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BMC Medical Genomics

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https://www.readbyqxmd.com/read/28716121/identification-of-trunk-mutations-in-gastric-carcinoma-a-case-study
#1
Zhan Zhou, Shanshan Wu, Jun Lai, Yuan Shi, Chixiao Qiu, Zhe Chen, Yufeng Wang, Xun Gu, Jie Zhou, Shuqing Chen
BACKGROUND: Intratumor heterogeneity (ITH) poses an urgent challenge for cancer precision medicine because it can cause drug resistance against cancer target therapy and immunotherapy. The search for trunk mutations that are present in all cancer cells is therefore critical for each patient. CASE PRESENTATION: In this study, we aimed to evaluate the efficiency of multiregional sequencing for the identification of trunk mutations present in all regions of a tumor as a case study...
July 17, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28629370/pharmacogenetic-testing-through-the-direct-to-consumer-genetic-testing-company-23andme
#2
Mengfei Lu, Cathryn M Lewis, Matthew Traylor
BACKGROUND: Rapid advances in scientific research have led to an increase in public awareness of genetic testing and pharmacogenetics. Direct-to-consumer (DTC) genetic testing companies, such as 23andMe, allow consumers to access their genetic information directly through an online service without the involvement of healthcare professionals. Here, we evaluate the clinical relevance of pharmacogenetic tests reported by 23andMe in their UK tests. METHODS: The research papers listed under each 23andMe report were evaluated, extracting information on effect size, sample size and ethnicity...
June 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28592245/in-silico-identification-of-potential-key-regulatory-factors-in-smoking-induced-lung-cancer
#3
Salem A El-Aarag, Amal Mahmoud, Medhat H Hashem, Hatem Abd Elkader, Alaa E Hemeida, Mahmoud ElHefnawi
BACKGROUND: Lung cancer is a leading cause of cancer-related death worldwide and is the most commonly diagnosed cancer. Like other cancers, it is a complex and highly heterogeneous disease involving multiple signaling pathways. Identifying potential therapeutic targets is critical for the development of effective treatment strategies. METHODS: We used a systems biology approach to identify potential key regulatory factors in smoking-induced lung cancer. We first identified genes that were differentially expressed between smokers with normal lungs and those with cancerous lungs, then integrated these differentially expressed genes (DEGs) with data from a protein-protein interaction database to build a network model with functional modules for pathway analysis...
June 7, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28549443/quantitative-analysis-of-cryptic-splicing-associated-with-tdp-43-depletion
#4
Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M Isaacs, Vincent Plagnol
BACKGROUND: Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown...
May 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28545463/cve-an-r-package-for-interactive-variant-prioritisation-in-precision-oncology
#5
Andreas Mock, Suzanne Murphy, James Morris, Francesco Marass, Nitzan Rosenfeld, Charlie Massie
BACKGROUND: An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browser interface. RESULTS: Leveraging Oncotator and the Drug Gene Interaction Database, CVE offers exploration of variants within single or multiple tumour exomes to identify drivers, resistance mechanisms and to assess druggability. We present example applications including the analysis of an individual patient and a cohort-wide study, and provide a first extension of CVE by adding a tumour-specific co-expression network...
May 25, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589862/taking-promoters-out-of-enhancers-in-sequence-based-predictions-of-tissue-specific-mammalian-enhancers
#6
Julia Herman-Izycka, Michal Wlasnowolski, Bartek Wilczynski
BACKGROUND: Many genetic diseases are caused by mutations in non-coding regions of the genome. These mutations are frequently found in enhancer sequences, causing disruption to the regulatory program of the cell. Enhancers are short regulatory sequences in the non-coding part of the genome that are essential for the proper regulation of transcription. While the experimental methods for identification of such sequences are improving every year, our understanding of the rules behind the enhancer activity has not progressed much in the last decade...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589861/evolution-of-translational-bioinformatics-lessons-learned-from-tbc-2016
#7
Kye Hwa Lee, Ju Han Kim
No abstract text is available yet for this article.
