Abstract:
BACKGROUND:Population stratification can cause spurious associations in a genome-wide association study (GWAS), and occurs when differences in allele frequencies of single nucleotide polymorphisms (SNPs) are due to ancestral differences between cases and controls rather than the trait of interest. Principal components analysis (PCA) is the established approach to detect population substructure using genome-wide data and to adjust the genetic association for stratification by including the top principal components in the analysis. An alternative solution is genetic matching of cases and controls that requires, however, well defined population strata for appropriate selection of cases and controls. RESULTS:We developed a novel algorithm to cluster individuals into groups with similar ancestral backgrounds based on the principal components computed by PCA. We demonstrate the effectiveness of our algorithm in real and simulated data, and show that matching cases and controls using the clusters assigned by the algorithm substantially reduces population stratification bias. Through simulation we show that the power of our method is higher than adjustment for PCs in certain situations. CONCLUSIONS:In addition to reducing population stratification bias and improving power, matching creates a clean dataset free of population stratification which can then be used to build prediction models without including variables to adjust for ancestry. The cluster assignments also allow for the estimation of genetic heterogeneity by examining cluster specific effects.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Solovieff N,Hartley SW,Baldwin CT,Perls TT,Steinberg MH,Sebastiani Pdoi
10.1186/1471-2156-11-108subject
Has Abstractpub_date
2010-12-09 00:00:00pages
108issn
1471-2156pii
1471-2156-11-108journal_volume
11pub_type
杂志文章相关文献
BMC GENETICS文献大全abstract:BACKGROUND:Cymbidium is a genus of 68 species in the orchid family, with extremely high ornamental value. Marker-assisted selection has proven to be an effective strategy in accelerating plant breeding for many plant species. Analysis of cymbidiums genetic background by molecular markers can be of great value in assist...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-014-0124-5
更新日期:2014-12-05 00:00:00
abstract:BACKGROUND:The Gpnmb gene encodes a transmembrane protein whose function(s) remain largely unknown. Here, we assess if a mutant allele of Gpnmb confers susceptibility to glaucoma by altering immune functions. DBA/2J mice have a mutant Gpnmb gene and they develop a form of glaucoma preceded by a pigment dispersing iris ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-30
更新日期:2008-04-10 00:00:00
abstract:BACKGROUND:The oxytocin (OT) system is known to be implicated in the regulation of complex social behavior, particularly empathy and parenting. The goal of this study was to estimate the gender and population differences in polymorphisms of two oxytocin receptor gene SNPs, rs53576 and rs2254298, in four populations. R...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0323-8
更新日期:2016-01-06 00:00:00
abstract:BACKGROUND:Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0607-x
更新日期:2018-04-03 00:00:00
abstract:BACKGROUND:Analyses of genetic data at the level of haplotypes provide increased accuracy and power to infer genotype-phenotype correlations and evolutionary history of a locus. However, empirical determination of haplotypes is expensive and laborious. Therefore, several methods of inferring haplotypes from unphased ge...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-5-22
更新日期:2004-08-03 00:00:00
abstract:BACKGROUND:Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poor...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-15
更新日期:2014-02-03 00:00:00
abstract:BACKGROUND:In mice MEOX2/TCF15 heterodimers are highly expressed in heart endothelial cells and are involved in the transcriptional regulation of lipid transport. In a general population, we investigated whether genetic variation in these genes predicted coronary heart disease (CHD). RESULTS:In 2027 participants rando...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0272-2
更新日期:2015-10-01 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:Despite several thousands of years of close contacts, there are genetic differences between the neighbouring countries of Finland and Sweden. Within Finland, signs of an east-west duality have been observed, whereas the population structure within Sweden has been suggested to be more subtle. With a fine-scal...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-54
更新日期:2008-08-19 00:00:00
abstract:BACKGROUND:Discerning the traits evolving under neutral conditions from those traits evolving rapidly because of various selection pressures is a great challenge. We propose a new method, composite selection signals (CSS), which unifies the multiple pieces of selection evidence from the rank distribution of its diverse...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-34
更新日期:2014-03-17 00:00:00
abstract:BACKGROUND:Spotted wilt caused by tomato spotted wilt virus (TSWV) is one of the major peanut (Arachis hypogaea L.) diseases in the southeastern United States. Occurrence, severity, and symptoms of spotted wilt disease are highly variable from season to season, making it difficult to efficiently evaluate breeding popul...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0435-9
更新日期:2016-09-06 00:00:00
abstract:BACKGROUND:Neutrophil cytosolic factor-1 (NCF1) is a component of NADPH oxidase. The NCF1 gene colocalizes with two pseudogenes (NCF1B and NCF1C). These two pseudogenes have a GT deletion in exon 2, resulting in a frameshift and an early stop codon. Here, we report a copy number variation (CNV) of the NCF1 pseudogenes ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-13
