Abstract:
:The genetic study of disease-associated phenotypes has become common because such phenotypes are often easier to measure and in many cases are under greater genetic control than the complex disease itself. Some disease-associated phenotypes are rare, however, making it difficult to evaluate their effects due to small informative sample sizes. In addition, analyzing numerous phenotypes introduces the issue of multiple comparisons. To address these issues, we have developed a hierarchical model (HM) for multiple phenotypes that provides more accurate effect estimates with a lower false-positive rate. We evaluated the validity and power of HM in association studies of multiple phenotypes using randomly selected cases and controls from the simulated data set in the Genetic Analysis Workshop 14. In particular, we first analyzed the association between each of the 12 subclinical phenotypes and single-nucleotide polymorphisms within the known causal loci using a conventional logistic regression model (LRM). Then we added a second-stage model by regressing all of the logistic coefficients of the phenotypes obtained from LRM on a Z matrix that incorporates the clinical correlation of the phenotypes. Specially, the 12 phenotypes were grouped into 3 clusters: 1) communally shared emotions; 2) behavioral related; and 3) anxiety related. A semi-Bayes HM effect estimate for each phenotype was calculated and compared with those from LRM. We observed that using HM to evaluate the association between SNPs and multiple related phenotypes slightly increased power for detecting the true associations and also led to fewer false-positive results.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Liu X,Jorgenson E,Witte JSdoi
10.1186/1471-2156-6-S1-S104keywords:
subject
Has Abstractpub_date
2005-12-30 00:00:00pages
S104issn
1471-2156pii
1471-2156-6-S1-S104journal_volume
6 Suppl 1pub_type
杂志文章相关文献
BMC GENETICS文献大全abstract:BACKGROUND:Hybrid breakdown has been well documented in various species. Relationships between genomic heterozygosity and traits-fitness have been extensively explored especially in the natural populations. But correlations between genomic heterozygosity and vegetative and reproductive traits in cotton interspecific po...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0366-5
更新日期:2016-04-12 00:00:00
abstract:BACKGROUND:Structured association mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required t...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-24
更新日期:2012-04-03 00:00:00
abstract:BACKGROUND:Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing of mtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from North America and Europe are genetically distinct. These observations are supported by karyotype ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-105
更新日期:2010-11-23 00:00:00
abstract:BACKGROUND:Boar taint is an unpleasant condition of pork, mainly due to the accumulation of androstenone and skatole in male pigs at onset of puberty. This condition is the cause of considerable economic losses in the pig industry and the most common practice to control it is to castrate male piglets. Because of the ec...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-35
更新日期:2011-04-20 00:00:00
abstract:BACKGROUND:The cultivated peanut (Arachis hypogaea L.) is an important oil and food crop in the world. Pod- and kernel-related traits are direct factors involved in determining the yield of the peanut. However, the genetic basis underlying pod- and kernel-related traits in the peanut remained largely unknown, which ham...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0337-x
更新日期:2016-01-25 00:00:00
abstract:BACKGROUND:Grass carp (Ctenopharyngodon idellus, GC), as the highest-output fish in China, is economically important. The production of gynogenetic grass carp (GGC) will provide important germplasm resource for producing improved GC. At present, knowledge regarding the heterologous sperm DNA in gynogenetic offspring is...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0712-x
更新日期:2019-01-07 00:00:00
abstract:BACKGROUND:Dyslexia is a polygenic speech and language disorder characterized by an unexpected difficulty in reading in children and adults despite normal intelligence and schooling. Increasing evidence reveals that different speech and language disorders could share common genetic factors. As previous study reported a...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0172-5
更新日期:2015-02-03 00:00:00
abstract:BACKGROUND:Lone atrial flutter (AFL) and atrial fibrillation (AF) are common and sometimes consequential cardiac conduction disorders with a strong heritability, as underlined by recent genome-wide association studies that identified genetic modifiers. Follow-up family-based genetic analysis also identified Mendelian t...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0177-0
更新日期:2015-02-11 00:00:00
abstract:BACKGROUND:Hexaploid wheat (Triticum aestivum L.) possesses a large genome that contains 1.6 x 1010 bp of DNA. Isolation of a large number of gene sequences from complex gene families with a high level of gene sequence identity from genomic DNA is therefore difficult and time-consuming. Bacterial artificial chromosome ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-18
更新日期:2007-05-04 00:00:00
abstract:BACKGROUND:MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immu...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-57
更新日期:2012-07-13 00:00:00
abstract:BACKGROUND:Feed efficiency is one of the major components determining costs of animal production. Residual feed intake (RFI) is defined as the difference between the observed and the expected feed intake given a certain production. Residual feed intake 1 (RFI1) was calculated based on regression of individual daily fee...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-27
更新日期:2014-02-17 00:00:00
abstract:BACKGROUND:A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems le...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-73
更新日期:2008-11-18 00:00:00
abstract:BACKGROUND:Grain zinc and iron concentration is a complex trait that is controlled by quantitative trait loci (QTL) and is important for maintaining body health. Despite the substantial effort that has been put into identifying QTL for grain zinc and iron concentration, the integration of independent QTL is useful for ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0176-1
