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 serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots. METHOD:To facilitate the studies of the underlying mechanism, we developed a database named LDSplitDB which provides an integrative and interactive data mining and visualization platform for the genome-wide association studies of recombination hotspots. It contains the pre-computed association maps of the major histocompatibility complex (MHC) region in the 1000 Genomes Project and the HapMap Phase III datasets, and a genome-scale study of the European population from the HapMap Phase II dataset. Besides the recombination profiles, related data of genes, SNPs and different types of epigenetic modifications, which could be associated with meiotic recombination, are provided for comprehensive analysis. To meet the computational requirement of the rapidly increasing population genomics data, we prepared a lookup table of 400 haplotypes for recombination rate estimation using the well-known LDhat algorithm which includes all possible two-locus haplotype configurations. CONCLUSION:To the best of our knowledge, LDSplitDB is the first large-scale database for the association analysis of human recombination hotspots with DNA sequence polymorphisms. It provides valuable resources for the discovery of the mechanism of meiotic recombination hotspots. The information about MHC in this database could help understand the roles of recombination in human immune system. DATABASE URL: http://histone.scse.ntu.edu.sg/LDSplitDB.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Guo J,Chen H,Yang P,Lee YT,Wu M,Przytycka TM,Kwoh CK,Zheng Jdoi
10.1186/s12920-018-0351-0subject
Has Abstractpub_date
2018-04-20 00:00:00pages
27issue
Suppl 2issn
1755-8794pii
10.1186/s12920-018-0351-0journal_volume
11pub_type
杂志文章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: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 exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00757-2
更新日期:2020-07-29 00:00:00
abstract::During June 10-12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics rang...
journal_title:BMC medical genomics
pub_type: 社论
doi:10.1186/s12920-018-0448-5
更新日期:2019-01-31 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:Reliability of real-time PCR (RT-qPCR) data is dependent on the use of appropriate reference gene(s) for normalization. To date, no validated reference genes have been reported for normalizing gene expression in human myocardium. This study aimed to identify validated reference genes for use in gene expressi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-64
更新日期:2008-12-29 00:00:00
abstract:BACKGROUND:The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of s...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-20
更新日期:2013-06-10 00:00:00
abstract:BACKGROUND: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 outcome and the frequently strong noise due to microarray handling effects. Effective strategies to reso...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0187-4
更新日期:2016-06-10 00:00:00
abstract:BACKGROUND:The right dataset is essential to obtain the right insights in data science; therefore, it is important for data scientists to have a good understanding of the availability of relevant datasets as well as the content, structure, and existing analyses of these datasets. While a number of efforts are underway ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0411-5
更新日期:2018-11-20 00:00:00
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: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: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:One of the major goals of genomic medicine is the identification of causal genomic variants in a patient and their relation to the observed clinical phenotypes. Prioritizing the genomic variants by considering only the genotype information usually identifies a few hundred potential variants. Narrowing it dow...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0372-8
更新日期:2018-07-06 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: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:Aberrant epigenetic profiles are concomitant with a spectrum of developmental defects and diseases. Role of methylation is an increasingly accepted factor in the pathophysiology of diabetes and its associated complications. This study aims to examine the correlation between oxidative stress and methylation o...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-29
更新日期:2014-05-30 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 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: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:A molecular characterization of Alzheimer's Disease (AD) is the key to the identification of altered gene sets that lead to AD progression. We rely on the assumption that candidate marker genes for a given disease belong to specific pathogenic pathways, and we aim at unveiling those pathways stable across ti...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-55
更新日期:2011-07-05 00:00:00
abstract:BACKGROUND:Urothelial carcinoma (UC) is characterized by nonrandom chromosomal aberrations, varying from one or a few changes in early-stage and low-grade tumors, to highly rearranged karyotypes in muscle-invasive lesions. Recent array-CGH analyses have shed further light on the genomic changes underlying the neoplasti...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-3
更新日期:2008-01-31 00:00:00
abstract:BACKGROUND:DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related individual differences in the sensitivity to methylation rigorously, we performed a systematic anal...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0217-2
更新日期:2016-08-26 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:Type 1 diabetes (T1D) is a complex disease and harmful to human health, and most of the existing biomarkers are mainly to measure the disease phenotype after the disease onset (or drastic deterioration). Until now, there is no effective biomarker which can predict the upcoming disease (or pre-disease state) ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S2-S8
更新日期:2013-01-01 00:00:00
abstract::Sickle cell disease and β thalassemia are common severe diseases with little effective pathophysiologically-based treatment. Their phenotypic heterogeneity prompted genomic approaches to identify modifiers that ultimately might be exploited therapeutically. Fetal hemoglobin (HbF) is the major modulator of the phenotyp...
journal_title:BMC medical genomics
pub_type: 杂志文章,评审
doi:10.1186/s12920-015-0120-2
更新日期:2015-07-29 00:00:00
abstract:BACKGROUND:A clinical overlap exists between mosaic Neurofibromatosis Type 2 and sporadic Schwannomatosis conditions. In these cases a molecular analysis of tumors is recommended for a proper genetic diagnostics. This analysis is challenged by the fact that schwannomas in both conditions bear a somatic double inactivat...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0076-2
更新日期:2015-01-24 00:00:00
abstract:BACKGROUND:Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide. At present no reliable biomarkers are available to guide the management of this condition. Microarray technology may allow appropriate biomarkers to be identified but present platforms are lacking disease focus and are thu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-20
更新日期:2008-05-30 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:Uric acid is the primary byproduct of purine metabolism. Hyperuricemia is associated with body mass index (BMI), sex, and multiple complex diseases including gout, hypertension (HTN), renal disease, and type 2 diabetes (T2D). Multiple genome-wide association studies (GWAS) in individuals of European ancestry...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-17
更新日期:2011-02-04 00:00:00
abstract:BACKGROUND:At least 90% of human genes are alternatively spliced. Alternative splicing has an important function regulating gene expression and miss-splicing can contribute to risk for human diseases, including Alzheimer's disease (AD). METHODS:We developed a splicing decision model as a molecular mechanism to identif...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0453-8
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was f...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0397-z
更新日期:2018-10-11 00:00:00