Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma
Childhood-onset asthma is highly affected by genetic components. In recent years, many genome-wide association studies (GWAS) have reported a large group of genetic variants and susceptible genes associated wi...BMC Medical Genomics 2020 13:123Machine learning based refined differential gene expression analysis of pediatric sepsis
Differential expression (DE) analysis of transcriptomic data enables genome-wide analysis of gene expression changes associated with biological conditions of interest. Such analysis often provides a wide list ...BMC Medical Genomics 2020 13:122Constructing cancer patient-specific and group-specific gene networks with multi-omics data
Cancer is a complex and heterogeneous disease with many possible genetic and environmental causes. The same treatment for patients of the same cancer type often results in different outcomes in terms of effica...BMC Medical Genomics 2020 13(Suppl 6):81This article is part of a Supplement: Volume 13 Supplement 6A machine learning framework for genotyping the structural variations with copy number variant
Genotyping of structural variation is an important computational problem in next generation sequence data analysis. However, in cancer genomes, the copy number variant(CNV) often coexists with other types of s...BMC Medical Genomics 2020 13(Suppl 6):79This article is part of a Supplement: Volume 13 Supplement 6A novel neoantigen discovery approach based on chromatin high order conformation
High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify ...BMC Medical Genomics 2020 13(Suppl 6):62This article is part of a Supplement: Volume 13 Supplement 6Association of blood pressure with cognitive function at midlife: a Mendelian randomization study
Whether high blood pressure has a causal effect on cognitive function as early as middle age is unclear. We investigated whether high blood pressure (BP) causally impairs cognitive function at midlife using Me...BMC Medical Genomics 2020 13:121Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease
Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture...BMC Medical Genomics 2020 13:120Unraveling the molecular heterogeneity in type 2 diabetes: a potential subtype discovery followed by metabolic modeling
Type 2 diabetes mellitus (T2DM) is a complex multifactorial disease with a high prevalence worldwide. Insulin resistance and impaired insulin secretion are the two major abnormalities in the pathogenesis of T2...BMC Medical Genomics 2020 13:119HDNA methylation data-based molecular subtype classification related to the prognosis of patients with hepatocellular carcinoma
DNA methylation is a common chemical modification of DNA in the carcinogenesis of hepatocellular carcinoma (HCC).BMC Medical Genomics 2020 13:118Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives
In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes. Typically, hapl...BMC Medical Genomics 2020 13:117Breast and prostate cancers harbor common somatic copy number alterations that consistently differ by race and are associated with survival
Pan-cancer studies of somatic copy number alterations (SCNAs) have demonstrated common SCNA patterns across cancer types, but despite demonstrable differences in aggressiveness of some cancers by race, pan-can...BMC Medical Genomics 2020 13:116Comparative transcriptome analysis of Parkinson’s disease and Hutchinson-Gilford progeria syndrome reveals shared susceptible cellular network processes
Parkinson’s Disease (PD) and Hutchinson-Gilford Progeria Syndrome (HGPS) are two heterogeneous disorders, which both display molecular and clinical alterations associated with the aging process. However, simil...BMC Medical Genomics 2020 13:114Clinical, genomics and networking analyses of a high-altitude native American Ecuadorian patient with congenital insensitivity to pain with anhidrosis: a case report
Congenital insensitivity to pain with anhidrosis (CIPA) is an extremely rare autosomal recessive disorder characterized by insensitivity to pain, inability to sweat and intellectual disability. CIPA is caused ...BMC Medical Genomics 2020 13:113Bioinformatic analysis revealing mitotic spindle assembly regulated NDC80 and MAD2L1 as prognostic biomarkers in non-small cell lung cancer development
Lung cancer has been the leading cause of tumor related death, and 80% ~ 85% of it is non-small cell lung cancer (NSCLC). Even with the rising molecular targeted therapies, for example EGFR, ROS1 and ALK, the ...BMC Medical Genomics 2020 13:112Fusion transcript detection using spatial transcriptomics
Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high sp...BMC Medical Genomics 2020 13:110A novel use for Levey-Jennings charts in prenatal molecular diagnosis