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:Previous investigations have highlighted the importance of genetic variation in the determination of bitter tasting ability, however have left unaddressed questions as to within group variation in tasting ability or the possibility of genetic prescription of intermediate tasting ability. Our aim was to exami...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-51
更新日期:2007-07-28 00:00:00
abstract:BACKGROUND:Retinal function is ordered by interactions between transcriptional and posttranscriptional regulators at the molecular level. These regulators include transcription factors (TFs) and posttranscriptional factors such as microRNAs (miRs). Some studies propose that miRs predominantly target the TFs rather than...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0201-4
更新日期:2015-04-24 00:00:00
abstract::Previous genome scan linkage analyses of the disease Kofendrerd Personality Disorder (KPD) with microsatellites led to detect some regions on chromosomes 1, 3, 5, and 9 that were identical for the three populations AI, KA, and DA but with large differences in significance levels. These differences in results may be ex...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S140
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Non-synonymous polymorphisms within the prion protein gene (PRNP) influence the susceptibility and incubation time for transmissible spongiform encephalopathies (TSE) in some species such as sheep and humans. In cattle, none of the known polymorphisms within the PRNP coding region has a major influence on su...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-15
更新日期:2007-04-16 00:00:00
abstract:BACKGROUND:Arabian horses are commonly believed to be one of the oldest and the most popular horse breeds in the world, characterized by favourable stamina traits and exercise phenotypes. During intensive training, the rates of lactate production and utilization are critical to avoid muscle fatigue and a decrease in ex...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0774-4
更新日期:2019-09-11 00:00:00
abstract:BACKGROUND:Studies on genetic effects of coffee consumption are scarce for Asian populations. We conducted a genome-wide association study (GWAS) of habitual coffee consumption in Japan using a self-reporting online survey. RESULTS:Candidate genetic loci associated with habitual coffee consumption were searched within...
journal_title:BMC genetics
pub_type: 杂志文章,meta分析
doi:10.1186/s12863-019-0763-7
更新日期:2019-07-26 00:00:00
abstract:BACKGROUND:Cytoplasmic effects on agronomic traits--involving cytoplasmic and nuclear genomes of either different species or different cultivars--are well documented in wheat but have seldom been demonstrated in rice (Oryza sativa L.). To detect cytoplasmic effects, we introgressed the nuclear genomes of three indica c...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-53
更新日期:2011-06-01 00:00:00
abstract:BACKGROUND:Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations to high-altitude adaptation in Asiatic toads (Bufo gargarizans), we implemented a reciprocal transpla...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0529-z
更新日期:2017-07-03 00:00:00
abstract:BACKGROUND:Two key questions in understanding the genetic control of behaviors are: what genes are involved and how these genes interact. To answer these questions at a systems level, we conducted high-content profiling of Drosophila larval locomotor behaviors for over 100 genotypes. RESULTS:We studied 69 genes whose ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0513-7
更新日期:2017-05-12 00:00:00
abstract:BACKGROUND:Many QTL have been detected in pigs, but very few of them have been fine-mapped up to the causal mutation. On SSC2, the IGF2-intron3-G3072A mutation has been described as the causative polymorphism for a QTL underlying muscle mass and backfat deposition, but further studies have demonstrated that at least on...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-92
更新日期:2011-10-27 00:00:00
abstract:BACKGROUND:The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-58
更新日期:2011-07-04 00:00:00
abstract:BACKGROUND:ENU-mutagenesis is a powerful technique to identify genes regulating mammalian development. To functionally annotate the distal region of mouse chromosome 4, we performed an ENU-mutagenesis screen using a balancer chromosome targeted to this region of the genome. RESULTS:We isolated 11 lethal lines that map...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-12
更新日期:2009-03-06 00:00:00
abstract:BACKGROUND:Hu sheep, a unique Chinese breed with high reproductive performance, are also well known for their rare white lambskin in China. The quality of lambskin is affected by hair follicles, and dermal papilla cells are an important component of hair follicles that plays a key role in hair follicle growth and devel...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0770-8
更新日期:2019-08-27 00:00:00
abstract:BACKGROUND:Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-21
更新日期:2011-01-31 00:00:00
abstract:BACKGROUND:Human glycosylase IV is involved in GLUT2 transporter regulation in pancreatic beta cells. A KO of this gene along with a high fat diet in a mice model has been associated with the development of type 2 diabetes (T2D). The aims of this study were to measure and compare the MGAT4A mRNA levels in white blood c...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-73
更新日期:2007-10-22 00:00:00
abstract:BACKGROUND:The Tnfrh1 gene (gene symbol Tnfrsf23) is located near one end of a megabase-scale imprinted region on mouse distal chromosome 7, about 350 kb distant from the nearest known imprinting control element. Within 20 kb of Tnfrh1 is a related gene called Tnfrh2 (Tnfrsf22) These duplicated genes encode putative de...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-3-11
更新日期:2002-06-27 00:00:00
abstract:BACKGROUND:Genomic information can be used to predict not only continuous but also categorical (e.g. binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-87
更新日期:2014-07-22 00:00:00