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    796 results match your criteria BMC Medical Genomics [Journal]

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    Bioinformatics prediction of miR-30a targets and its inhibition of cell proliferation of osteosarcoma by up-regulating the expression of PTEN.
    BMC Med Genomics 2017 Nov 15;10(1):64. Epub 2017 Nov 15.
    Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
    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. Read More

    Targeted/exome sequencing identified mutations in ten Chinese patients diagnosed with Noonan syndrome and related disorders.
    BMC Med Genomics 2017 Oct 30;10(1):62. Epub 2017 Oct 30.
    Department of Pediatric Endocrinology/Genetics, Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, 1665 Kongjiang Road, Shanghai, 200092, China.
    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). Read More

    A method to reduce ancestry related germline false positives in tumor only somatic variant calling.
    BMC Med Genomics 2017 Oct 19;10(1):61. Epub 2017 Oct 19.
    Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA.
    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. Read More

    The establishment and application of preimplantation genetic haplotyping in embryo diagnosis for reciprocal and Robertsonian translocation carriers.
    BMC Med Genomics 2017 Oct 17;10(1):60. Epub 2017 Oct 17.
    Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, 588 Fangxie Rd, Shanghai, 200011, China.
    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. Read More

    Differential gene expression in disease: a comparison between high-throughput studies and the literature.
    BMC Med Genomics 2017 Oct 11;10(1):59. Epub 2017 Oct 11.
    Biogen, Cambridge, MA, USA.
    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. Read More

    RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking.
    BMC Med Genomics 2017 Oct 6;10(1):58. Epub 2017 Oct 6.
    Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, USA.
    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. Read More

    Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory.
    BMC Med Genomics 2017 Oct 6;10(1):57. Epub 2017 Oct 6.
    Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA.
    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. Read More

    Genomic diversity and phylogeography of norovirus in China.
    BMC Med Genomics 2017 Oct 3;10(Suppl 3):51. Epub 2017 Oct 3.
    Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Rd, Shanghai, 200032, People's Republic of China.
    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. Read More

    A systematic review and integrative approach to decode the common molecular link between levodopa response and Parkinson's disease.
    BMC Med Genomics 2017 Sep 19;10(1):56. Epub 2017 Sep 19.
    Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Mall Road, New Delhi, -110007, India.
    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. Read More

    Assessing the activity of nonsense-mediated mRNA decay in lung cancer.
    BMC Med Genomics 2017 Sep 6;10(1):55. Epub 2017 Sep 6.
    State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
    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. Read More

    A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA.
    BMC Med Genomics 2017 Aug 31;10(1):54. Epub 2017 Aug 31.
    Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.
    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. Read More

    De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance.
    BMC Med Genomics 2017 Aug 29;10(1):53. Epub 2017 Aug 29.
    Integrated Cancer Research Center, School of Biological Sciences, and Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, 315 Ferst Dr, Atlanta, GA, 30332, USA.
    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. Read More

    Integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support: a prospective observational study.
    BMC Med Genomics 2017 Aug 29;10(1):52. Epub 2017 Aug 29.
    Department of Medicine, Division of Cardiology, University of California Los Angeles, 100 UCLA Medical Plaza, Suite 630, Los Angeles, California, 90095, USA.
    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. Read More

    Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis.
    BMC Med Genomics 2017 Aug 8;10(1):50. Epub 2017 Aug 8.
    Faculty of Pharmacy, University of Porto, Porto, Portugal.
    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. Read More

    Secure searching of biomarkers through hybrid homomorphic encryption scheme.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):42. Epub 2017 Jul 26.
    Department of Mathematical Sciences, Seoul National University, GwanAkRo 1, Seoul, 08826, Republic of Korea.
    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. Read More

    PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):48. Epub 2017 Jul 26.
    Department of Biomedical Informatics, University of California San Diego, La Jolla, 92093, CA, USA.
    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. Read More

    Aftermath of bustamante attack on genomic beacon service.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):43. Epub 2017 Jul 26.
    Department of Computer Science, University of Manitoba, Winnipeg, Canada.
    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. Read More

    Efficient and secure outsourcing of genomic data storage.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):46. Epub 2017 Jul 26.
    Laboratory for Communications and Applications - LCA 1, École Polytechnique Fédérale de Lausanne, Route Cantonale, Lausanne, 1015, Switzerland.
    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. Read More

    Secure approximation of edit distance on genomic data.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):41. Epub 2017 Jul 26.
    Department of Computer Science, University of Manitoba, Winnipeg, Canada.
    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. Read More

    BLOOM: BLoom filter based oblivious outsourced matchings.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):44. Epub 2017 Jul 26.
    Communication and Distributed Systems (COMSYS), RWTH Aachen University, Ahornstrasse 55, Aachen, 52074, Germany.
    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. Read More

    Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):39. Epub 2017 Jul 26.
    Department of Electrical Engineering and Computer Science, Vanderbilt University, 2525 West End Avenue, Suite 800, 37203, Nashville, TN, USA.
    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. Read More

    Private queries on encrypted genomic data.
    BMC Med Genomics 2017 Jul 26;10(Suppl 2):45. Epub 2017 Jul 26.
    Princeton University, 304 Washington Rd, Princeton, NJ 08544, USA.
    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.

