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BMC Medical Genomics

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https://www.readbyqxmd.com/read/28927418/a-systematic-review-and-integrative-approach-to-decode-the-common-molecular-link-between-levodopa-response-and-parkinson-s-disease
#1
Debleena Guin, Manish Kumar Mishra, Puneet Talwar, Chitra Rawat, Suman S Kushwaha, Shrikant Kukreti, Ritushree Kukreti
BACKGROUND: PD is a progressive neurodegenerative disorder commonly treated by levodopa. The findings from genetic studies on adverse effects (ADRs) and levodopa efficacy are mostly inconclusive. Here, we aim to identify predictive genetic biomarkers for levodopa response (LR) and determine common molecular link with disease susceptibility. A systematic review for LR was conducted for ADR, and drug efficacy, independently. All included articles were assessed for methodological quality on 14 parameters...
September 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28874147/assessing-the-activity-of-nonsense-mediated-mrna-decay-in-lung-cancer
#2
Meng Wang, Peiwei Zhang, Yufei Zhu, Xiangyin Kong, Zhenguo Zhang, Landian Hu
BACKGROUND: Inhibition of nonsense-mediated mRNA decay (NMD) in tumor cells can suppress tumor growth through expressing new antigens whose mRNAs otherwise are degraded by NMD. Thus NMD inhibition is a promising approach for developing cancer therapies. Apparently, the success of this approach relies on the basal NMD activity in cancer cells. If NMD is already strongly inhibited in tumors, the approach would not work. Therefore, it is crucial to assess NMD activity in cancers to forecast the efficacy of NMD-inhibition based therapy...
September 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28859641/a-streamlined-method-for-analysing-genome-wide-dna-methylation-patterns-from-low-amounts-of-ffpe-dna
#3
Jackie L Ludgate, James Wright, Peter A Stockwell, Ian M Morison, Michael R Eccles, Aniruddha Chatterjee
BACKGROUND: Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis...
August 31, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28851357/de-novo-assembly-and-characterization-of-breast-cancer-transcriptomes-identifies-large-numbers-of-novel-fusion-gene-transcripts-of-potential-functional-significance
#4
Vinay K Mittal, John F McDonald
BACKGROUND: Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach for the identification of chimeric transcripts of potential functional significance. We report here the development and use of an integrated computational pipeline for the de novo assembly and characterization of chimeric transcripts in 55 primary breast cancer and normal tissue samples...
August 29, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28851355/integrative-model-of-leukocyte-genomics-and-organ-dysfunction-in-heart-failure-patients-requiring-mechanical-circulatory-support-a-prospective-observational-study
#5
Nicholas Wisniewski, Galyna Bondar, Christoph Rau, Jay Chittoor, Eleanor Chang, Azadeh Esmaeili, Martin Cadeiras, Mario Deng
BACKGROUND: The implantation of mechanical circulatory support devices in heart failure patients is associated with a systemic inflammatory response, potentially leading to death from multiple organ dysfunction syndrome. Previous studies point to the involvement of many mechanisms, but an integrative hypothesis does not yet exist. Using time-dependent whole-genome mRNA expression in circulating leukocytes, we constructed a systems-model to improve mechanistic understanding and prediction of adverse outcomes...
August 29, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28789679/consensus-strategy-in-genes-prioritization-and-combined-bioinformatics-analysis-for-preeclampsia-pathogenesis
#6
Eduardo Tejera, Maykel Cruz-Monteagudo, Germán Burgos, María-Eugenia Sánchez, Aminael Sánchez-Rodríguez, Yunierkis Pérez-Castillo, Fernanda Borges, Maria Natália Dias Soeiro Cordeiro, César Paz-Y-Miño, Irene Rebelo
BACKGROUND: Preeclampsia is a multifactorial disease with unknown pathogenesis. Even when recent studies explored this disease using several bioinformatics tools, the main objective was not directed to pathogenesis. Additionally, consensus prioritization was proved to be highly efficient in the recognition of genes-disease association. However, not information is available about the consensus ability to early recognize genes directly involved in pathogenesis. Therefore our aim in this study is to apply several theoretical approaches to explore preeclampsia; specifically those genes directly involved in the pathogenesis...
