology Source Type: research

Circulating cell-free DNA mutation patterns in early and late stage colon and pancreatic cancer
Publication date: Available online 9 November 2018Source: Cancer GeneticsAuthor(s): Eveline E. Vietsch, Garrett T. Graham, Justine N. McCutcheon, Aamir Javaid, Giuseppe Giaccone, John L. Marshall, Anton WellsteinCancer is a heterogeneous disease harboring diverse subclonal populations that can be discriminated by their DNA mutations. Environmental pressure selects subclones that ultimately drive disease progression and tumor relapse. Circulating cell-free DNA (ccfDNA) can be used to approximate the mutational makeup of cancer lesions and can serve as a marker for monitoring disease progression at the molecular level withou...
Source: Cancer Genetics - November 11, 2018 Category: Cancer & Oncology Source Type: research

Establishing a Human Adrenocortical Carcinoma (ACC)-Specific Gene Mutation Signature
Publication date: Available online 9 November 2018Source: Cancer GeneticsAuthor(s): Chinmay Satish Rahane, Arne Kutzner, Klaus HeeseAbstractAdrenocortical carcinoma (ACC) is a rare and aggressive tumor whose molecular signaling pathways are not fully understood. Using an in-silico clinical data analysis approach we retrieved human gene mutation data from the highly reputed Cancer Genome Atlas (TCGA). ACC-specific gene mutations were correlated with proliferation marker FAM72 expression and Mutsig along with the algorithmic implementation of the 20/20 rule were used to validate their oncogenic potential. The newly identifie...
Source: Cancer Genetics - November 9, 2018 Category: Cancer & Oncology Source Type: research

A new complex rearrangement in infant ALL: t(X;11;17)(p11.2;q23;q12)
We present a case of an infant who developed pro-B acute lymphoblastic leukemia with a rare and complex MLL-translocation. Cytogenetic analysis of bone marrow cells at diagnosis showed a 46,XY,t(X;11)(p11.2;q23)[13]/46,XY[7] karyotype. Fluorescence in situ hybridization analysis using a break apart specific probes showed a split in the MLL gene. Long distance inverse-PCR and next generation sequencing analysis depicted a complex rearrangement t(X;11;17)(p11.2;q23;q12) involving MLL, MLLT6 and the genomic region Xp11.23, 41 bases upstream of the WDR45 gene. WDR45 encodes a beta-propeller protein essential for autophagocytos...
Source: Cancer Genetics - November 7, 2018 Category: Cancer & Oncology Source Type: research

Clinical Impact of MYC Abnormalities in Plasma Cell Myeloma
In this study we evaluated the karyotypes obtained in a single institution to identify recurring cytogenetic abnormalities. We constructed evolutionary pathways to differentiate abnormalities present at the beginning of evolution from those that developed later in evolution. We then estimated genetic progression scores and the clinical impact of the cytogenetic abnormalities on survival. In addition, we also evaluated the clinical significance of MYC related abnormalities (translocations and numerical changes) in disease evolution and on survival. Our results indicate that PCM with MYC related abnormalities in general have...
Source: Cancer Genetics - October 31, 2018 Category: Cancer & Oncology Source Type: research

A new complex rearrangement in infant ALL: t(X;11;17)(p11.2;q23;q12).
We present a case of an infant who developed pro-B acute lymphoblastic leukemia with a rare and complex MLL-translocation. Cytogenetic analysis of bone marrow cells at diagnosis showed a 46,XY,t(X;11)(p11.2;q23)[13]/46,XY[7] karyotype. Fluorescence in situ hybridization analysis using a break apart specific probes showed a split in the MLL gene. Long distance inverse-PCR and next generation sequencing analysis depicted a complex rearrangement t(X;11;17)(p11.2;q23;q12) involving MLL, MLLT6 and the genomic region Xp11.23, 41 bases upstream of the WDR45 gene. WDR45 encodes a beta-propeller protein essential for autophagocytos...
Source: Cancer Genetics - October 29, 2018 Category: Cancer & Oncology Source Type: research