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589859/integrative-information-theoretic-network-analysis-for-genome-wide-association-study-of-aspirin-exacerbated-respiratory-disease-in-korean-population
#8
Sehee Wang, Hyun-Hwan Jeong, Dokyoon Kim, Kyubum Wee, Hae-Sim Park, Seung-Hyun Kim, Kyung-Ah Sohn
BACKGROUND: Aspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589857/identification-of-epigenetic-interactions-between-mirna-and-dna-methylation-associated-with-gene-expression-as-potential-prognostic-markers-in-bladder-cancer
#9
Manu Shivakumar, Younghee Lee, Lisa Bang, Tullika Garg, Kyung-Ah Sohn, Dokyoon Kim
BACKGROUND: One of the fundamental challenges in cancer is to detect the regulators of gene expression changes during cancer progression. Through transcriptional silencing of critical cancer-related genes, epigenetic change such as DNA methylation plays a crucial role in cancer. In addition, miRNA, another major component of epigenome, is also a regulator at the post-transcriptional levels that modulate transcriptome changes. However, a mechanistic role of synergistic interactions between DNA methylation and miRNA as epigenetic regulators on transcriptomic changes and its association with clinical outcomes such as survival have remained largely unexplored in cancer...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589856/association-analysis-of-rare-variants-near-the-apoe-region-with-csf-and-neuroimaging-biomarkers-of-alzheimer-s-disease
#10
Kwangsik Nho, Sungeun Kim, Emrin Horgusluoglu, Shannon L Risacher, Li Shen, Dokyoon Kim, Seunggeun Lee, Tatiana Foroud, Leslie M Shaw, John Q Trojanowski, Paul S Aisen, Ronald C Petersen, Clifford R Jack, Michael W Weiner, Robert C Green, Arthur W Toga, Andrew J Saykin
BACKGROUND: The APOE ε4 allele is the most significant common genetic risk factor for late-onset Alzheimer's disease (LOAD). The region surrounding APOE on chromosome 19 has also shown consistent association with LOAD. However, no common variants in the region remain significant after adjusting for APOE genotype. We report a rare variant association analysis of genes in the vicinity of APOE with cerebrospinal fluid (CSF) and neuroimaging biomarkers of LOAD. METHODS: Whole genome sequencing (WGS) was performed on 817 blood DNA samples from the Alzheimer's Disease Neuroimaging Initiative (ADNI)...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589855/identifying-subtype-specific-associations-between-gene-expression-and-dna-methylation-profiles-in-breast-cancer
#11
Garam Lee, Lisa Bang, So Yeon Kim, Dokyoon Kim, Kyung-Ah Sohn
BACKGROUND: Breast cancer is a complex disease in which different genomic patterns exists depending on different subtypes. Recent researches present that multiple subtypes of breast cancer occur at different rates, and play a crucial role in planning treatment. To better understand underlying biological mechanisms on breast cancer subtypes, investigating the specific gene regulatory system via different subtypes is desirable. METHODS: Gene expression, as an intermediate phenotype, is estimated based on methylation profiles to identify the impact of epigenomic features on transcriptomic changes in breast cancer...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589854/a-disease-similarity-matrix-based-on-the-uniqueness-of-shared-genes
#12
Matthew B Carson, Cong Liu, Yao Lu, Caiyan Jia, Hui Lu
BACKGROUND: Complex diseases involve many genes, and these genes are often associated with several different illnesses. Disease similarity measurement can be based on shared genotype or phenotype. Quantifying relationships between genes can reveal previously unknown connections and form a reference base for therapy development and drug repurposing. METHODS: Here we introduce a method to measure disease similarity that incorporates the uniqueness of shared genes...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28589853/n-of-1-pathways-mixenrich-advancing-precision-medicine-via-single-subject-analysis-in-discovering-dynamic-changes-of-transcriptomes
#13
Qike Li, A Grant Schissler, Vincent Gardeux, Ikbel Achour, Colleen Kenost, Joanne Berghout, Haiquan Li, Hao Helen Zhang, Yves A Lussier
BACKGROUND: Transcriptome analytic tools are commonly used across patient cohorts to develop drugs and predict clinical outcomes. However, as precision medicine pursues more accurate and individualized treatment decisions, these methods are not designed to address single-patient transcriptome analyses. We previously developed and validated the N-of-1-pathways framework using two methods, Wilcoxon and Mahalanobis Distance (MD), for personal transcriptome analysis derived from a pair of samples of a single patient...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28535813/erratum-to-mirna-profiling-of-whole-trabecular-bone-identification-of-osteoporosis-related-changes-in-mirnas-in-human-hip-bones
#14
Laura De-Ugarte, Guy Yoskovitz, Susana Balcells, Robert Güerri-Fernández, Santos Martinez-Diaz, Leonardo Mellibovsky, Roser Urreizti, Xavier Nogués, Daniel Grinberg, Natalia García-Giralt, Adolfo Díez-Pérez
No abstract text is available yet for this article.
