Abstract:
BACKGROUND:Genotyping technologies enable us to genotype multiple Single Nucleotide Polymorphisms (SNPs) within selected genes/regions, providing data for haplotype association analysis. While haplotype-based association analysis is powerful for detecting untyped causal alleles in linkage-disequilibrium (LD) with neighboring SNPs/haplotypes, the inclusion of extraneous SNPs could reduce its power by increasing the number of haplotypes with each additional SNP. METHODS:Here, we propose a haplotype-based stepwise procedure (HBSP) to eliminate extraneous SNPs. To evaluate its properties, we applied HBSP to both simulated and real data, generated from a study of genetic associations of the bactericidal/permeability-increasing (BPI) gene with pulmonary function in a cohort of patients following bone marrow transplantation. RESULTS:Under the null hypothesis, use of the HBSP gave results that retained the desired false positive error rates when multiple comparisons were considered. Under various alternative hypotheses, HBSP had adequate power to detect modest genetic associations in case-control studies with 500, 1,000 or 2,000 subjects. In the current application, HBSP led to the identification of two specific SNPs with a positive validation. CONCLUSION:These results demonstrate that HBSP retains the essence of haplotype-based association analysis while improving analytic power by excluding extraneous SNPs. Minimizing the number of SNPs also enables simpler interpretation and more cost-effective applications.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Yang Y,Li SS,Chien JW,Andriesen J,Zhao LPdoi
10.1186/1471-2156-9-90subject
Has Abstractpub_date
2008-12-22 00:00:00pages
90issn
1471-2156pii
1471-2156-9-90journal_volume
9pub_type
杂志文章相关文献
BMC GENETICS文献大全abstract:BACKGROUND:Currently, a commonly used strategy for mapping complex quantitative traits is to use a genome-wide linkage analysis to narrow suspected genes to regions on a scale of centiMorgans (cM), followed by an association analysis to fine map the genetic variation in regions showing linkage. Two important questions ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-7-5
更新日期:2006-01-20 00:00:00
abstract:BACKGROUND:Oculocutaneous albinism (OCA) is an autosomal recessive hereditary pigmentation disorder affecting humans and several other animal species. Oculocutaneous albinism was studied in a herd of Murrah buffalo to determine the clinical presentation and genetic basis of albinism in this species. RESULTS:Clinical e...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-62
更新日期:2012-07-20 00:00:00
abstract:BACKGROUND:Genetic maps based on single-nucleotide polymorphisms (SNP) are increasingly being used as an alternative to microsatellite maps. This study compares linkage results for both types of maps for a neurophysiology phenotype and for an alcohol dependence phenotype. Our analysis used two SNP maps on the Illumina ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S122
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Genome-wide association studies involve detecting association between millions of genetic variants and a trait, which typically use univariate regression to test association between each single variant and the phenotype. Alternatively, Lasso penalized regression allows one to jointly model the relationship b...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0533-3
更新日期:2017-07-24 00:00:00
abstract:BACKGROUND:Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo)...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-33
更新日期:2008-04-19 00:00:00
abstract::Genetic epidemiologists have taken the challenge to identify genetic polymorphisms involved in the development of diseases. Many have collected data on large numbers of genetic markers but are not familiar with available methods to assess their association with complex diseases. Statistical methods have been developed...