Identification of eight meta-signature miRNAs as potential biomarkers for Oropharyngeal Cancers
ConclusionEight important miRNAs were identified by meta-analysis as well as the corresponding target genes and transcription factors. The potential functions were revealed, which will provide novel insights for the target treatment of OC. (Source: Cancer Genetics)
Source: Cancer Genetics - October 24, 2018 Category: Cancer & Oncology Source Type: research

Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group
Publication date: Available online 6 October 2018Source: Cancer GeneticsAuthor(s): Xinjie Xu, Christine Bryke, Madina Sukhanova, Emma Huxley, D.P. Dash, Amanda Dixon-Mciver, Min Fang, Patricia T. Griepp, Jennelle C. Hodge, Anwar Iqbal, Sally Jeffries, Rashmi Kanagal-Shamanna, Fabiola Quintero-Rivera, Shashi Shetty, Marilyn L. Slovak, Ashwini Yenamandra, Patrick A. Lennon, Gordana RacaAbstractStructural genomic abnormalities, including balanced chromosomal rearrangements, copy number gains and losses and copy-neutral loss-of-heterozygosity (CN-LOH) represent an important category of diagnostic, prognostic and therapeutic ma...
Source: Cancer Genetics - October 20, 2018 Category: Cancer & Oncology Source Type: research

Identification and characterization of a novel nuclear structure containing members of the homologous recombination and DNA damage response pathways
Publication date: Available online 18 October 2018Source: Cancer GeneticsAuthor(s): Megan L Sierant, Scott K DaveyAbstractThe human RAD9A protein is required for successful execution of the G2/M DNA damage checkpoint. Along with RAD1 and HUS1, RAD9A exists in a heterotrimeric ring-shaped complex which is necessary for activation of the CHK1 checkpoint kinase. RAD9A is also required for proper localization of both TopBP1 and the Claspin adaptor protein during the DNA damage response. We have shown large, RAD9A-dense nuclear foci containing several members of the homologous recombination pathway as well as BRCA1 and the DNA ...
Source: Cancer Genetics - October 19, 2018 Category: Cancer & Oncology Source Type: research

Assessing Copy Number Aberrations and Copy-Neutral Loss-of-Heterozygosity Across the Genome as Best Practice: An Evidence-Based Review from the Cancer Genomics Consortium (CGC) Working Group for Chronic Lymphocytic Leukemia
Publication date: Available online 16 October 2018Source: Cancer GeneticsAuthor(s): Kathy Chun, Gail D. Wenger, Alka Chaubey, D.P. Dash, Rashmi Kanagal-Shamanna, Sibel Kanturci, Ravindra Kolhe, Daniel L. Van Dyke, Lu Wang, Daynna J. Wolff, Patricia M. MironAbstractThe prognostic role of cytogenetic analysis is well-established in B-cell chronic lymphocytic leukemia (CLL). Approximately 80% of patients have a cytogenetic aberration. Interphase FISH panels have been the gold standard for cytogenetic evaluation, but conventional cytogenetics allows detection of additional abnormalities, including translocations, complex karyo...
Source: Cancer Genetics - October 16, 2018 Category: Cancer & Oncology Source Type: research

An expression quantitative trait locus variant for LKB1 gene predicts the clinical outcomes of chemotherapy in patients with non-small cell lung cancer
ConclusionsOur results suggest that rs10414193A>G may be useful for the prediction of clinical outcomes of chemotherapy in advanced NSCLC. (Source: Cancer Genetics)
Source: Cancer Genetics - October 16, 2018 Category: Cancer & Oncology Source Type: research

