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Clinical genomics

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https://www.readbyqxmd.com/read/28212573/dynamic-variations-in-epithelial-to-mesenchymal-transition-emt-atm-and-slfn11-govern-response-to-parp-inhibitors-and-cisplatin-in-small-cell-lung-cancer
#1
C Allison Stewart, Pan Tong, Robert J Cardnell, Triparna Sen, Lerong Li, Carl M Gay, Fatemah Masrorpour, You Fan, Rasha O Bara, Ying Feng, Yuanbin Ru, Junya Fujimoto, Samrat T Kundu, Leonard E Post, Karen Yu, Yuqiao Shen, Bonnie S Glisson, Ignatio Wistuba, John V Heymach, Don L Gibbons, Jing Wang, Lauren Averett Byers
Small cell lung cancer (SCLC) is one of the most aggressive forms of cancer, with a 5-year survival <7%. A major barrier to progress is the absence of predictive biomarkers for chemotherapy and novel targeted agents such as PARP inhibitors. Using a high-throughput, integrated proteomic, transcriptomic, and genomic analysis of SCLC patient-derived xenografts (PDXs) and profiled cell lines, we identified biomarkers of drug sensitivity and determined their prevalence in patient tumors. In contrast to breast and ovarian cancer, PARP inhibitor response was not associated with mutations in homologous recombination (HR) genes (e...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212566/genetic-characterization-of-polish-ccrcc-patients-somatic-mutation-analysis-of-pbrm1-bap1-and-kdmc5-genomic-snp-array-analysis-in-tumor-biopsy-and-preliminary-results-of-chromosome-aberrations-analysis-in-plasma-cell-free-dna
#2
Katarzyna Kluzek, Malgorzata I Srebniak, Weronika Majer, Agnieszka Ida, Tomasz Milecki, Kinga Huminska, Robert M van der Helm, Adrian Silesian, Tomasz M Wrzesinski, Jacek Wojciechowicz, Berna H Beverloo, Zbigniew Kwias, Hans A R Bluyssen, Joanna Wesoly
BACKGROUND: Mutation analysis and cytogenetic testing in clear cell renal cell carcinoma (ccRCC) is not yet implemented in a routine diagnostics of ccRCC. MATERIAL AND METHODS: We characterized the chromosomal alterations in 83 ccRCC tumors from Polish patients using whole genome SNP genotyping assay. Moreover, the utility of next generation sequencing of cell free DNA (cfDNA) in patients plasma as a potential tool for non-invasive cytogenetic analysis was tested...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212402/graph-gpa-a-graphical-model-for-prioritizing-gwas-results-and-investigating-pleiotropic-architecture
#3
Dongjun Chung, Hang J Kim, Hongyu Zhao
Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. However, identification of risk variants associated with complex diseases remains challenging as they are often affected by many genetic variants with small or moderate effects. There has been accumulating evidence suggesting that different complex traits share common risk basis, namely pleiotropy...
February 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28212293/targeting-angiogenesis-in-biliary-tract-cancers-an-open-option
#4
REVIEW
Valeria Simone, Oronzo Brunetti, Luigi Lupo, Mario Testini, Eugenio Maiorano, Michele Simone, Vito Longo, Christian Rolfo, Marc Peeters, Aldo Scarpa, Amalia Azzariti, Antonio Russo, Domenico Ribatti, Nicola Silvestris
Biliary tract cancers (BTCs) are characterized by a bad prognosis and the armamentarium of drugs for their treatment is very poor. Although the inflammatory status of biliary tract represents the first step in the cancerogenesis, the microenvironment also plays a key role in the pathogenesis of BTCs, promoting tumor angiogenesis, invasion and metastasis. Several molecules, such as vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF), are involved in the angiogenesis process and their expression on tumor samples has been explored as prognostic marker in both cholangiocarcinoma and gallbladder cancer...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28212290/defining-clinical-response-criteria-and-early-response-criteria-for-precision-oncology-current-state-of-the-art-and-future-perspectives
#5
Vivek Subbiah, Hubert H Chuang, Dhiraj Gambhire, Kalevi Kairemo
In this era of precision oncology, there has been an exponential growth in the armamentarium of genomically targeted therapies and immunotherapies. Evaluating early responses to precision therapy is essential for "go" versus "no go" decisions for these molecularly targeted drugs and agents that arm the immune system. Many different response assessment criteria exist for use in solid tumors and lymphomas. We reviewed the literature using the Medline/PubMed database for keywords "response assessment" and various known response assessment criteria published up to 2016...