    Methods: We devise a novel string matching protocol to enable privacy-preserving queries on homomorphically encrypted data. Read More

    Identification of trunk mutations in gastric carcinoma: a case study.
    BMC Med Genomics 2017 Jul 17;10(1):49. Epub 2017 Jul 17.
    College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China.
    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. Read More

    Pharmacogenetic testing through the direct-to-consumer genetic testing company 23andMe.
    BMC Med Genomics 2017 Jun 19;10(1):47. Epub 2017 Jun 19.
    Department of Medical and Molecular Genetics, King's College London, 8th Floor Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
    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. Read More

    In silico identification of potential key regulatory factors in smoking-induced lung cancer.
    BMC Med Genomics 2017 Jun 7;10(1):40. Epub 2017 Jun 7.
    Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Center, Cairo, Egypt.
    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. Read More

    Taking promoters out of enhancers in sequence based predictions of tissue-specific mammalian enhancers.
    BMC Med Genomics 2017 May 24;10(Suppl 1):34. Epub 2017 May 24.
    Institute of Informatics, University of Warsaw, Banacha 2, Warsaw, 02-097, Poland.
    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. Read More

    Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population.
    BMC Med Genomics 2017 May 24;10(Suppl 1):31. Epub 2017 May 24.
    Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
    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. Read More

    Identification of epigenetic interactions between miRNA and DNA methylation associated with gene expression as potential prognostic markers in bladder cancer.
    BMC Med Genomics 2017 May 24;10(Suppl 1):30. Epub 2017 May 24.
    Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA.
    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. Read More

    Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer's disease.
    BMC Med Genomics 2017 May 24;10(Suppl 1):29. Epub 2017 May 24.
    Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA.
    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. Read More

    Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer.
    BMC Med Genomics 2017 May 24;10(Suppl 1):28. Epub 2017 May 24.
    Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
    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. Read More

    A disease similarity matrix based on the uniqueness of shared genes.
    BMC Med Genomics 2017 May 24;10(Suppl 1):26. Epub 2017 May 24.
    Department of Bioengineering, University of Illinois at Chicago, 851 S Morgan St, Chicago, IL, 60607, USA.
    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. Read More

    N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.
    BMC Med Genomics 2017 May 24;10(Suppl 1):27. Epub 2017 May 24.
    Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, 85721, USA.
    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. Read More

    Quantitative analysis of cryptic splicing associated with TDP-43 depletion.
    BMC Med Genomics 2017 May 26;10(1):38. Epub 2017 May 26.
    University College London Genetics Institute, Gower Street, London, UK.
    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. Read More

    CVE: an R package for interactive variant prioritisation in precision oncology.
    BMC Med Genomics 2017 May 25;10(1):37. Epub 2017 May 25.
    Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
    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. Read More

    Erratum to: MiRNA profiling of whole trabecular bone: identification of osteoporosis-related changes in MiRNAs in human hip bones.
    BMC Med Genomics 2017 May 23;10(1):36. Epub 2017 May 23.
    Musculoskeletal research group, IMIM (Hospital del Mar Medical Research Institute), Red Temática de Investigación Cooperativa en Envejecimiento y Fragilidad (RETICEF), ISCIII, Barcelona, Spain.

    Challenges and strategies for implementing genomic services in diverse settings: experiences from the Implementing GeNomics In pracTicE (IGNITE) network.
    BMC Med Genomics 2017 May 22;10(1):35. Epub 2017 May 22.
    Duke Center for Applied Genomics & Precision Medicine, Duke University, Durham, NC, USA.
    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. Read More

    Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing.
    BMC Med Genomics 2017 May 19;10(1):33. Epub 2017 May 19.
    Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.
    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. Read More

    Diet and exercise changes following direct-to-consumer personal genomic testing.
    BMC Med Genomics 2017 May 2;10(1):24. Epub 2017 May 2.
    Division of Genetics, Department of Medicine, Brigham and Women's Hospital, EC Alumnae Building, Suite 301, 41 Avenue Louis Pasteur, Boston, MA, 02115, USA.
    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. Read More

    Post-operative atrial fibrillation examined using whole-genome RNA sequencing in human left atrial tissue.
    BMC Med Genomics 2017 May 2;10(1):25. Epub 2017 May 2.
    Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital/Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
    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. Read More