Assessing Copy Number Aberrations and Copy Neutral Loss of Heterozygosity Across the Genome as Best Practice: An Evidence Based Review of Clinical Utility from the Cancer Genomics Consortium (CGC) Working Group for Myelodysplastic Syndrome, Myelodysplastic/Myeloproliferative and Myeloproliferative Neoplasms
Publication date: Available online 10 October 2018Source: Cancer GeneticsAuthor(s): Rashmi Kanagal-Shamanna, Jennelle C. Hodge, Tracy Tucker, Shashi Shetty, Ashwini Yenamandra, Amanda Dixon-McIver, Christine Bryke, Emma Huxley, Patrick A. Lennon, Gordana Raca, Xinjie Xu, Sally Jeffries, Fabiola Quintero-Rivera, Patricia T. Greipp, Marilyn L. Slovak, M. Anwar Iqbal, Min FangAbstractMultiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines...
Source: Cancer Genetics - October 11, 2018 Category: Cancer & Oncology Source Type: research

The role of E-cadherin and Runx3 in Helicobacter Pylori – Associated gastric carcinoma is achieved through regulating P21waf and P27 expression
Publication date: December 2018Source: Cancer Genetics, Volumes 228–229Author(s): Abeer A. Bahnassy, Thanaa El-A Helal, Ibrahim MH. El-Ghazawy, Gamal F. Samaan, Moataz M. Galal el-Din, Mona S. Abdellateif, Eman Desouky, Abdel-Rahman N. ZekriAbstractBackgroundWe assessed the role of E-cadherin (CDH1), runt-related transcription factor 3, p21waf and p27 promoter methylation (PM) and protein expression in Helicobacter pylori (HP)-associated gastric carcinomas (GCs) and adjacent non-neoplastic tissues (ANNTs).Patients and methods192 cases were assessed for PM and protein expression of CDH1, RUNX3, p21waf and p27 by methy...
Source: Cancer Genetics - October 9, 2018 Category: Cancer & Oncology Source Type: research

BAP1 gene mutations in Egyptian patients with advanced sporadic malignant Pleural mesothelioma (MPM): Relation with clinical outcomes and survival
Publication date: Available online 8 October 2018Source: Cancer GeneticsAuthor(s): Raghda Shehab El-Din, Abeer A Bahnasy, Nagwa Ali Sabri, Chahd.A. Abdel-Rahman, Ahmed El BastawisyABSTRACTBackgroundMalignant Pleural Mesothelioma (MPM) is a lethal cancer with few therapeutic options. Patients with MPM have a poor prognosis, with estimated 1 year median survival and currently no treatment is curative. The BRCA associated protein 1 (BAP1) has the highest prevalence of protein-altering mutations identified in MPM.AimsAssessment of the frequency and pattern of BAP1 gene mutations in Egyptian patients with advanced sporadic MPM ...
Source: Cancer Genetics - October 8, 2018 Category: Cancer & Oncology Source Type: research

Assessing Copy Number Aberrations and Copy-Neutral Loss-of-Heterozygosity Across the Genome as Best Practice in Diagnostic Evaluation of Acute Myeloid Leukemia: An Evidence-Based Review from the Cancer Genomics Consortium (CGC) Myeloid Neoplasms Working Group
Publication date: Available online 6 October 2018Source: Cancer GeneticsAuthor(s): Xinjie Xu, Christine Bryke, Madina Sukhanova, Emma Huxley, D P Dash, Amanda Dixon-Mciver, Min Fang, Patricia T. Griepp, Jennelle C. Hodge, Anwar Iqbal, Sally Jeffries, Rashmi Kanagal-Shamanna, Fabiola Quintero-Rivera, Shashi Shetty, Marilyn L Slovak, Ashwini Yenamandra, Patrick A Lennon, Gordana RacaAbstractStructural genomic abnormalities, including balanced chromosomal rearrangements, copy number gains and losses and copy-neutral loss-of-heterozygosity (CN-LOH) represent an important category of diagnostic, prognostic and therapeutic marke...
Source: Cancer Genetics - October 7, 2018 Category: Cancer & Oncology Source Type: research

