Abstract:
BACKGROUND:Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse sample of asthmatic children and to assess subphenotype-specific genetic ancestry in African-American asthmatic children. METHODS:A total of 1211 asthmatic children including 813 in the Childhood Asthma Management Program and 398 in the Childhood Asthma Research and Education program were studied. Unsupervised cluster analysis on clinical phenotypes was conducted to identify homogeneous subphenotypes. Subphenotype-specific genetic ancestry was estimated for 167 African-American asthmatic children. Genetic ancestry association with subphenotypes/clinical phenotypes were determined. RESULTS:Three distinct subphenotypes were identified: a moderate atopic dermatitis (AD) group with negative skin prick test (SPT) and preserved lung function; a high AD group with positive SPT and airway hyperresponsiveness; and a low AD group with positive SPT and lower lung function. African ancestry at asthma genome-wide association study (GWAS) SNPs differed between subphenotypes (64, 89, and 94% for the three subphenotypes, respectively) and was inversely correlated with AD; each additional 10% increase in African ancestry was associated with 1.5 fold higher in IgE and 6.3 higher odds of positive SPT (all p-values < 0.0001). CONCLUSIONS:By conducting phenotype-based cluster analysis and assessing subphenotype-specific genetic ancestry, we were able to identify homogeneous subphenotypes for childhood asthma that showed significant variation in genetic ancestry of African-American asthmatic children. This finding demonstrates the utility of these complementary approaches to understand and refine childhood asthma subphenotypes and enable more targeted therapy.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Ding L,Li D,Wathen M,Altaye M,Mersha TBdoi
10.1186/s12920-018-0367-5subject
Has Abstractpub_date
2018-05-31 00:00:00pages
51issue
1issn
1755-8794pii
10.1186/s12920-018-0367-5journal_volume
11pub_type
杂志文章abstract:BACKGROUND:To explore long-non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression profiles and their biological functions in the urine samples in calcium oxalate (CaOx) patients. METHODS:Five CaOx kidney stone patients were recruited in CaOx stone group and six healthy people were included as co...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0502-y
更新日期:2019-04-29 00:00:00
abstract:BACKGROUND:Despite being caused by mutations in different genes, diseases in the same phenotypic series are clinically similar, as reported in Part I of this study. Here, in Part II, we hypothesized that the phenotypic series too might be clinically similar. Furthermore, on the assumption that gene mutations indirectly...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00793-y
更新日期:2020-09-24 00:00:00
abstract:BACKGROUND:Rhodesiense sleeping sickness is caused by infection with T. b rhodesiense parasites resulting in an acute disease that is fatal if not treated in time. The aim of this study was to understand the global impact of active T. b rhodesiense infection on the patient's immune response in the early and late stages...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-0666-5
更新日期:2020-01-30 00:00:00
abstract:BACKGROUND:Bladder cancer has numerous genomic features that are potentially actionable by targeted agents. Nevertheless, both pre-clinical and clinical research using molecular targeted agents have been very limited in bladder cancer. RESULTS:We created the Genomics of Drug Sensitivity in Bladder Cancer (GDBC) databa...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0406-2
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:The early diagnosis of lung cancer has been a critical problem in clinical practice for a long time and identifying differentially expressed gene as disease marker is a promising solution. However, the most existing gene differential expression analysis (DEA) methods have two main drawbacks: First, these met...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0630-4
更新日期:2019-12-20 00:00:00
abstract: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, a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0297-7
更新日期:2017-10-06 00:00:00
abstract:BACKGROUND: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 interesting approach is the entropy-based IGENT method by Kwon et al. that promises an efficient de...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-0703-4
更新日期:2020-04-23 00:00:00
abstract:BACKGROUND:Balanced reciprocal chromosomal translocations (RCTs) are the ones of the most common structural aberrations in the population, with an incidence of 1:625. RCT carriers usually do not demonstrate changes in phenotype, except when the translocation results in gene interruption. However, these people are at ri...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0384-4
更新日期:2018-08-20 00:00:00
abstract:BACKGROUND:Current prostate cancer prognostic models are based on pre-treatment prostate specific antigen (PSA) levels, biopsy Gleason score, and clinical staging but in practice are inadequate to accurately predict disease progression. Hence, we sought to develop a molecular panel for prostate cancer progression by re...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-8
更新日期:2010-03-16 00:00:00
abstract:BACKGROUND:While most pediatric sarcomas respond to front-line therapy, some bone sarcomas do not show radiographic response like soft-tissue sarcomas (rhabdomyosarccomas) but do show 90% necrosis. Though, new therapies are urgently needed to improve survival and quality of life in pediatric patients with sarcomas. Com...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0456-5
更新日期:2019-01-31 00:00:00
abstract:BACKGROUNDS:Recent large-scale genetic studies often involve clustered phenotypes such as repeated measurements. Compared to a series of univariate analyses of single phenotypes, an analysis of clustered phenotypes can be useful for substantially increasing statistical power to detect more genetic associations. Moreove...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0517-4
