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BMC Medical Genomics

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https://www.readbyqxmd.com/read/29141684/bioinformatics-prediction-of-mir-30a-targets-and-its-inhibition-of-cell-proliferation-of-osteosarcoma-by-up-regulating-the-expression-of-pten
#1
Biao Zhong, Shang Guo, Wei Zhang, Chi Zhang, Yukai Wang, Changqing Zhang
BACKGROUND: MiRNAs are frequently abnormally expressed in the progression of human osteosarcoma. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is one of the tumor suppressors in various types of human cancer. In the present study, we detected how hsa-miR-30a-3p regulated PTEN and further tested the role of hsa-miR-30a-3p in the cell proliferation of osteosarcoma cells. METHODS: The levels of miR-30a were determined by real time PCR. The expression of PTEN was tested by western blotting analysis...
November 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29084544/targeted-exome-sequencing-identified-mutations-in-ten-chinese-patients-diagnosed-with-noonan-syndrome-and-related-disorders
#2
Shanshan Xu, Yanjie Fan, Yu Sun, Lili Wang, Xuefan Gu, Yongguo Yu
BACKGROUND: Noonan syndrome (NS) and Noonan syndrome with multiple lentigines (NSML) are autosomal dominant developmental disorders. NS and NSML are caused by abnormalities in genes that encode proteins related to the RAS-MAPK pathway, including PTPN11, RAF1, BRAF, and MAP2K. In this study, we diagnosed ten NS or NSML patients via targeted sequencing or whole exome sequencing (TS/WES). METHODS: TS/WES was performed to identify mutations in ten Chinese patients who exhibited the following manifestations: potential facial dysmorphisms, short stature, congenital heart defects, and developmental delay...
October 30, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29052513/a-method-to-reduce-ancestry-related-germline-false-positives-in-tumor-only-somatic-variant-calling
#3
Rebecca F Halperin, John D Carpten, Zarko Manojlovic, Jessica Aldrich, Jonathan Keats, Sara Byron, Winnie S Liang, Megan Russell, Daniel Enriquez, Ana Claasen, Irene Cherni, Baffour Awuah, Joseph Oppong, Max S Wicha, Lisa A Newman, Evelyn Jaigge, Seungchan Kim, David W Craig
BACKGROUND: Significant clinical and research applications are driving large scale adoption of individualized tumor sequencing in cancer in order to identify tumors-specific mutations. When a matched germline sample is available, somatic mutations may be identified using comparative callers. However, matched germline samples are frequently not available such as with archival tissues, which makes it difficult to distinguish somatic from germline variants. While population databases may be used to filter out known germline variants, recent studies have shown private germline variants result in an inflated false positive rate in unmatched tumor samples, and the number germline false positives in an individual may be related to ancestry...
October 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29041973/the-establishment-and-application-of-preimplantation-genetic-haplotyping-in-embryo-diagnosis-for-reciprocal-and-robertsonian-translocation-carriers
#4
Shuo Zhang, Caixia Lei, Junping Wu, Jing Zhou, Haiyan Sun, Jing Fu, Yijuan Sun, Xiaoxi Sun, Daru Lu, Yueping Zhang
BACKGROUND: Preimplantation genetic diagnosis (PGD) is now widely used to select embryos free of chromosomal copy number variations (CNV) from chromosome balanced translocation carriers. However, it remains a difficulty to distinguish in embryos between balanced and structurally normal chromosomes efficiently. METHODS: For this purpose, genome wide preimplantation genetic haplotyping (PGH) analysis was utilized based on single nucleotide polymorphism (SNP) microarray...
October 17, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29020950/differential-gene-expression-in-disease-a-comparison-between-high-throughput-studies-and-the-literature
#5
Raul Rodriguez-Esteban, Xiaoyu Jiang
BACKGROUND: Differential gene expression is important to understand the biological differences between healthy and diseased states. Two common sources of differential gene expression data are microarray studies and the biomedical literature. METHODS: With the aid of text mining and gene expression analysis we have examined the comparative properties of these two sources of differential gene expression data. RESULTS: The literature shows a preference for reporting genes associated to higher fold changes in microarray data, rather than genes that are simply significantly differentially expressed...
October 11, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28985737/rna-sequencing-identifies-novel-non-coding-rna-and-exon-specific-effects-associated-with-cigarette-smoking
#6
Margaret M Parker, Robert P Chase, Andrew Lamb, Alejandro Reyes, Aabida Saferali, Jeong H Yun, Blanca E Himes, Edwin K Silverman, Craig P Hersh, Peter J Castaldi
BACKGROUND: Cigarette smoking is the leading modifiable risk factor for disease and death worldwide. Previous studies quantifying gene-level expression have documented the effect of smoking on mRNA levels. Using RNA sequencing, it is possible to analyze the impact of smoking on complex regulatory phenomena (e.g. alternative splicing, differential isoform usage) leading to a more detailed understanding of the biology underlying smoking-related disease. METHODS: We used whole-blood RNA sequencing to describe gene and exon-level expression differences between 229 current and 286 former smokers in the COPDGene study...
October 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28985730/clinical-utility-of-the-low-density-infinium-qc-genotyping-array-in-a-genomics-based-diagnostics-laboratory
#7
Petr Ponomarenko, Alex Ryutov, Dennis T Maglinte, Ancha Baranova, Tatiana V Tatarinova, Xiaowu Gai
BACKGROUND: With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests. METHODS: We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing...
October 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28984198/genomic-diversity-and-phylogeography-of-norovirus-in-china
#8
Niu Qiao, He Ren, Lei Liu
BACKGROUND: Little is known about the phylogeography of norovirus (NoV) in China. In norovirus, a clear understanding for the characteristics of tree topology, migration patterns and its demographic dynamics in viral circulation are needed to identify its prevalence trends, which can help us better prepare for its epidemics as well as develop useful control strategies. The aim of this study was to explore the genetic diversity, temporal distribution, demographic dynamics and migration patterns of NoV that circulated in China...
October 3, 2017: BMC Medical Genomics
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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