Screening and characterization of BRCA2 c.156_157insAlu in Brazil: results from 1380 individuals from the South and Southeast.
In conclusion, the present study reports a low albeit relevant frequency of the Portuguese BRCA2 founder mutation c.156_157insAlu in Brazilian patients at-risk for HBOC Brazilian population. (Source: Cancer Genetics)
Source: Cancer Genetics - October 6, 2018 Category: Cancer & Oncology Source Type: research

Assessing Genome-wide Copy Number Aberrations and Copy-Neutral Loss-of-Heterozygosity as Best Practice: An Evidence-Based Review from the Cancer Genomics Consortium Working Group for Plasma Cell Disorders
ConclusionWe present an overview of current practices in plasma cell neoplasm testing as well as an algorithm for integrated FISH and CMA testing to guide treatment of this disease. (Source: Cancer Genetics)
Source: Cancer Genetics - October 5, 2018 Category: Cancer & Oncology Source Type: research

Myeloproliferative neoplasm with ABL1/ETV6 rearrangement mimics chronic myeloid leukemia and responds to tyrosine kinase inhibitors
We report a 47-year-old man who presented with MPN with clinicopathologic features resembling chronic myeloid leukemia, but there was no evidence of t(9;22)(p34.1;q11.2) or BCR-ABL1 fusion. Conventional cytogenetics and fluorescence in situ hybridization analysis showed ins(12;9)(p13;q34q34) that led to ETV6-ABL1 fusion. The patient responded well to tyrosine kinase inhibitor therapy and achieved remission for 7 years. (Source: Cancer Genetics)
Source: Cancer Genetics - October 4, 2018 Category: Cancer & Oncology Source Type: research

The Role of E-Cadherin and Runx3 in Helicobacter Pylori- Associated Gastric Carcinoma Is Achieved Through Regulating P21waf and P27 Expression
Publication date: Available online 19 September 2018Source: Cancer GeneticsAuthor(s): Abeer A. Bahnassy, Thanaa El-A Helal, Ibrahim MH. El-Ghazawy, Gamal F. Samaan, Moataz M. Galal el-Din, Mona S. Abdellateif, Eman Desouky, Abdel-Rahman N. ZekriABSTRACTBackground: We assessed the role of E-cadherin (CDH1), runt-related transcription factor 3, p21waf and p27 promoter methylation (PM) and protein expression in Helicobacter pylori (HP)-associated gastric carcinomas (GCs) and adjacent non-neoplastic tissues (ANNTs).Patients and methods: 192 cases were assessed for PM and protein expression of CDH1, RUNX3, p21waf and p27 by met...
Source: Cancer Genetics - September 21, 2018 Category: Cancer & Oncology Source Type: research

Validation of a Next-Generation Sequencing Oncology Panel Optimized for Low Input DNA
Publication date: Available online 19 September 2018Source: Cancer GeneticsAuthor(s): Robyn T. Sussman, Sydney Shaffer, Elizabeth M. Azzato, Daniel DeSloover, Midhat S. Farooqi, Anders Meyer, David B. Lieberman, Ashkan Bigdeli, Carmela Paolillo, Karthik Ganapathy, Shrey Sukhadia, Jason N. Rosenbaum, Robert D. Daber, Jennifer J.D. MorrissetteAbstractOne caveat of next-generation sequencing (NGS)-based clinical oncology testing is the high amount of input DNA required. We sought to develop a focused NGS panel that could capture hotspot regions in relevant genes requiring 0.5-10 ng input DNA. The resulting Penn Precision Pane...
Source: Cancer Genetics - September 21, 2018 Category: Cancer & Oncology Source Type: research

Primary extranodal diffuse large B-cell lymphomas: many sites, many entities? Clinico-pathological, immunohistochemical and cytogenetic study of 106 cases.
In conclusion, our data suggest that immunophenotypic, genetic and survival characteristics of EN-DLBCL are related to the specific primary site of the disease. (Source: Cancer Genetics)
Source: Cancer Genetics - August 29, 2018 Category: Cancer & Oncology Source Type: research

