Abstract:
:Genotype data from the Illumina Linkage III SNP panel (n = 4,720 SNPs) and the Affymetrix 10 k mapping array (n = 11,120 SNPs) were used to test the effects of linkage disequilibrium (LD) between SNPs in a linkage analysis in the Collaborative Study on the Genetics of Alcoholism pedigree collection (143 pedigrees; 1,614 individuals). The average r2 between adjacent markers across the genetic map was 0.099 +/- 0.003 in the Illumina III panel and 0.17 +/- 0.003 in the Affymetrix 10 k array. In order to determine the effect of LD between marker loci in a nonparametric multipoint linkage analysis, markers in strong LD with another marker (r2 > 0.40) were removed (n = 471 loci in the Illumina panel; n = 1,804 loci in the Affymetrix panel) and the linkage analysis results were compared to the results using the entire marker sets. In all analyses using the ALDX1 phenotype, 8 linkage regions on 5 chromosomes (2, 7, 10, 11, X) were detected (peak markers p < 0.01), and the Illumina panel detected an additional region on chromosome 6. Analysis of the same pedigree set and ALDX1 phenotype using short tandem repeat markers (STRs) resulted in 3 linkage regions on 3 chromosomes (peak markers p < 0.01). These results suggest that in this pedigree set, LD between loci with spacing similar to the SNP panels tested may not significantly affect the overall detection of linkage regions in a genome scan. Moreover, since the data quality and information content are greatly improved in the SNP panels over STR genotyping methods, new linkage regions may be identified due to higher information content and data quality in a dense SNP linkage panel.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Murray SSdoi
10.1186/1471-2156-6-S1-S85keywords:
subject
Has Abstractpub_date
2005-12-30 00:00:00pages
S85issn
1471-2156pii
1471-2156-6-S1-S85journal_volume
6 Suppl 1pub_type
杂志文章相关文献
BMC GENETICS文献大全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:Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 3...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-7-10
更新日期:2006-02-16 00:00:00
abstract:BACKGROUND:Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with th...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-018-0670-3
更新日期:2018-08-29 00:00:00
abstract::Alcohol dependence is a serious public health problem. We studied data from families participating in the Collaborative Study on the Genetics of Alcoholism (COGA) and made available to participants in the Genetic Analysis Workshop 14 (GAW14) in order to search for genes predisposing to alcohol dependence. Using factor...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S15
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-74
更新日期:2008-11-19 00:00:00
abstract:BACKGROUND:Transgenic poplar (Populus × euramericana 'Guariento') plants harboring five exogenous, stress-related genes exhibit increased tolerance to multiple stresses including drought, salt, waterlogging, and insect feeding, but the complex mechanisms underlying stress tolerance in these plants have not been elucida...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-S1-S7
更新日期:2014-01-01 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: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:Congenital fibrosis of the extraocular muscles types 1 and 3 (CFEOM1/CFEOM3) are autosomal dominant strabismus disorders that appear to result from maldevelopment of ocular nuclei and nerves. We previously reported that most individuals with CFEOM1 and rare individuals with CFEOM3 harbor heterozygous mutatio...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-26
更新日期:2007-05-18 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: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: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:Somatolactin alpha (SLa) is a fish-specific peptide hormone secreted from the pituitary. In medaka, SLa functions to darken the skin color and lack of SLa makes it pale. Transcription of SLa is enhanced or suppressed when fish are kept in dark or bright conditions, respectively, indicating SLa's important ro...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-13-64
更新日期:2012-07-24 00:00:00
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 ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-108
更新日期:2010-12-09 00:00:00
abstract:BACKGROUND:Genome-wide association studies (GWAS) are a widely used study design for detecting genetic causes of complex diseases. Current studies provide good coverage of common causal SNPs, but not rare ones. A popular method to detect rare causal variants is haplotype testing. A disadvantage of this approach is that...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-80
更新日期:2010-09-09 00:00:00
abstract:BACKGROUND:Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been f...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-26
更新日期:2005-05-19 00:00:00
abstract:BACKGROUND:Meta-analysis is a popular methodology in several fields of medical research, including genetic association studies. However, the methods used for meta-analysis of association studies that report haplotypes have not been studied in detail. In this work, methods for performing meta-analysis of haplotype assoc...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-12-8
更新日期:2011-01-19 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:The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a re...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0514-6
更新日期:2017-05-19 00:00:00
abstract::The Framingham Heart Study offspring cohort, a complex data set with irregularly spaced longitudinal phenotype data, was made available as part of Genetic Analysis Workshop 13. To allow an analysis of all of the data simultaneously, a mixed-model- based random-regression (RR) approach was used. The RR accounted for th...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-4-S1-S22
更新日期:2003-12-31 00:00:00
abstract:BACKGROUND:Nucleotide 1311 polymorphism at exon 11 of G6PD gene is widely prevalent in various populations of the world. The aim of the study was to evaluate 1311 polymorphism in subjects carrying G6PD Mediterranean gene and in general population living in Pakistan. RESULTS:Patients already known to be G6PD deficient ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-10-41
更新日期:2009-07-30 00:00:00
abstract:BACKGROUND:Alcoholism is a serious public health problem. It has both genetic and environmental causes. In an effort to gain understanding of the underlying genetic susceptibility to alcoholism, a long-term study has been undertaken. The Collaborative Study on the Genetics of Alcoholism (COGA) provides a rich source of...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S131
更新日期:2005-12-30 00:00:00
abstract:BACKGROUND:India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Drav...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-86
更新日期:2014-07-22 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: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 neigh...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-90
更新日期:2008-12-22 00:00:00
abstract:BACKGROUND:RNA sequencing (RNA-seq) technology has identified multiple differentially expressed (DE) genes associated to complex disease, however, these genes only explain a modest part of variance. Omnigenic model assumes that disease may be driven by genes with indirect relevance to disease and be propagated by funct...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0739-7
更新日期:2019-03-19 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:Sry is a gene known to be essential for testis determination but is also transcribed in adult male tissues. The laboratory rat, Rattus norvegicus, has multiple Y chromosome copies of Sry while most mammals have only a single copy. DNA sequence comparisons with other rodents with multiple Sry copies are incon...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-8-11
更新日期:2007-04-04 00:00:00
abstract:BACKGROUND:The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed was rescued from extinction and population sizes have been gradually increasing over the past few ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-019-0757-5
更新日期:2019-08-05 00:00:00
abstract:BACKGROUND:