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  1. Research article

    The establishment and application of preimplantation genetic haplotyping in embryo diagnosis for reciprocal and Robertsonian translocation carriers

    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 t...

    Shuo Zhang, Caixia Lei, Junping Wu, Jing Zhou, Haiyan Sun, Jing Fu, Yijuan Sun, Xiaoxi Sun, Daru Lu and Yueping Zhang

    BMC Medical Genomics 2017 10:60

    Published on: 17 October 2017

  2. Research article

    RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking

    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 seque...

    Margaret M. Parker, Robert P. Chase, Andrew Lamb, Alejandro Reyes, Aabida Saferali, Jeong H. Yun, Blanca E. Himes, Edwin K. Silverman, Craig P. Hersh and Peter J. Castaldi

    BMC Medical Genomics 2017 10:58

    Published on: 6 October 2017

  3. Research article

    Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory

    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 pharmaco...

    Petr Ponomarenko, Alex Ryutov, Dennis T. Maglinte, Ancha Baranova, Tatiana V. Tatarinova and Xiaowu Gai

    BMC Medical Genomics 2017 10:57

    Published on: 6 October 2017

  4. Research article

    A systematic review and integrative approach to decode the common molecular link between levodopa response and Parkinson’s disease

    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 ...

    Debleena Guin, Manish Kumar Mishra, Puneet Talwar, Chitra Rawat, Suman S. Kushwaha, Shrikant Kukreti and Ritushree Kukreti

    BMC Medical Genomics 2017 10:56

    Published on: 19 September 2017

  5. Research article

    Assessing the activity of nonsense-mediated mRNA decay in lung cancer

    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 ...

    Meng Wang, Peiwei Zhang, Yufei Zhu, Xiangyin Kong, Zhenguo Zhang and Landian Hu

    BMC Medical Genomics 2017 10:55

    Published on: 6 September 2017

  6. Technical advance

    A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA

    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 nu...

    Jackie L. Ludgate, James Wright, Peter A. Stockwell, Ian M. Morison, Michael R. Eccles and Aniruddha Chatterjee

    BMC Medical Genomics 2017 10:54

    Published on: 31 August 2017

  7. Research article

    Integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support: a prospective observational study

    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. ...

    Nicholas Wisniewski, Galyna Bondar, Christoph Rau, Jay Chittoor, Eleanor Chang, Azadeh Esmaeili, Martin Cadeiras and Mario Deng

    BMC Medical Genomics 2017 10:52

    Published on: 29 August 2017

  8. Research article

    De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance

    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 ...

    Vinay K. Mittal and John F. McDonald

    BMC Medical Genomics 2017 10:53

    Published on: 29 August 2017

  9. Research article

    Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis

    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. Addit...

    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 and Irene Rebelo

    BMC Medical Genomics 2017 10:50

    Published on: 8 August 2017

  10. Research

    Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services

    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 deca...

    Zhiyu Wan, Yevgeniy Vorobeychik, Murat Kantarcioglu and Bradley Malin

    BMC Medical Genomics 2017 10(Suppl 2):39

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  11. Research

    Efficient and secure outsourcing of genomic data storage

    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...

    João Sá Sousa, Cédric Lefebvre, Zhicong Huang, Jean Louis Raisaro, Carlos Aguilar-Melchor, Marc-Olivier Killijian and Jean-Pierre Hubaux

    BMC Medical Genomics 2017 10(Suppl 2):46

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  12. Research

    BLOOM: BLoom filter based oblivious outsourced matchings

    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...

    Jan Henrik Ziegeldorf, Jan Pennekamp, David Hellmanns, Felix Schwinger, Ike Kunze, Martin Henze, Jens Hiller, Roman Matzutt and Klaus Wehrle

    BMC Medical Genomics 2017 10(Suppl 2):44

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  13. Research

    Private queries on encrypted genomic data

    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...

    Gizem S. Çetin, Hao Chen, Kim Laine, Kristin Lauter, Peter Rindal and Yuhou Xia

    BMC Medical Genomics 2017 10(Suppl 2):45

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  14. Research

    Aftermath of bustamante attack on genomic beacon service

    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 all...

    Md Momin Al Aziz, Reza Ghasemi, Md Waliullah and Noman Mohammed

    BMC Medical Genomics 2017 10(Suppl 2):43

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  15. Research

    Secure approximation of edit distance on genomic data

    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 ...

    Md Momin Al Aziz, Dima Alhadidi and Noman Mohammed

    BMC Medical Genomics 2017 10(Suppl 2):41

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  16. Research

    PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension

    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 cha...

    Feng Chen, Chenghong Wang, Wenrui Dai, Xiaoqian Jiang, Noman Mohammed, Md Momin Al Aziz, Md Nazmus Sadat, Cenk Sahinalp, Kristin Lauter and Shuang Wang

    BMC Medical Genomics 2017 10(Suppl 2):48

    Published on: 26 July 2017

    This article is part of a Supplement: Volume 10 Supplement 2

  17. Case report

    Identification of trunk mutations in gastric carcinoma: a case study

    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 ...

    Zhan Zhou, Shanshan Wu, Jun Lai, Yuan Shi, Chixiao Qiu, Zhe Chen, Yufeng Wang, Xun Gu, Jie Zhou and Shuqing Chen

    BMC Medical Genomics 2017 10:49

    Published on: 17 July 2017

  18. Research article

    In silico identification of potential key regulatory factors in smoking-induced lung cancer

    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 pat...

    Salem A. El-aarag, Amal Mahmoud, Medhat H. Hashem, Hatem Abd Elkader, Alaa E. Hemeida and Mahmoud ElHefnawi

    BMC Medical Genomics 2017 10:40

    Published on: 7 June 2017

  19. Research article

    Quantitative analysis of cryptic splicing associated with TDP-43 depletion

    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 ...

    Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs and Vincent Plagnol

    BMC Medical Genomics 2017 10:38

    Published on: 26 May 2017

  20. Software

    CVE: an R package for interactive variant prioritisation in precision oncology

    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 browse...

    Andreas Mock, Suzanne Murphy, James Morris, Francesco Marass, Nitzan Rosenfeld and Charlie Massie

    BMC Medical Genomics 2017 10:37

    Published on: 25 May 2017

  21. Research

    Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer’s disease

    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. Howev...

    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 Jr., Michael W. Weiner, Robert C. Green, Arthur W. Toga…

    BMC Medical Genomics 2017 10(Suppl 1):29

    Published on: 24 May 2017

    This article is part of a Supplement: Volume 10 Supplement 1

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