Evaluation of commercial kits for purification of circulating free DNA
This study represents the first to use a comprehensive size distribution of spiked-in DNA fragments to evaluate commercial cfDNA kits. The commonly used spin column-based Qiagen QIAamp circulating nucleic acid kit was found to be the most consistent performing kit across the two evaluation assays employed. The Qiagen QIAamp minElute ccfDNA mini kit represented the best performing magnetic bead-based kit and provides an alternative based on lower cost/sample with a simpler workflow than spin column-based kits. (Source: Cancer Genetics)
Source: Cancer Genetics - August 29, 2018 Category: Cancer & Oncology Source Type: research

Identification of key genes and construction of microRNA-mRNA regulatory networks in non-small cell lung cancer
In conclusion, a set of differentially expressed microRNAs in NSCLC was identified and the CCND1 gene was determined as the potential prognostic biomarkers for NSCLC, providing useful information for discovery of future therapeutic targets and candidates in the clinical management of NSCLC. (Source: Cancer Genetics)
Source: Cancer Genetics - August 27, 2018 Category: Cancer & Oncology Source Type: research

Myeloproliferative Neoplasm with ABL1/ETV6 Rearrangement Mimics Chronic Myeloid Leukemia and Responses to Tyrosine Kinase Inhibitors
We report a 47-year-old man who presented with MPN with clinicopathologic features resembling chronic myeloid leukemia, but there was no evidence of t(9;22)(p34.1;q11.2) or BCR-ABL1 fusion. Conventional cytogenetics and fluorescence in situ hybridization analysis showed ins(12;9)(p13;q34q34) that led to ETV6-ABL1 fusion. The patient responded well to tyrosine kinase inhibitor therapy and achieved remission for 7 years. (Source: Cancer Genetics)
Source: Cancer Genetics - August 27, 2018 Category: Cancer & Oncology Source Type: research

Primary aneurysmal bone cyst with a novel SPARC-USP6 translocation identified by next-generation sequencing
Publication date: Available online 20 July 2018Source: Cancer GeneticsAuthor(s): Daja Šekoranja, Emanuela Bostjančič, Vladka Salapura, Blaž Mavčič, Jože PižemAbstractAneurysmal bone cyst (ABC) is a benign but locally aggressive, mostly pediatric neoplasm, with characteristic USP6 gene rearrangement that distinguishes it from a secondary ABC and other primary bone tumors. With the advent of next-generation sequencing (NGS) technology, several hitherto unknown USP6 fusion partners have been identified in ABC. Accordingly, we present a case of an 18-year-old male with a solid sub-periosteal primary ABC in the di...
Source: Cancer Genetics - July 20, 2018 Category: Cancer & Oncology Source Type: research

A rare case of Hepatosplenic γδ T-cell lymphoma expressing CD19 with ring chromosome 7 and trisomy 8
We describe the clinical, immunophenotypic and cytogenetic analysis in a 24-year-old woman. We present an unusual case of TCRγδ positive T-cell lymphoma with aberrant expression of CD19, which is a B-cell lymphoid marker, with amplification of 7q region and subsequent formation of ring chromosome 7 and trisomy 8. This is the second case of HSTL, positive for CD19 and first case presenting with ring chromosome 7 and trisomy 8 in a CD19 positive HSTL which is a rare finding in T-cell lymphoma and needs to be explored further. (Source: Cancer Genetics)
Source: Cancer Genetics - July 20, 2018 Category: Cancer & Oncology Source Type: research