更新日期:2010-02-23 00:00:00
abstract:BACKGROUND:The disease gene of fragile X syndrome, FMR1 gene, encodes fragile X mental retardation protein (FMRP). The alternative splicing (AS) of FMR1 can affect the structure and function of FMRP. However, the biological functions of alternatively spliced isoforms remain elusive. In a previous study, we identified a...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00870-2
更新日期:2020-06-18 00:00:00
abstract:BACKGROUND:We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. RESULTS:Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One h...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-8
更新日期:2008-01-22 00:00:00
abstract:BACKGROUND:In this article, I propose a model-selection-free method to map multiple quantitative trait loci (QTL) in variance component model, which is useful in outbred populations. The new method can estimate the variance of zero-effect QTL infinitely to zero, but nearly unbiased for non-zero-effect QTL. It is analog...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-30
更新日期:2010-04-29 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:Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two major challenges arise in haplotype-based association analysis of family data. First, haplotypes may ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00902-x
更新日期:2020-09-07 00:00:00
abstract::Only one genome scan to date has attempted to make use of the longitudinal data available in the Framingham Heart Study, and this attempt yielded evidence of linkage to a gene for mean systolic blood pressure. We show how the additional information available in these longitudinal data can be utilized to examine linkag...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-S1-S82
更新日期:2003-12-31 00:00:00
abstract:BACKGROUND:The high mobility group A1 proteins (HMGA1a/HMGA1b) are highly conserved between mammalian species and widely described as participating in various cellular processes. By inducing DNA conformation changes the HMGA1 proteins indirectly influence the binding of various transcription factors and therefore effec...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-49
更新日期:2008-07-23 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:BACKGROUND:Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bu...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0671-2
更新日期:2018-09-20 00:00:00
abstract::An empirical comparison between three different methods for estimation of pair-wise identity-by-descent (IBD) sharing at marker loci was conducted in order to quantify the resulting differences in power and localization precision in variance components-based linkage analysis. On the examined simulated, error-free data...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-S1-S72
更新日期:2003-12-31 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:There have been inconsistent results from case-control studies assessing the association of the PON1 Q192R polymorphism with coronary heart disease (CHD). Most studies have included predominantly men and the association in women is unclear. Since lipid levels vary between the sexes the antioxidant effect of ...
journal_title:BMC genetics
pub_type: 杂志文章,meta分析,评审
doi:10.1186/1471-2156-5-17
更新日期:2004-06-23 00:00:00
abstract:BACKGROUND:Intronic DNA sequences of the canine arrestin (SAG) gene was screened to identify potential disease causing mutations in dogs with generalized progressive retinal atrophy (gPRA). The intronic sequences flanking each of the 16 exons were obtained from clones of a canine genomic library. RESULTS:Using polymer...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-3-12
更新日期:2002-07-17 00:00:00
abstract:BACKGROUND:Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this rese...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0596-1
更新日期:2018-01-15 00:00:00
abstract:BACKGROUND:Koala (Koa) is a dominant mutation in mice causing bushy muzzle and pinna, and is associated with a chromosomal inversion on the distal half of chromosome 15. To identify the gene responsible for the Koa phenotypes, we investigated phenotypes of Koa homozygous mice and determined the breakpoints of the inver...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-60
更新日期:2009-09-22 00:00:00
abstract:BACKGROUND:The current genetic structure of Iberian populations has presumably been affected by the complex orography of its territory, the different people and civilizations that settled there, its ancient and complex history, the diverse and persistent sociocultural patterns in its different regions, and also by the ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-37
更新日期:2007-06-27 00:00:00
abstract::A simple multipoint procedure to test for parent-of-origin effects in samples of affected siblings is discussed. The procedure consists of artificially changing all full sibs to half-sibs, with distinct mothers or fathers depending on the parental origin to be evaluated, then analyzing these families with commonly use...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S159
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Many QTL studies have two common features: (1) often there is missing marker information, (2) among many markers involved in the biological process only a few are causal. In statistics, the second issue falls under the headings "sparsity" and "causal inference". The goal of this work is to develop a two-step...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-14-125
更新日期:2013-12-30 00:00:00