Characterization 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 13:84MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
The majority of copy number callers requires high read coverage data that is often achieved with elevated material input, which increases the heterogeneity of tissue samples. However, to gain insights into sma...BMC Medical Genomics 2020 13:76Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining study
Recurrent pregnancy loss (RPL) is a significant adverse pregnancy complication, with an incompletely understood pathology. While many entities were proposed to elucidate the pathogenic basis of RPL, only few w...BMC Medical Genomics 2020 13:75Using 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 13:73Mitochondrial tRNA methylation in Alzheimer’s disease and progressive supranuclear palsy
Methylation of mitochondrial tRNAs (mt-tRNA) at the 9th position (“p9 site”) is known to impact translational efficiency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation ...BMC Medical Genomics 2020 13:71The diagnostic yield of intellectual disability: combined whole genome low-coverage sequencing and medical exome sequencing
Intellectual disability (ID) is a heterogeneous neurodevelopmental disorder with a complex genetic underpinning in its etiology. Chromosome microarray (CMA) is recommended as the first-tier diagnostic test for...BMC Medical Genomics 2020 13:70ERα-related chromothripsis enhances concordant gene transcription on chromosome 17q11.1-q24.1 in luminal breast cancer
Chromothripsis is an event of genomic instability leading to complex chromosomal alterations in cancer. Frequent long-range chromatin interactions between transcription factors (TFs) and targets may promote ex...BMC Medical Genomics 2020 13:69Molecular diagnosis in recessive pediatric neurogenetic disease can help reduce disease recurrence in families
The causes for thousands of individually rare recessive diseases have been discovered since the adoption of next generation sequencing (NGS). Following the molecular diagnosis in older children in a family, pa...BMC Medical Genomics 2020 13:68MyoMiner: explore gene co-expression in normal and pathological muscle
High-throughput transcriptomics measures mRNA levels for thousands of genes in a biological sample. Most gene expression studies aim to identify genes that are differentially expressed between different biolog...BMC Medical Genomics 2020 13:67Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1
Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11.22 duplication patients and is associated with nonsyndromic ...BMC Medical Genomics 2020 13:66Modified entropy-based procedure detects gene-gene-interactions in unconventional genetic models
Since it is assumed that genetic interactions play an important role in understanding the mechanisms of complex diseases, different statistical approaches have been suggested in recent years for this task. One...BMC Medical Genomics 2020 13:65Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood
Circular RNAs are non-coding RNA molecules with gene regulatory potential that have been associated with several human diseases. They are stable and present in the circulation, making them excellent candidates...BMC Medical Genomics 2020 13:64A case report of familial 4q13.3 microdeletion in three individuals with syndromic intellectual disability
Interstitial 4q deletions are rare chromosomal alterations. Most of the previously reported deletions involving the 4q13.3 region are large chromosomal alterations with a common loss of band 4q21 resulting in ...BMC Medical Genomics 2020 13:63Prevalence of clinically actionable disease variants in exceptionally long-lived families
Phenotypic expression of pathogenic variants in individuals with no family history of inherited disorders remains unclear.BMC Medical Genomics 2020 13:61Absolute measurement of the tissue origins of cell-free DNA in the healthy state and following paracetamol overdose
Despite the emergence of cell-free DNA (cfDNA) as a clinical biomarker in cancer, the tissue origins of cfDNA in healthy individuals have to date been inferred only by indirect and relative measurement methods...BMC Medical Genomics 2020 13:60E. coli diversity: low in colorectal cancer
Escherichia coli are mostly commensals but also contain pathogenic lineages. It is largely unclear whether the commensal E. coli as the potential origins of pathogenic lineages may consist of monophyletic or poly...BMC Medical Genomics 2020 13:59Comprehensive chromosomal aberrations in a case of a patient with TCF3-HLF-positive BCP-ALL
The use of high-throughput analytical techniques has enabled the description of acute lymphoblastic leukaemia (ALL) subtypes. The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with...BMC Medical Genomics 2020 13:58Differential co-expression analysis reveals early stage transcriptomic decoupling in alzheimer’s disease
Alzheimer’s disease (AD) is one of the leading causes of death in the US and there is no validated drugs to stop, slow or prevent AD. Despite tremendous effort on biomarker discovery, existing findings are mos...BMC Medical Genomics 2020 13(Suppl 5):53This article is part of a Supplement: Volume 13 Supplement 5Pseudogene-gene functional networks are prognostic of patient survival in breast cancer
Given the vast range of molecular mechanisms giving rise to breast cancer, it is unlikely universal cures exist. However, by providing a more precise prognosis for breast cancer patients through integrative mo...BMC Medical Genomics 2020 13(Suppl 5):51This article is part of a Supplement: Volume 13 Supplement 5Highly robust model of transcription regulator activity predicts breast cancer overall survival
While several multigene signatures are available for predicting breast cancer prognosis, particularly in early stage disease, effective molecular indicators are needed, especially for triple-negative carcinoma...BMC Medical Genomics 2020 13(Suppl 5):49This article is part of a Supplement: Volume 13 Supplement 5The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics
In this editorial, we briefly summarized the International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019) that was held on June 9–11, 2019 at Columbus, Ohio, USA. We further introduced the 19...BMC Medical Genomics 2020 13(Suppl 5):47This article is part of a Supplement: Volume 13 Supplement 5Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets
With the development of next generation sequencing (NGS) technology and genotype imputation methods, statistical methods have been proposed to test a set of genomic variants together to detect if any of them i...BMC Medical Genomics 2020 13(Suppl 5):46This article is part of a Supplement: Volume 13 Supplement 5An integrative, genomic, transcriptomic and network-assisted study to identify genes associated with human cleft lip with or without cleft palate
Cleft lip with or without cleft palate (CL/P) is one of the most common congenital human birth defects. A combination of genetic and epidemiology studies has contributed to a better knowledge of CL/P-associate...BMC Medical Genomics 2020 13(Suppl 5):39This article is part of a Supplement: Volume 13 Supplement 5
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