Clinical utility of emerging liquid biomarkers in advanced prostate cancer
Publication date: Available online 25 August 2017Source: Cancer GeneticsAuthor(s): Gillian Vandekerkhove, Kim N. Chi, Alexander W. WyattThe 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. In this context, minimally-invasive blood-based “liquid” biopsies are attractive...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker
Publication date: Available online 24 February 2018Source: Cancer GeneticsAuthor(s): Mersedeh RohanizadeganAbstractDespite all the advances in diagnosis and treatment of breast cancer, a large number of patients suffer from late diagnosis or recurrence of their disease. Current available imaging modalities do not reveal micrometastasis and tumor biopsy is an invasive method to detect early stage or recurrent cancer, signifying the need for an inexpensive, non-invasive diagnostic modality. Cell-free tumor DNA (ctDNA) has been tried for early detection and targeted therapy of breast cancer, but its diagnostic and prognostic ...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Comparison of 4 commercial kits for the extraction of circulating DNA from plasma
We describe the evaluation of 4 commercial DNA purification kits—QIAamp Circulating Nucleic Acids kit, QIAamp DNA Blood Mini kit, QIAamp Ultrasens Virus kit and the QIASymphony DSP Virus kit—for the extraction of high and low molecular weight DNA from blood plasma. Using qPCR to quantitate endogenous Alu sequences, as well as spiked exogenous high and low molecular weight zebrafish DNA, we found that the Circulating Nucleic Acids kit and the DSP kit were both efficient at purifying DNA from plasma regardless of fragment size, whereas the DNA Blood Mini kit was only able to effectively extract high molecular wei...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Circulating cell-free DNA for non-invasive cancer management
Publication date: Available online 11 March 2018Source: Cancer GeneticsAuthor(s): Caitlin M. Stewart, Dana W.Y. TsuiCell-free DNA (cfDNA) was first identified in human plasma in 1948 and is thought to be released from cells throughout the body into the circulatory system. In cancer, a portion of the cfDNA originates from tumour cells, referred to as circulating-tumour DNA (ctDNA), and can contain mutations corresponding to the patient's tumour, for instance specific TP53 alleles. Profiling of cfDNA has recently become an area of increasing clinical relevance in oncology, in particular due to advances in the sensitivity of ...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Identification of gene-specific DNA methylation signature for Colorectal Cancer
ConclusionsWith the six gene-specific DNA methylation signatures, patients in the training set were divided into low-risk and high- risk groups. What's more, gene-specific DNA methylation target genes were highly associated with protein phosphorylation, which indicated that further research on phosphorylation of target gene-coding protein might provide new sight on the treatment of CC. (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Corrigendum to “Potential circulating miRNA signature for early detection of NSCLC” [Cancer Genetics 216–217 (2017) 150–158]
Publication date: Available online 15 June 2018Source: Cancer GeneticsAuthor(s): Ayda Arab, Morteza Karimipoor, Shiva Irani, Arda Kiani, Sirous Zeinali, Elham Tafsiri, Kambiz Sheikhy (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Corrigendum to ``Survey of gynecological carcinosarcomas in families with breast and ovarian cancer predisposition'' [Cancer Genet. 221(2018) 38–45]
Publication date: Available online 29 June 2018Source: Cancer GeneticsAuthor(s): C.B. Ripamonti, S. Manoukian, B. Peissel, J. Azzollini, M.L. Carcangiu, P. Radice (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Editorial Board
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Non-invasive early detection of malignant pulmonary nodules by FISH-based sputum test
ConclusionsIn a cohort of patients with highly suspicious lung nodules, the LCD test is a non-invasive option with good sensitivity and a high positive predictive value. A positive LCD test reinforces the need to aggressively pursue a definitive diagnosis of suspicious nodules. (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Clonal neutrophil infiltrates in concurrent Sweet's syndrome and acute myeloid leukemia: A case report and literature review
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Wenbin Mo, Xiaoxue Wang, Yue Wang, Yan Li, Rui ZhangAbstractSweet's syndrome (SS), also known as acute febrile neutrophilic dermatosis is often associated with a hematological malignancy, especially acute myeloid leukemia (AML) and myeloid dysplasia syndrome. Histopathologically, SS is characterized by diffuse infiltrates in the upper dermis, predominantly consisting of mature neutrophils. The origin of neutrophils invading the skin remains unknown. Herein, we report a patient with concurrent acute monoblastic leukemia and SS who initial...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Challenges in next generation sequencing analysis of somatic mutations in transplant patients
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Hui Chen, Rajyalakshmi Luthra, Keyur P Patel, Mark Routbort, Asif Rashid, Sinchita Roy-Chowdhuri, Alexander Lazar, Russell Broaddus, Jawad Manekia, Rajesh R Singh, Anna YemelyanovaAbstractAnalysis of somatic mutations in solid tumors and hematologic malignancies using targeted next generation sequencing (NGS)-based assays has become part of routine oncology practice as well as clinical trials. The use of paired tumor-normal DNA samples increases confidence of somatic calls. NGS assays that utilize unique patient identifiers (SNP IDs) all...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