February 15, 2017: Diagnostics
https://www.readbyqxmd.com/read/28212287/big-data-analytics-for-genomic-medicine
#6
REVIEW
Karen Y He, Dongliang Ge, Max M He
Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28211990/homozygous-mutation-in-prune1-in-an-oji-cree-male-with-a-complex-neurological-phenotype
#7
Gregory Costain, Andrea Shugar, Pradeep Krishnan, Saadet Mahmutoglu, Suzanne Laughlin, Peter Kannu
The PRUNE1 gene encodes a member of the phosphoesterases (DHH) protein superfamily that is highly expressed in the human fetal brain and involved in the regulation of cell migration. Homozygous or compound heterozygous PRUNE1 mutations were recently identified in five individuals with brain malformations from four families. We present a case of a 2-year-old male with a complex neurological phenotype and abnormalities on brain MRI. Re-annotation of clinical whole-exome sequencing data revealed a homozygous likely pathogenic variant in PRUNE1 (c...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211977/1q21-3-deletion-involving-gatad2b-an-emerging-recurrent-microdeletion-syndrome
#8
Thipwimol Tim-Aroon, Natini Jinawath, Weerin Thammachote, Praweena Sinpitak, Anchalee Limrungsikul, Chaiyos Khongkhatithum, Duangrurdee Wattanasirichaigoon
GATAD2B gene is involved in chromatin modification and transcription activity. Loss-of-function mutations of GATAD2B have recently been defined to cause a recognizable syndrome with intellectual disability (ID). Human TPM3 gene encoding thin filament protein is associated with myopathies. Both genes are located on chromosome 1q21.3. We herein report an infant with feeding difficulty, developmental delay, hypotonia, and dysmorphic features including small palpebral fissures, telecanthus, sparse hair and eyebrow, cup-shaped ears, and clinodactyly...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211800/upregulated-mir-483-5p-expression-as-a-prognostic-biomarker-for-esophageal-squamous-cell-carcinoma
#9
Liying Xue, Jinglong Nan, Li Dong, Cuiying Zhang, Hui Li, Rentura Na, Huijie He, Yadi Wang
BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most common cause of cancer-associated mortality. Uncovering novel molecular biomarkers that can predict ESCC development will improve personalized therapy. OBJECTIVE: The goal of the current study was to investigate the expression pattern of miR-483-5p and determine its prognostic value in ESCC. METHODS: We first analyzed miRNA-seq data obtained from the Cancer Genome Atlas (TCGA) cohort to evaluate the prognostic value of miR-483-5p in ESCC...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28211564/the-genomics-of-inherited-bone-marrow-failure-from-mechanism-to-the-clinic
#10
REVIEW
Talia Wegman-Ostrosky, Sharon A Savage
The inherited bone marrow failure syndromes (IBMFS) typically present with significant cytopenias in at least one haematopoietic cell lineage that may progress to pancytopenia, and are associated with increased risk of cancer. Although the clinical features of the IBMFS are often diagnostic, variable disease penetrance and expressivity may result in diagnostic dilemmas. The discovery of the genetic aetiology of the IBMFS has been greatly facilitated by next-generation sequencing methods. This has advanced understanding of the underlying biology of the IBMFS and been essential in improving clinical management and genetic counselling for affected patients...