    Serum MicroRNA profile in patients with colon adenomas or cancer.
    BMC Med Genomics 2017 Apr 20;10(1):23. Epub 2017 Apr 20.
    National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.
    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. Read More

    Patient complexity and genotype-phenotype correlations in biliary atresia: a cross-sectional analysis.
    BMC Med Genomics 2017 Apr 17;10(1):22. Epub 2017 Apr 17.
    Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong.
    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. Read More

    GRMD cardiac and skeletal muscle metabolism gene profiles are distinct.
    BMC Med Genomics 2017 Apr 8;10(1):21. Epub 2017 Apr 8.
    Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, 2200 Pierce Avenue, 359A Preston Research Building, Nashville, TN, 37232, USA.
    Background: Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps remain in understanding mechanisms that contribute to the marked delay in cardiac compared to skeletal muscle dysfunction.

    Methods: To address this question, we analyzed cardiac and skeletal muscle tissue microarrays from golden retriever muscular dystrophy (GRMD) dogs, a genetically and clinically homologous model for DMD. Read More

    Revealing cancer subtypes with higher-order correlations applied to imaging and omics data.
    BMC Med Genomics 2017 Mar 31;10(1):20. Epub 2017 Mar 31.
    Biomedical Engineering, University of California, Santa Cruz, USA.
    Background: Patient stratification to identify subtypes with different disease manifestations, severity, and expected survival time is a critical task in cancer diagnosis and treatment. While stratification approaches using various biomarkers (including high-throughput gene expression measurements) for patient-to-patient comparisons have been successful in elucidating previously unseen subtypes, there remains an untapped potential of incorporating various genotypic and phenotypic data to discover novel or improved groupings.

    Methods: Here, we present HOCUS, a unified analytical framework for patient stratification that uses a community detection technique to extract subtypes out of sparse patient measurements. Read More

    Basal-like breast cancer: molecular profiles, clinical features and survival outcomes.
    BMC Med Genomics 2017 Mar 28;10(1):19. Epub 2017 Mar 28.
    Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine, Hunter Medical Research Institute, Lot 1, Kookaburra Circuit, New Lambton Heights, 2305, Australia.
    Background: Basal-like constitutes an important molecular subtype of breast cancer characterised by an aggressive behaviour and a limited therapy response. The outcome of patients within this subtype is, however, divergent. Some individuals show an increased risk of dying in the first five years, and others a long-term survival of over ten years after the diagnosis. Read More

    Gene and protein analysis reveals that p53 pathway is functionally inactivated in cytogenetically normal Acute Myeloid Leukemia and Acute Promyelocytic Leukemia.
    BMC Med Genomics 2017 Mar 24;10(1):18. Epub 2017 Mar 24.
    Department of Hematology, Hadassah-Hebrew University Medical Center, P.O. Box 12000, Jerusalem, 91120, Israel.
    Background: Mechanisms that inactivate the p53 pathway in Acute Myeloid Leukemia (AML), other than rare mutations, are still not well understood.

    Methods: We performed a bioinformatics study of the p53 pathway function at the gene expression level on our collection of 1153 p53-pathway related genes. Publically available Affymetrix data of 607 de-novo AML patients at diagnosis were analyzed according to the patients cytogenetic, FAB and molecular mutations subtypes. Read More

    Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing.
    BMC Med Genomics 2017 Mar 18;10(1):17. Epub 2017 Mar 18.
    Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, Leeds, UK.
    Background: The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material.

    Methods: We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples. Read More

    Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications.
    BMC Med Genomics 2017 Mar 16;10(1):16. Epub 2017 Mar 16.
    Department of Computer Science, Texas State University, 601 University Drive, San Marcos, USA.
    Background: The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent and low risk; however, it may transform into acute myeloid leukemia (AML), which is much more aggressive.

    Methods: We develop a novel network analysis approach that uses expression of eigengenes to delineate the biological differences between these two diseases. Read More

    CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data.
    BMC Med Genomics 2017 Mar 15;10(1):15. Epub 2017 Mar 15.
    School of Information Science and Technology, University of Science and Technology of China, Hefei, AH230027, China.
    Background: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. Read More

    Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer.
    BMC Med Genomics 2017 Mar 15;10(1):12. Epub 2017 Mar 15.
    Information Sciences Institute, University of Southern California, Marina Del Rey, USA.
    Background: De novo inference of clinically relevant gene function relationships from tumor RNA-seq remains a challenging task. Current methods typically either partition patient samples into a few subtypes or rely upon analysis of pairwise gene correlations that will miss some groups in noisy data. Leveraging higher dimensional information can be expected to increase the power to discern targetable pathways, but this is commonly thought to be an intractable computational problem. Read More

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