更新日期:2019-07-11 00:00:00
abstract:BACKGROUND:Acute erythro- and megakaryoblastic leukaemias are associated with very poor prognoses and the mechanism of blastic transformation is insufficiently elucidated. The murine Graffi leukaemia retrovirus induces erythro- and megakaryoblastic leukaemias when inoculated into NFS mice and represents a good model to...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-2
更新日期:2010-01-26 00:00:00
abstract:BACKGROUND:Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0404-4
更新日期:2018-10-20 00:00:00
abstract:BACKGROUND:Inflammation is a hallmark of many human diseases. Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research. When primary pathogenetic events remains unclear due to its immense complexity, construction and analysis of the gene regulatory netw...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-46
更新日期:2008-09-30 00:00:00
abstract:BACKGROUND:Gastric emptying is impaired in patients with gastroparesis whereas it is either unchanged or accelerated in obese individuals. The goal of the current study was to identify changes in gene expression in the stomach muscularis that may be contributing to altered gastric motility in idiopathic gastroparesis a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0550-3
更新日期:2019-06-20 00:00:00
abstract:BACKGROUND:Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. Th...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S1-S10
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely influenced by the rate of aqueous humor production by ciliary processes ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0177-6
更新日期:2016-03-22 00:00:00
abstract:BACKGROUND:According to the Genetic Analysis Workshops (GAW), hundreds of thousands of SNPs have been tested for association with rheumatoid arthritis. Traditional genome-wide association studies (GWAS) have been developed to identify susceptibility genes using a "most significant SNPs/genes" model. However, many minor...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-38
更新日期:2010-08-20 00:00:00
abstract:BACKGROUND: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 adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0226-1
更新日期:2016-10-19 00:00:00
abstract:BACKGROUND:Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serio...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0351-0
更新日期:2018-04-20 00:00:00
abstract:BACKGROUND:Cancer cells are characterized by massive dysegulation of physiological cell functions with considerable disruption of transcriptional regulation. Genome-wide transcriptome profiling can be utilized for early detection and molecular classification of cancers. Accurate discrimination of functionally different...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-53
更新日期:2011-06-30 00:00:00
abstract:BACKGROUND:Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization....
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-49
更新日期:2009-08-05 00:00:00
abstract:BACKGROUND:Recent advances in whole-genome association studies (WGASs) for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-62
更新日期:2008-12-18 00:00:00
abstract:BACKGROUND:The growing advances in DNA sequencing tools have made analyzing the human genome cheaper and faster. While such analyses are intended to identify complex variants, related to disease susceptibility and efficacy of drug responses, they have blurred the definitions of mutation and polymorphism. DISCUSSION:In...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0115-z
更新日期:2015-07-15 00:00:00
abstract:BACKGROUND:A plethora of cases are reported in the literature with iso- and ring-chromosome 18. However, co-occurrence of these two abnormalities in an individual along with a third cell line and absence of numerical anomaly is extremely rare. CASE PRESENTATION:A 7-year-old female was referred for diagnosis due to gro...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00796-9
更新日期:2020-09-24 00:00:00
abstract:BACKGROUND:Cardiac pathological hypertrophy is associated with a significantly increased risk of coronary heart disease and has been observed in diabetic patients treated with rosiglitazone whereas most published studies do not suggest a similar increase in risk of cardiovascular events in pioglitazone-treated diabetic...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-35
更新日期:2014-06-17 00:00:00
abstract:BACKGROUND:Hypermethylation of promoter CpG islands with associated loss of gene expression, and hypomethylation of CpG-rich repetitive elements that may destabilize the genome are common events in most, if not all, epithelial cancers. METHODS:The methylation of 6,502 CpG-rich sequences spanning the genome was analyze...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-47
更新日期:2008-09-30 00:00:00
abstract:BACKGROUND:Postmenopausal hormone therapy (HT) influences endogenous hormone concentrations and increases the risk of breast cancer. Gene expression profiling may reveal the mechanisms behind this relationship.Our objective was to explore potential associations between sex hormones and gene expression in whole blood fr...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-29
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:Intra-tumor heterogeneity stems from genetic, epigenetic, functional, and environmental differences among tumor cells. A major source of genetic heterogeneity comes from DNA sequence differences and/or whole chromosome and focal copy number variations (CNVs). Whole chromosome CNVs are caused by chromosomal i...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0532-5
更新日期:2019-05-31 00:00:00
abstract:BACKGROUND:Systemic sclerosis (SSc), a multi-organ disorder, is characterized by vascular abnormalities, dysregulation of the immune system, and fibrosis. The mechanisms underlying tissue pathology in SSc have not been entirely understood. This study intended to investigate the common and tissue-specific pathways invol...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0632-2
更新日期:2019-12-27 00:00:00