Abstract:
BACKGROUND:With the increasing amount of high-throughput genomic sequencing data, there is a growing demand for a robust and flexible tool to perform interaction analysis. The identification of SNP-SNP, SNP-CpG, and higher order interactions helps explain the genetic etiology of human diseases, yet genome-wide analysis for interactions has been very challenging, due to the computational burden and a lack of statistical power in most datasets. RESULTS:The wtest R package performs association testing for main effects, pairwise and high order interactions in genome-wide association study data, and cis-regulation of SNP and CpG sites in genome-wide and epigenome-wide data. The software includes a number of post-test diagnostic and analysis functions and offers an integrated toolset for genetic epistasis testing. CONCLUSIONS:The wtest is an efficient and powerful statistical tool for integrated genetic epistasis testing. The package is available in CRAN: https://CRAN.R-project.org/package=wtest.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Sun R,Xia X,Chong KC,Zee BC,Wu WKK,Wang MHdoi
10.1186/s12920-019-0638-9subject
Has Abstractpub_date
2019-12-24 00:00:00pages
180issue
Suppl 9issn
1755-8794pii
10.1186/s12920-019-0638-9journal_volume
12pub_type
杂志文章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:In addition to their well-documented ocular therapeutic effects, glucocorticoids (GCs) can cause sight-threatening side-effects including ocular hypertension presumably via morphological and biochemical changes in trabecular meshwork (TM) cells. In the present study, we directly compared the glucocorticoid r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-58
更新日期:2009-09-10 00:00:00
abstract:BACKGROUND:Integrating multiple data sources is indispensable in improving disease gene identification. It is not only due to the fact that disease genes associated with similar genetic diseases tend to lie close with each other in various biological networks, but also due to the fact that gene-disease associations are...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-8-S3-S2
更新日期:2015-01-01 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:The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-19
更新日期:2012-05-30 00:00:00
abstract:BACKGROUND:Urothelial carcinoma (UC) can arise at any location along the urothelial tract, including the urethra, bladder, ureter, or renal pelvis. Although tumors arising in these various locations have similar morphology, it is unclear whether the gene expression profiles are similar between the upper-tract (ureter a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-58
更新日期:2010-12-15 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:Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this study was to identify general and clinical-dependent biomarker genes and biological processes of three...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-49
更新日期:2011-06-07 00:00:00
abstract:BACKGROUND:Gulf War Illness (GWI) is a complex multi-symptom disorder that affects up to one in three veterans of this 1991 conflict and for which no effective treatment has been found. Discovering novel treatment strategies for such a complex chronic illness is extremely expensive, carries a high probability of failur...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0111-3
更新日期:2015-07-09 00:00:00
abstract:BACKGROUND: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. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. MET...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00743-8
更新日期:2020-07-17 00:00:00
abstract: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...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0282-1
更新日期:2017-07-26 00:00:00
abstract:BACKGROUND:The purpose of this paper is to describe the data collection efforts and validation of PhenX measures in the Personalized Medicine Research Project (PMRP) cohort. METHODS:Thirty-six measures were chosen from the PhenX Toolkit within the following domains: demographics; anthropometrics; alcohol, tobacco and ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-3
更新日期:2014-01-14 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:Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and micro RNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interactio...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0570-z
更新日期:2019-08-23 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:Glioblastoma multiforme (GBM) tends to occur between the ages of 45 and 70. This relatively early onset and its poor prognosis make the impact of GBM on public health far greater than would be suggested by its relatively low frequency. Tissue and blood samples have now been collected for a number of populati...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-63
更新日期:2011-08-09 00:00:00
abstract:BACKGROUND:Images embedded in biomedical publications carry rich information that often concisely summarize key hypotheses adopted, methods employed, or results obtained in a published study. Therefore, they offer valuable clues for understanding main content in a biomedical publication. Prior studies have pointed out ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S3-S8
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:With the introduction of increasingly powerful mass spectrometry (MS) techniques for clinical research, several recent large-scale MS proteomics studies have sought to characterize the entire human plasma proteome with a general objective for identifying thousands of proteins leaked from tissues in the circu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-12
更新日期:2008-04-25 00:00:00
abstract:BACKGROUND:The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcinogenesis and human cancer are operating in zebrafish. In order to determine the potential of zebrafis...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-41
更新日期:2011-05-16 00:00:00
abstract:BACKGROUND:Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0395-1
更新日期:2018-09-04 00:00:00
abstract:BACKGROUND:Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While a number of studies have proposed molecular signatures that characterize the spectrum of such transi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-017-0252-7
更新日期:2017-03-09 00:00:00
abstract:BACKGROUND:Expression quantitative trait loci (eQTL) are genomic regions regulating RNA transcript expression levels. Genome-wide Association Studies (GWAS) have identified many variants, often in non-coding regions, with unknown functions and eQTL provide a possible mechanism by which these variants may influence obse...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-31
更新日期:2014-06-03 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:While BMPR2 mutation strongly predisposes to pulmonary arterial hypertension (PAH), only 20% of mutation carriers develop clinical disease. This finding suggests that modifier genes contribute to FPAH clinical expression. Since modifiers are likely to be common alleles, this problem is not tractable by tradi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-45
更新日期:2008-09-29 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:Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-6
更新日期:2012-01-30 00:00:00
abstract:BACKGROUND:Prognostic signatures are vital to precision medicine. However, development of somatic mutation prognostic signatures for cancers remains a challenge. In this study we developed a novel method for discovering somatic mutation based prognostic signatures. RESULTS:Somatic mutation and clinical data for lung a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0454-7
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:The mechanisms underlying neurodegeneration in the striatum of Huntingon's Disease (HD) brain are currently unknown. While the striatum is massively degenerated in symptomatic individuals, which makes cellular characterization difficult, it is largely intact in asymptomatic HD gene positive (HD+) individuals...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0581-9
更新日期:2019-10-16 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: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