journal_title:BMC genetics
pub_type: 社论
doi:10.1186/1471-2156-7-23
更新日期:2006-04-21 00:00:00
abstract:BACKGROUND:Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum. RESULTS:In the present study, 15 new EST-SSR markers were developed from publicly available ESTs...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0261-5
更新日期:2015-08-19 00:00:00
abstract:BACKGROUND:Kernel length is an important target trait in barley (Hordeum vulgare L.) breeding programs. However, the number of known quantitative trait loci (QTLs) controlling kernel length is limited. In the present study, we aimed to identify major QTLs for kernel length, as well as putative candidate genes that migh...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0438-6
更新日期:2016-09-13 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:DNA methylation is an epigenetic modification that mainly repress expression of genes essential during embryogenesis and development. There are key ATPase-dependent enzymes that read or write DNA methylation to remodel chromatin and regulate gene expression. Structural maintenance of chromosome hinge domain ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-0809-x
更新日期:2020-01-15 00:00:00
abstract:BACKGROUND:Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present st...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0736-x
更新日期:2019-03-26 00:00:00
abstract:BACKGROUND:Compared to model-based approaches, nonparametric methods for quantitative trait loci mapping are more robust to deviations in distributional assumptions. In this study, we modify a nonparametric regression method and the "contrast function"- based regression method to analyze total cholesterol level in the ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-S1-S92
更新日期:2003-12-31 00:00:00
abstract:BACKGROUND:Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular r...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-63
更新日期:2014-05-27 00:00:00
abstract:BACKGROUND:Pulmonary arterial hypertension (PAH) is a rare vascular disorder characterized by a capillary wedge pressure ≤ 15 mmHg and a mean pulmonary arterial pressure ≥ 25 mmHg at rest. PAH can be idiopathic, heritable or associated with other conditions. The aim of this study was to analyze the Endoglin (ENG) gene ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0384-3
更新日期:2016-06-04 00:00:00
abstract:BACKGROUND:African Americans experience disproportionately higher prevalence of type 2 diabetes and related risk factors. Little research has been done on the association of ADIPOQ gene on type 2 diabetes, plasma adiponectin, blood glucose, HOMA-IR and body mass index (BMI) in African Americans. The objective of our re...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0319-4
更新日期:2015-12-23 00:00:00
abstract:BACKGROUND:Heritable factors are well known to increase the risk of cancer in families. Known susceptibility genes account for a small proportion of all colorectal cancer cases. The aim of this study was to identify the genetic background in a family suggested to segregate a dominant cancer syndrome with a high risk of...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0351-z
更新日期:2016-02-13 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:This study aimed to explore the molecular mechanism of estrogen-mediated neuroprotection in the relief of cerebral ischemic injury. The gene expression profiles were downloaded from Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified using limma package in R software. ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0630-y
更新日期:2018-07-20 00:00:00
abstract:BACKGROUND:We propose a gene-level association test that accounts for individual relatedness and population structures in pedigree data in the framework of linear mixed models (LMMs). Our method data-adaptively combines the results across a class of score-based tests, only requiring fitting a single null model (under t...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0639-2
更新日期:2018-09-17 00:00:00
abstract:BACKGROUND:Anopheles gambiae females are the world's most successful vectors of human malaria. However, a fraction of these mosquitoes is refractory to Plasmodium development. L3-5, a laboratory selected refractory strain, encapsulates transforming ookinetes/early oocysts of a wide variety of Plasmodium species. Previo...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-16
更新日期:2003-10-24 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:BACKGROUND:The Glued gene of Drosophila melanogaster encodes the homologue of the vertebrate p150Glued subunit of dynactin. The Glued1 mutation compromises the dynein-dynactin retrograde motor complex and causes disruptions to the adult eye and the CNS, including sensory neurons and the formation of the giant fiber sys...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-77
更新日期:2009-11-30 00:00:00
abstract::The study of change in intermediate phenotypes over time is important in genetics. In this paper we explore a new approach to phenotype definition in the genetic analysis of longitudinal phenotypes. We utilized data from the longitudinal Framingham Heart Study Family Cohort to investigate the familial aggregation and ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-S1-S12
更新日期:2003-12-31 00:00:00
abstract:BACKGROUND:Egg production is the most economically-important trait in layers as it directly influences benefits of the poultry industry. To better understand the genetic architecture of egg production, we measured traits including age at first egg (AFE), weekly egg number (EN) from onset of laying eggs to 80 weeks whic...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0771-7
更新日期:2019-08-14 00:00:00
abstract:BACKGROUND:Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleoti...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0185-0
更新日期:2015-03-12 00:00:00
abstract::A thorough genetic mapping study was performed to identify predisposing genes for alcoholism dependence using the Collaborative Study on the Genetics of Alcoholism (COGA) data. The procedure comprised whole-genome linkage and confirmation analyses, single locus and haplotype fine mapping analyses, and gene x environme...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S30
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Acipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, high chromosome numbers, presence of numerous microchromosomes and propensity to interspecific hybridiz...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0484-8
更新日期:2017-03-02 00:00:00
abstract:BACKGROUND:Land plants have evolved several measures to maintain their life against abiotic stresses. The accumulation of proline is the most generalized response of plants under drought, heat or salt stress conditions. It is known as an osmoprotectant which also acts as an instant source of energy during drought recov...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-61
更新日期:2012-07-20 00:00:00
abstract:BACKGROUND:Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. RESULTS:In this work, 15 wheat CAMTA genes ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00916-5
更新日期:2020-09-14 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