February 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28211357/preimplantation-genetic-diagnosis-and-screening-by-array-comparative-genomic-hybridisation-experience-of-more-than-100-cases-in-a-single-centre
#11
J Fc Chow, W Sb Yeung, V Cy Lee, E Yl Lau, P C Ho, E Hy Ng
INTRODUCTION: Preimplantation genetic screening has been proposed to improve the in-vitro fertilisation outcome by screening for aneuploid embryos or blastocysts. This study aimed to report the outcome of 133 cycles of preimplantation genetic diagnosis and screening by array comparative genomic hybridisation. METHODS: This study of case series was conducted in a tertiary assisted reproductive centre in Hong Kong. Patients who underwent preimplantation genetic diagnosis for chromosomal abnormalities or preimplantation genetic screening between 1 April 2012 and 30 June 2015 were included...
February 17, 2017: Hong Kong Medical Journal, Xianggang Yi Xue za Zhi
https://www.readbyqxmd.com/read/28211229/serum-micrornas-as-predictors-for-liver-fibrosis-staging-in-hepatitis-c-virus-associated-chronic-liver-disease-patients
#12
Olfat G Shaker, Mahmoud A Senousy
Accurate staging of liver fibrosis is important for clinical decision making and personalized management. Liver fibrosis is influenced by patients' genomics, including IFNL3 genotype and microRNA expression. However, incorporating microRNAs into fibrosis prediction algorithms has not been investigated. We examined the potential of 8 selected serum microRNAs; miR-122, miR-126, miR-129, miR-199a, miR-155, miR-203a, miR-221, and miR-223 as non-invasive biomarkers to stage liver fibrosis in HCV-associated chronic liver disease (HCV-CLD)...
February 17, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28211009/pneumococcal-predictive-proteins-selected-by-microbial-genomic-approach-are-serotype-cross-reactive-and-bind-to-host-extracellular-matrix-proteins
#13
Ana Paula Corrêa Argondizzo, Cláudio Marcos Rocha-de-Souza, Marta de Almeida Santiago, Ricardo Galler, Joice Neves Reis, Marco Alberto Medeiros
Streptococcus pneumoniae is a colonizer of the human nasopharynx, which accounts for most of the community-acquired pneumonia cases and can cause non-invasive and invasive diseases. Current available vaccines are serotype-specific and the use of recombinant proteins associated with virulence is an alternative to compose vaccines and to overcome these problems. In a previous work, we describe the identification of proteins in S. pneumoniae by reverse vaccinology and the genetic diversity of these proteins in clinical isolates...
February 17, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28210881/comprehensive-genomic-profiling-of-malignant-phyllodes-tumors-of-the-breast
#14
Sahar Nozad, Christine E Sheehan, Laurie M Gay, Julia A Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Alexa B Schrock, Kim M Hirshfield, Nadia Ali, Shridar Ganesan, Siraj M Ali, Vincent A Miller, Philip J Stephens, Jeffrey S Ross, Jon H Chung
PURPOSE: Malignant phyllodes tumors (MPT) are exceptionally rare, and the genomic drivers of these tumors are still being elucidated. We performed comprehensive genomic profiling (CGP) of MPT to identify genomic alterations that will inform approaches to targeted therapy for patients with MPT, including relapsed, refractory, and metastatic disease. METHODS: DNA was extracted from formalin-fixed, paraffin-embedded samples from 24 consecutive patient cases of MPT...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28210865/the-impact-of-melanoma-genetics-on-treatment-response-and-resistance-in-clinical-and-experimental-studies
#15
M Kunz, M Hölzel
Recent attempts to characterize the melanoma mutational landscape using high-throughput sequencing technologies have identified new genes and pathways involved in the molecular pathogenesis of melanoma. Apart from mutated BRAF, NRAS, and KIT, a series of new recurrently mutated candidate genes with impact on signaling pathways have been identified such as NF1, PTEN, IDH1, RAC1, ARID2, and TP53. Under targeted treatment using BRAF and MEK1/2 inhibitors either alone or in combination, a majority of patients experience recurrences, which are due to different genetic mechanisms such as gene amplifications of BRAF or NRAS, MEK1/2 and PI3K mutations...
