BMC Medical Genomics
Bioinformatic and algorithmical studies
Section edited by Youping Deng
This section considers studies on the development and application of novel computational and statistical methods to the analysis of genomic data for the study of health and disease.
- RESEARCH ARTICLE
A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without
Systemic Lupus Erythematosus (SLE) is a complex, multi-systemic, autoimmune disease for which the underlying aetiological mechanisms are poorly understood. The genetic and molecular processes underlying lupus ...BMC Medical Genomics 2016 9:66Published on: 15 November 2016 - RESEARCH ARTICLE
Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing
The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adeq...BMC Medical Genomics 2016 9:64Published on: 19 October 2016 - TECHNICAL ADVANCE
Protecting genomic data analytics in the cloud: state of the art and opportunities
The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, ...BMC Medical Genomics 2016 9:63Published on: 13 October 2016 - RESEARCH ARTICLE
An adaptive detection method for fetal chromosomal aneuploidy using cell-free DNA from 447 Korean women
Noninvasive prenatal testing (NIPT) using massively parallel sequencing of cell-free DNA (cfDNA) is increasingly being used to predict fetal chromosomal abnormalities. However, concerns over erroneous predicti...BMC Medical Genomics 2016 9:61Published on: 3 October 2016 - DEBATE
Explorations to improve the completeness of exome sequencing
Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a defin...BMC Medical Genomics 2016 9:56Published on: 27 August 2016 - RESEARCH ARTICLE
Reproducible detection of disease-associated markers from gene expression data
Detection of disease-associated markers plays a crucial role in gene screening for biological studies. Two-sample test statistics, such as the t-statistic, are widely used to rank genes based on gene expression d...BMC Medical Genomics 2016 9:53Published on: 18 August 2016 - RESEARCH ARTICLE
Dealing with prognostic signature instability: a strategy illustrated for cardiovascular events in patients with end-stage renal disease
Identification of prognostic gene expression markers from clinical cohorts might help to better understand disease etiology. A set of potentially important markers can be automatically selected when linking ge...BMC Medical Genomics 2016 9:43Published on: 20 July 2016 - RESEARCH ARTICLE
Study design and data analysis considerations for the discovery of prognostic molecular biomarkers: a case study of progression free survival in advanced serous ovarian cancer
Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outc...BMC Medical Genomics 2016 9:27Published on: 10 June 2016 - TECHNICAL ADVANCE
A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer
Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significa...BMC Medical Genomics 2016 9:19Published on: 11 April 2016 - SOFTWARE
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient...BMC Medical Genomics 2015 8:24Published on: 21 May 2015 - RESEARCH ARTICLE
Co-expression network of neural-differentiation genes shows specific pattern in schizophrenia
Schizophrenia is a neurodevelopmental disorder with genetic and environmental factors contributing to its pathogenesis, although the mechanism is unknown due to the difficulties in accessing diseased tissue du...BMC Medical Genomics 2015 8:23Published on: 16 May 2015 - RESEARCH ARTICLE
Systems biology of myasthenia gravis, integration of aberrant lncRNA and mRNA expression changes
A novel class of transcripts, long non-coding RNAs (lncRNAs), has recently emerged as a key player in several biological processes, and important roles for these molecules have been reported in a number of com...BMC Medical Genomics 2015 8:13Published on: 18 March 2015 - SOFTWARE
ASEQ: fast allele-specific studies from next-generation sequencing data
Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. S...BMC Medical Genomics 2015 8:9Published on: 1 March 2015 - RESEARCH ARTICLE
Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer – the INNODIAG study
Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data...BMC Medical Genomics 2015 8:3Published on: 7 February 2015 - RESEARCH ARTICLE
Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans
African Americans (AA) have more pronounced insulin resistance and higher insulin secretion than European Americans (Caucasians or CA) when matched for age, gender, and body mass index (BMI). We hypothesize th...BMC Medical Genomics 2015 8:4Published on: 7 February 2015 - RESEARCH ARTICLE
Meta-analysis of prostate cancer gene expression data identifies a novel discriminatory signature enriched for glycosylating enzymes
Tumorigenesis is characterised by changes in transcriptional control. Extensive transcript expression data have been acquired over the last decade and used to classify prostate cancers. Prostate cancer is, how...BMC Medical Genomics 2014 7:513Published on: 31 December 2014 - RESEARCH ARTICLE
A 3-biomarker-panel predicts renal outcome in patients with proteinuric renal diseases
Clinical and histological parameters are valid prognostic markers in renal disease, although they may show considerable interindividual variability and sometimes limited prognostic value. Novel molecular marke...BMC Medical Genomics 2014 7:75Published on: 24 December 2014 - RESEARCH ARTICLE
Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS)
The incidence of Acute Megakaryoblastic Leukemia (AMKL) is 500-fold higher in children with Down Syndrome (DS) compared with non-DS children, but the relevance of trisomy 21 as a specific background of AMKL in...BMC Medical Genomics 2014 7:63Published on: 5 December 2014 - RESEARCH ARTICLE
Evaluation of an integrated clinical workflow for targeted next-generation sequencing of low-quality tumor DNA using a 51-gene enrichment panel
Improvements in both performance and cost for next-generation sequencing (NGS) have spurred its rapid adoption for clinical applications. We designed and optimized a pan-cancer target-enrichment panel for 51 w...BMC Medical Genomics 2014 7:62Published on: 14 November 2014 - RESEARCH ARTICLE
Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor
Cytokine-induced killer (CIK) cells are an emerging approach of cancer treatment. Our previous study have shown that CIK cells stimulated with combination of IL-2 and IL-15 displayed improved proliferation cap...BMC Medical Genomics 2014 7:49Published on: 9 August 2014
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