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 other substances; cardiovascular; environmental exposures; cancer; psychiatric; neurology; and physical activity and physical fitness. Eligibility criteria for the current study included: living PMRP subjects with known addresses who consented to future contact and were not currently living in a nursing home, available GWAS data from eMERGE I for subjects where age-related cataract, HDL, dementia and resistant hypertension were the primary phenotypes, thus biasing the sample to the older PMRP participants. The questionnaires were mailed twice. Data from the PhenX measures were compared with information from PMRP questionnaires and data from Marshfield Clinic electronic medical records. RESULTS:Completed PhenX questionnaires were returned by 2271 subjects for a final response rate of 70%. The mean age reported on the PhenX questionnaire (73.1 years) was greater than the PMRP questionnaire (64.8 years) because the data were collected at different time points. The mean self-reported weight, and subsequently calculated BMI, were less on the PhenX survey than the measured values at the time of enrollment into PMRP (PhenX means 173.5 pounds and BMI 28.2 kg/m2 versus PMRP 182.9 pounds and BMI 29.6 kg/m2). There was 95.3% agreement between the two questionnaires about having ever smoked at least 100 cigarettes. 139 (6.2%) of subjects indicated on the PhenX questionnaire that they had been told they had a stroke. Of them, only 15 (10.8%) had no electronic indication of a prior stroke or TIA. All of the age-and gender-specific 95% confidence limits around point estimates for major depressive episodes overlap and show that 31% of women aged 50-64 reported symptoms associated with a major depressive episode. CONCLUSIONS:The approach employed resulted in a high response rate and valuable data for future gene/environment analyses. These results and high response rate highlight the utility of the PhenX Toolkit to collect valid phenotypic data that can be shared across groups to facilitate gene/environment studies.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
McCarty CA,Berg R,Rottscheit CM,Waudby CJ,Kitchner T,Brilliant M,Ritchie MDdoi
10.1186/1755-8794-7-3subject
Has Abstractpub_date
2014-01-14 00:00:00pages
3issn
1755-8794pii
1755-8794-7-3journal_volume
7pub_type
杂志文章abstract:BACKGROUND:Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-32
更新日期:2013-09-17 00:00:00
abstract:BACKGROUND:The gene expression profile of cytologically-normal bronchial airway epithelial cells has previously been shown to be altered in patients with lung cancer. Although bronchoscopy is often used for the diagnosis of lung cancer, its sensitivity is imperfect, especially for small and peripheral suspicious lesion...
journal_title:BMC medical genomics
pub_type: 杂志文章,多中心研究
doi:10.1186/s12920-015-0091-3
更新日期:2015-05-06 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:The noninvasive prenatal diagnosis procedures that are currently used to detect genetic diseases do not achieve desirable levels of sensitivity and specificity. Recently, fetal methylated DNA biomarkers in maternal peripheral blood have been explored for the noninvasive prenatal detection of genetic disorder...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-26
更新日期:2012-06-18 00:00:00
abstract:BACKGROUND:Infant birth weight is a complex quantitative trait associated with both neonatal and long-term health outcomes. Numerous studies have been published in which candidate genes (IGF1, IGF2, IGF2R, IGF binding proteins, PHLDA2 and PLAGL1) have been associated with birth weight, but these studies are difficult t...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-10
更新日期:2012-04-12 00:00:00
abstract:BACKGROUND:DNA methylation is thought to be extensively involved in the pathogenesis of many diseases, including major psychosis. However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expression. METHODS:We analyzed...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0139-4
更新日期:2015-10-14 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: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:Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients. METHODS:We designed a panel ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0475-x
更新日期:2019-01-28 00:00:00
abstract:BACKGROUND: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 Mendelian Randomization (MR). METHODS:We applied a two-sample MR approach to investigate the causal r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00769-y
更新日期:2020-08-26 00:00:00
abstract:BACKGROUND:We explored the imputation performance of the program IMPUTE in an admixed sample from Mexico City. The following issues were evaluated: (a) the impact of different reference panels (HapMap vs. 1000 Genomes) on imputation; (b) potential differences in imputation performance between single-step vs. two-step (...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-12
更新日期:2012-05-01 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: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...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0638-9
更新日期:2019-12-24 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: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:Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metast...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-56
更新日期:2008-11-11 00:00:00
abstract:BACKGROUND:Prevalence of obesity is increasing to pandemic proportions. However, obese subjects differ in insulin resistance, adipokine production and co-morbidities. Based on fasting plasma analysis, obese subjects were grouped as Low Acylation Stimulating protein (ASP) and Triglyceride (TG) (LAT) vs High ASP and TG (...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-3
更新日期:2010-01-27 00:00:00
abstract:BACKGROUND:Phelan-McDermid syndrome (PMS, OMIM#606232), or 22q13 deletion syndrome, is a rare genetic disorder caused by deletion of the distal long arm of chromosome 22 with a variety of clinical features that display considerably heterogeneous degrees of severity. The SHANK3 gene is understood to be the critical gene...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00802-0
更新日期:2020-10-06 00:00:00
abstract:BACKGROUND:Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0093-1
更新日期:2015-05-06 00:00:00
abstract:BACKGROUND:DNA methylation is a key epigenetic regulator contributing to cancer development. To understand the role of DNA methylation in tumorigenesis, it is important to investigate and compare differential methylation (DM) patterns between normal and case samples across different cancer types. However, current pan-c...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00780-3
更新日期:2020-10-22 00:00:00
abstract:BACKGROUND:Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstructive CAD likelihood would have diagnostic utility. RESULTS:Microarray analysis of RNA samples from...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-26
更新日期:2011-03-28 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:As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during the advanced stage of the disease and exhibits a low five-year survival rate. The importance of tumor microenvironment (TME) in tumor initiation and metastasis is widely recognized. In...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-0707-0
更新日期:2020-03-30 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: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:Birt-Hogg-Dubé syndrome (BHD) is an autosomal dominant disorder caused by germline mutations in the folliculin gene (FLCN). Nearly 150 pathogenic mutations have been identified in FLCN. The most frequent pattern is a frameshift mutation within a coding exon. In addition, splice-site mutations have been repor...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0359-5
更新日期:2018-05-02 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: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: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::In this issue of BMC Medical Genomics Griffin et al. present a user-friendly and freely accessible HIV-associated neurocognitive disorder (HAND) genomic database that compiles viral (HIV-1) genetic sequences and other relevant clinical and treatment data. We discuss the benefits and caveats of public data sharing in N...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-015-0150-9
更新日期:2015-11-11 00:00:00