February 16, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28210784/novel-aids-therapies-based-on-gene-editing
#16
REVIEW
Kamel Khalili, Martyn K White, Jeffrey M Jacobson
HIV/AIDS remains a major public health issue. In 2014, it was estimated that 36.9 million people are living with HIV worldwide, including 2.6 million children. Since the advent of combination antiretroviral therapy (cART), in the 1990s, treatment has been so successful that in many parts of the world, HIV has become a chronic condition in which progression to AIDS has become increasingly rare. However, while people with HIV can expect to live a normal life span with cART, lifelong medication is required and cardiovascular, renal, liver, and neurologic diseases are still possible, which continues to prompt research for a cure for HIV...
February 16, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28210550/evaluating-the-performance-of-national-comprehensive-cancer-network-nccn-breast-and-ovarian-genetic-familial-high-risk-assessment-referral-criteria-for-breast-cancer-women-in-an-asian-surgical-breast-clinic
#17
Geok-Hoon Lim, Eillen Borje, John C Allen
BACKGROUND: Globally, resources for genomic services vary. Current National Comprehensive Cancer Network (NCCN) breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation are useful, but lack specificity for reliably excluding patients with low a priori risk. This may result in patient overload in lesser-equipped genetics clinics. Since we use Manchester and the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk assessment models in our genetics clinic to determine whether genetic testing is warranted, we chose Manchester and BOADICEA as the reference standard to compare how the NCCN breast and ovarian genetic/familial high risk assessment criteria for further genetic risk evaluation performs against these two risk assessment models in referring breast cancer patients for genetic evaluation...
February 2017: Gland Surgery
https://www.readbyqxmd.com/read/28210247/genome-insight-and-comparative-pathogenomic-analysis-of-nesterenkonia-jeotgali-strain-cd08_7-isolated-from-duodenal-mucosa-of-celiac-disease-patient
#18
Atul M Chander, Ramesan G Nair, Gurwinder Kaur, Rakesh Kochhar, Devinder K Dhawan, Sanjay K Bhadada, Shanmugam Mayilraj
Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1(T), Nesterenkonia sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28210080/il23r-single-nucleotide-polymorphisms-could-be-either-beneficial-or-harmful-in-ulcerative-colitis
#19
Sarah Fischer, Erzsébet Kövesdi, Lili Magyari, Veronika Csöngei, Kinga Hadzsiev, Béla Melegh, Péter Hegyi, Patrícia Sarlós
AIM: To investigate the association of seven single nucleotide polymorphisms (SNPs) of the IL23R gene with the clinical picture of ulcerative colitis (UC). METHODS: Genomic DNA samples of 131 patients (66 males, 65 females, mean age 55.4 ± 15.8 years) with Caucasian origin, diagnosed with UC were investigated. The diagnosis of UC was based on the established clinical, endoscopic, radiological, and histopathological guidelines. DNA was extracted from peripheral blood leukocytes by routine salting out method...
January 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28209835/draft-genome-sequence-of-a-colistin-resistant-klebsiella-pneumoniae-clinical-strain-carrying-the-blandm-1-carbapenemase-gene
#20
Zhihong Yao, Yu Feng, Ji Lin, Zhiyong Zong
Klebsiella pneumoniae strain WCHKP1845, recovered from the sputum of a patient with pneumonia, was resistant to colistin and carried the carbapenemase gene blaNDM-1 Here, we report its 5.4-Mb draft genome sequence, comprising 140 contigs with an average 57.33% G+C content. The genome contains 5,118 coding sequences and 88 tRNA genes.
February 16, 2017: Genome Announcements
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