Differentially expressed LncRNAs as potential prognostic biomarkers for glioblastoma
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Mei Shao, Wenyun Liu, Yu WangAbstractGlioblastoma (GBM) is the most common and aggressive brain tumor with the poor clinical outcome. LncRNAs (Long non-coding RNAs) play an important role in the occurrence and development of glioblastoma. We aimed to explore the role that lncRNAs play in regulating glioblastoma and the pathways they are enriched in. The expression data of a total of 516 GBM samples were downloaded from TCGA (The Cancer Genome Atlas). We identified the differentially expressed lncRNAs between cancer and normal tissues a...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

SH2B3 aberrations enriched in iAMP21 B lymphoblastic leukemia
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): LB Baughn, MM Meredith, L Oseth, TA Smolarek, B HirschAbstractAcute lymphoblastic leukemia (ALL) represents the most common childhood malignancy. Although survival for pediatric B-ALL has approached 90%, variability in outcome among and within cytogenetically defined subgroups persists. While G-banding and fluorescence in situ hybridization (FISH) have been used to characterize leukemic clones, there is added value of chromosomal microarray and next generation sequencing in screening genome-wide for copy number aberrations, copy neutral ...
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

1. Clinical utility of mate pair sequencing to detect diagnostic and prognostic chromosomal rearrangements and copy number changes in patients with acute myeloid leukemia
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Linda Baughn, Stephanie Smoley, Beth Pitel, George Vasmatzis, Sarah Johnson, James Smadbeck, Jess Peterson, Daniel Van Dyke, Rhett Ketterling, Robert Jenkins, Nicole Hoppman, Hutton Kearney, Patricia Greipp (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

2. Distinct genetic signature of a high risk AML subgroup with ERG amplification
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Iya Znoyko, Cynthia Schandl, Daynna Wolff (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

3. Building risk scores for evaluating survival after hematopoietic cell transplantation for AML using pre-transplant cytogenetic data
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Yi Li, Ted Gooley, Chris Davis, Emily Silgard, Mohamed L. Sorror, Masumi Ueda, Jennifer E. Nyland, Lue Zhao, Min Fang (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

4. Coordinating variant interpretation knowledgebases improves clinical interpretation of genomic variants in cancers
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Alex Wagner, Brian Walsh, Dmitriy Sonkin, Rodrigo Dienstmann, Xuan Shirley Li, Jacques S. Beckmann, Georgia Mayfield, David Tamborero, Nuria Lopez-Bigas, Jeremy Goecks, Adam Margolin, Malachi Griffith, Obi Griffith (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

5. Progress and future of the compendium of Cancer Genome Aberrations (CCGA)
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Jennelle C. Hodge, Linda Cooley, Hui Chen, Fei Yang, Obi Griffith, Linda Baughn, Scott Newman, Daynna J. Wolff (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

6. Human ring chromosome registry: Developing an interactive web resource for constitutional and cancer cytogenomic diagnosis
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Peining Li, Autumn DiAdamo, Brittany Grommisch, Hongyan Chai, Qiping Hu (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research

7. Data and knowledge sharing to improve patient care: The VICC and MCG experience
Publication date: October 2018Source: Cancer Genetics, Volumes 226–227Author(s): Ingrid Anderson, Neha Jain, Michele LeNoue-Newton, Christine Micheel, Mia Levy (Source: Cancer Genetics)
Source: Cancer Genetics - July 10, 2018 Category: Cancer & Oncology Source Type: research