The goal of this study was to determine whether Levey-Jennings charts, which are widely used in clinical laboratories, can be used to create standardized internal quality controls (IQCs) for prenatal molecular...BMC Medical Genomics 2020 13:109Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma
Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exa...BMC Medical Genomics 2020 13:108Analysis of exosomal circRNAs upon irradiation in pancreatic cancer cell repopulation
Pancreatic cancer is one of the most malignant tumors. However, radiotherapy can lead to tumor recurrence, which is caused by the residual surviving cells repopulation stimulated by some molecular released fro...BMC Medical Genomics 2020 13:107Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics
We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workf...BMC Medical Genomics 2020 13:106Characterization of genetic and phenotypic heterogeneity of obstructive sleep apnea using electronic health records
Obstructive sleep apnea (OSA) is defined by frequent episodes of reduced or complete cessation of airflow during sleep and is linked to negative health outcomes. Understanding the genetic factors influencing e...BMC Medical Genomics 2020 13:105Decentralized genomics audit logging via permissioned blockchain ledgering
One of the tasks in the iDASH Secure Genome Analysis Competition in 2018 was to develop blockchain-based immutable logging and querying for a cross-site genomic dataset access audit trail. The specific challen...BMC Medical Genomics 2020 13(Suppl 7):102This article is part of a Supplement: Volume 13 Supplement 7Semi-Parallel logistic regression for GWAS on encrypted data
The sharing of biomedical data is crucial to enable scientific discoveries across institutions and improve health care. For example, genome-wide association studies (GWAS) based on a large number of samples ca...BMC Medical Genomics 2020 13(Suppl 7):99This article is part of a Supplement: Volume 13 Supplement 7- BMC Medical Genomics 2020 13(Suppl 7):98This article is part of a Supplement: Volume 13 Supplement 7
Efficient logging and querying for blockchain-based cross-site genomic dataset access audit
Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module...BMC Medical Genomics 2020 13(Suppl 7):91This article is part of a Supplement: Volume 13 Supplement 7Achieving GWAS with homomorphic encryption
One way of investigating how genes affect human traits would be with a genome-wide association study (GWAS). Genetic markers, known as single-nucleotide polymorphism (SNP), are used in GWAS. This raises privac...BMC Medical Genomics 2020 13(Suppl 7):90This article is part of a Supplement: Volume 13 Supplement 7Privacy-preserving semi-parallel logistic regression training with fully homomorphic encryption
Privacy-preserving computations on genomic data, and more generally on medical data, is a critical path technology for innovative, life-saving research to positively and equally impact the global population. I...BMC Medical Genomics 2020 13(Suppl 7):88This article is part of a Supplement: Volume 13 Supplement 7Optimized homomorphic encryption solution for secure genome-wide association studies
Genome-Wide Association Studies (GWAS) refer to observational studies of a genome-wide set of genetic variants across many individuals to see if any genetic variants are associated with a certain trait. A typi...BMC Medical Genomics 2020 13(Suppl 7):83This article is part of a Supplement: Volume 13 Supplement 7Leveraging blockchain for immutable logging and querying across multiple sites
Blockchain has emerged as a decentralized and distributed framework that enables tamper-resilience and, thus, practical immutability for stored data. This immutability property is important in scenarios where ...BMC Medical Genomics 2020 13(Suppl 7):82This article is part of a Supplement: Volume 13 Supplement 7Using blockchain to log genome dataset access: efficient storage and query
Genomic variants are considered sensitive information, revealing potentially private facts about individuals. Therefore, it is important to control access to such data. A key aspect of controlled access is sec...BMC Medical Genomics 2020 13(Suppl 7):78This article is part of a Supplement: Volume 13 Supplement 7Privacy-preserving approximate GWAS computation based on homomorphic encryption
One of three tasks in a secure genome analysis competition called iDASH 2018 was to develop a solution for privacy-preserving GWAS computation based on homomorphic encryption. The scenario is that a data holde...BMC Medical Genomics 2020 13(Suppl 7):77This article is part of a Supplement: Volume 13 Supplement 7Privately computing set-maximal matches in genomic data