August 8, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786366/secure-searching-of-biomarkers-through-hybrid-homomorphic-encryption-scheme
#7
Miran Kim, Yongsoo Song, Jung Hee Cheon
BACKGROUND: As genome sequencing technology develops rapidly, there has lately been an increasing need to keep genomic data secure even when stored in the cloud and still used for research. We are interested in designing a protocol for the secure outsourcing matching problem on encrypted data. METHOD: We propose an efficient method to securely search a matching position with the query data and extract some information at the position. After decryption, only a small amount of comparisons with the query information should be performed in plaintext state...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786365/presage-privacy-preserving-genetic-testing-via-software-guard-extension
#8
Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter, Shuang Wang
BACKGROUND: Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genomic data. METHODS: We present one of the first implementations of Software Guard Extension (SGX) based securely outsourced genetic testing framework, which leverages multiple cryptographic protocols and minimal perfect hash scheme to enable efficient and secure data storage and computation outsourcing...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786364/aftermath-of-bustamante-attack-on-genomic-beacon-service
#9
Md Momin Al Aziz, Reza Ghasemi, Md Waliullah, Noman Mohammed
BACKGROUND: With the enormous need for federated eco-system for holding global genomic and clinical data, Global Alliance for Genomic and Health (GA4GH) has created an international website called beacon service which allows a researcher to find out whether a specific dataset can be utilized to his or her research beforehand. This simple webservice is quite useful as it allows queries like whether a certain position of a target chromosome has a specific nucleotide. However, the increased integration of individuals genomic data into clinical practice and research raised serious privacy concern...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786363/efficient-and-secure-outsourcing-of-genomic-data-storage
#10
João Sá Sousa, Cédric Lefebvre, Zhicong Huang, Jean Louis Raisaro, Carlos Aguilar-Melchor, Marc-Olivier Killijian, Jean-Pierre Hubaux
BACKGROUND: Cloud computing is becoming the preferred solution for efficiently dealing with the increasing amount of genomic data. Yet, outsourcing storage and processing sensitive information, such as genomic data, comes with important concerns related to privacy and security. This calls for new sophisticated techniques that ensure data protection from untrusted cloud providers and that still enable researchers to obtain useful information. METHODS: We present a novel privacy-preserving algorithm for fully outsourcing the storage of large genomic data files to a public cloud and enabling researchers to efficiently search for variants of interest...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786362/secure-approximation-of-edit-distance-on-genomic-data
#11
Md Momin Al Aziz, Dima Alhadidi, Noman Mohammed
BACKGROUND: Edit distance is a well established metric to quantify how dissimilar two strings are by counting the minimum number of operations required to transform one string into the other. It is utilized in the domain of human genomic sequence similarity as it captures the requirements and leads to a better diagnosis of diseases. However, in addition to the computational complexity due to the large genomic sequence length, the privacy of these sequences are highly important. As these genomic sequences are unique and can identify an individual, these cannot be shared in a plaintext...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786361/bloom-bloom-filter-based-oblivious-outsourced-matchings
#12
Jan Henrik Ziegeldorf, Jan Pennekamp, David Hellmanns, Felix Schwinger, Ike Kunze, Martin Henze, Jens Hiller, Roman Matzutt, Klaus Wehrle
BACKGROUND: Whole genome sequencing has become fast, accurate, and cheap, paving the way towards the large-scale collection and processing of human genome data. Unfortunately, this dawning genome era does not only promise tremendous advances in biomedical research but also causes unprecedented privacy risks for the many. Handling storage and processing of large genome datasets through cloud services greatly aggravates these concerns. Current research efforts thus investigate the use of strong cryptographic methods and protocols to implement privacy-preserving genomic computations...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786360/controlling-the-signal-practical-privacy-protection-of-genomic-data-sharing-through-beacon-services
#13
Zhiyu Wan, Yevgeniy Vorobeychik, Murat Kantarcioglu, Bradley Malin
BACKGROUND: Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can be applied to discern the presence of a known individual's DNA sequence in the pool of subjects. Recently, it was shown that the Beacon Project of the Global Alliance for Genomics and Health, a web service for querying about the presence (or absence) of a specific allele, was vulnerable...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28786359/private-queries-on-encrypted-genomic-data
#14
Gizem S Çetin, Hao Chen, Kim Laine, Kristin Lauter, Peter Rindal, Yuhou Xia
BACKGROUND: One of the tasks in the iDASH Secure Genome Analysis Competition in 2016 was to demonstrate the feasibility of privacy-preserving queries on homomorphically encrypted genomic data. More precisely, given a list of up to 100,000 mutations, the task was to encrypt the data using homomorphic encryption in a way that allows it to be stored securely in the cloud, and enables the data owner to query the dataset for the presence of specific mutations, without revealing any information about the dataset or the queries to the cloud...
July 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28716121/identification-of-trunk-mutations-in-gastric-carcinoma-a-case-study
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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