May 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28532511/challenges-and-strategies-for-implementing-genomic-services-in-diverse-settings-experiences-from-the-implementing-genomics-in-practice-ignite-network
#15
Nina R Sperber, Janet S Carpenter, Larisa H Cavallari, Laura J Damschroder, Rhonda M Cooper-DeHoff, Joshua C Denny, Geoffrey S Ginsburg, Yue Guan, Carol R Horowitz, Kenneth D Levy, Mia A Levy, Ebony B Madden, Michael E Matheny, Toni I Pollin, Victoria M Pratt, Marc Rosenman, Corrine I Voils, Kristen W Weitzel, Russell A Wilke, R Ryanne Wu, Lori A Orlando
BACKGROUND: To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges. METHODS: We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies...
May 22, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28526081/comprehensive-detection-of-germline-variants-by-msk-impact-a-clinical-diagnostic-platform-for-solid-tumor-molecular-oncology-and-concurrent-cancer-predisposition-testing
#16
Donavan T Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E Robson, Kenneth Offit, Michael F Berger, Khedoudja Nafa, Marc Ladanyi, Liying Zhang
BACKGROUND: The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families. METHODS: Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes...
May 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28464943/diet-and-exercise-changes-following-direct-to-consumer-personal-genomic-testing
#17
Daiva Elena Nielsen, Deanna Alexis Carere, Catharine Wang, J Scott Roberts, Robert C Green
BACKGROUND: The impacts of direct-to-consumer personal genomic testing (PGT) on health behaviors such as diet and exercise are poorly understood. Our investigation aimed to evaluate diet and exercise changes following PGT and to determine if changes were associated with genetic test results obtained from PGT. METHODS: Customers of 23andMe and Pathway Genomics completed a web-based survey prior to receiving PGT results (baseline) and 6 months post-results. Fruit and vegetable intake (servings/day), and light, vigorous and strength exercise frequency (days/week) were assessed...
May 2, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28464817/post-operative-atrial-fibrillation-examined-using-whole-genome-rna-sequencing-in-human-left-atrial-tissue
#18
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jochen D Muehlschlegel, Simon C Body
BACKGROUND: Both ambulatory atrial fibrillation (AF) and post-operative AF (poAF) are associated with substantial morbidity and mortality. Analyzing the tissue-specific gene expression in the left atrium (LA) can identify novel genes associated with AF and further the understanding of the mechanism by which previously identified genetic variants associated with AF mediate their effects. METHODS: LA free wall samples were obtained intraoperatively immediately prior to mitral valve surgery in 62 Caucasian individuals...
May 2, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28427387/serum-microrna-profile-in-patients-with-colon-adenomas-or-cancer
#19
Yajie Zhang, Min Li, Yijiang Ding, Zhimin Fan, Jinchun Zhang, Hongying Zhang, Bin Jiang, Yong Zhu
BACKGROUND: Colon cancer, one of the most common causes of cancer-related deaths, arises from adenomatous polyps. In these years, circulating microRNAs (miRNAs) have attracted increasing attention as novel biomarkers for colon cancers. The dysregulated circulating miRNAs in patients with colon adenomas has not been well-understood. METHODS: Here, we aimed to identify miRNA profile in the serum of patients with colon adenomas or colon cancer by using microarray. Then we validated eight differentially expressed miRNAs (DEMs) by qRT-PCR and predicted their targets...
April 20, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28416017/patient-complexity-and-genotype-phenotype-correlations-in-biliary-atresia-a-cross-sectional-analysis
#20
Guo Cheng, Patrick Ho-Yu Chung, Edwin Kin-Wai Chan, Man-Ting So, Pak-Chung Sham, Stacey S Cherny, Paul Kwong-Hang Tam, Maria-Mercè Garcia-Barceló
BACKGROUND: Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering the BA phenotypic variance is a priority in clinics and can be achieved by the integrative analysis of genotype and phenotype. We aim to explore the BA phenotypic features and to delineate the source of its variance. METHODS: The study is a cross-sectional observational study collating with case/control association analysis...
April 17, 2017: BMC Medical Genomics
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