Finding long matches in deoxyribonucleic acid (DNA) sequences in large aligned genetic sequences is a problem of great interest. A paradigmatic application is the identification of distant relatives via large ...BMC Medical Genomics 2020 13(Suppl 7):72This article is part of a Supplement: Volume 13 Supplement 7Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Atrial fibrillation (AF) is at least partially heritable, affecting 2–3% of the population in Europe and the USA. However, a substantial proportion of heritability is still lacking. In the present study, we ai...BMC Medical Genomics 2020 13:104What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations
Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Fi...BMC Medical Genomics 2020 13:103Next-generation sequencing analysis of endometrial screening liquid-based cytology specimens: a comparative study to tissue specimens
Liquid-based cytology (LBC) is now a widely used method for cytologic screening and cancer diagnosis. Since the cells are fixed with alcohol-based fixatives, and the specimens are stored in a liquid condition,...BMC Medical Genomics 2020 13:101Genome-wide identification of methylated CpG sites in nongenital cutaneous warts
Low-risk HPV infection has not been the subject of epigenetic investigation. The present study was carried out in order to investigate the methylation status of CpG sites in non-genital cutaneous warts.BMC Medical Genomics 2020 13:100Mitochondrial GWAS and association of nuclear – mitochondrial epistasis with BMI in T1DM patients
BMI is a strong indicator of complications from type I diabetes, especially under intensive treatment.BMC Medical Genomics 2020 13:97A rare Down syndrome foetus with de novo 21q;21q rearrangements causing false negative results in non-invasive prenatal testing: a case report
Non-invasive prenatal testing (NIPT) has been established as a routine prenatal screening to assess the risk of common foetal aneuploidy disorder (trisomy 21, 18, and 13). NIPT has high sensitivity and high sp...BMC Medical Genomics 2020 13:96Statistical driver genes as a means to uncover missing heritability for age-related macular degeneration
Age-related macular degeneration (AMD) is a progressive retinal disease contributing to blindness worldwide. Multiple estimates for AMD heritability (h2) exist; however, a substantial proportion of h2 is not attr...BMC Medical Genomics 2020 13:95Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples
Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently...BMC Medical Genomics 2020 13:94Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure
Left-sided heart failure (HF) is documented as a key prognostic factor in HF. However, the relative molecular mechanisms underlying left-sided HF is unknown. The purpose of this study is to unearth significant...BMC Medical Genomics 2020 13:93Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression
The role of histone modifications is poorly characterized in breast cancer, especially within the major subtypes. While epigenetic modifications may enhance the adaptability of a cell to both therapy and the s...BMC Medical Genomics 2020 13:92Genetic colocalization atlas points to common regulatory sites and genes for hematopoietic traits and hematopoietic contributions to disease phenotypes
Genetic associations link hematopoietic traits and disease end-points, but most causal variants and genes underlying these relationships are unknown. Here, we used genetic colocalization to nominate loci and g...BMC Medical Genomics 2020 13:89Long non-coding RNA profiling of pediatric Medulloblastoma
Medulloblastoma (MB) is one of the most common malignant cancers in children. MB is primarily classified into four subgroups based on molecular and clinical characteristics as (1) WNT (2) Sonic-hedgehog (SHH) ...BMC Medical Genomics 2020 13:87Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension
Pulmonary arterial hypertension (PAH) is a life-threatening condition. The aim of this study was to explore potential crucial genes and pathways associated with PAH based on integrative analyses of gene expres...BMC Medical Genomics 2020 13:86Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants
Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea an...BMC Medical Genomics 2020 13:85Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer
A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains ...BMC Medical Genomics 2020 13:84Using Ethereum blockchain to store and query pharmacogenomics data via smart contracts
As pharmacogenomics data becomes increasingly integral to clinical treatment decisions, appropriate data storage and sharing protocols need to be adopted. One promising option for secure, high-integrity storag...BMC Medical Genomics 2020 13:74Leukocyte telomere length in patients with transfusion-dependent thalassemia
Thalassemia is a hereditary hemolytic anemia with a severity ranging from mild, non-transfusion dependent to severe chronic anemia requiring lifelong transfusion. Transfusional iron overload is a major complic...BMC Medical Genomics 2020 13:73
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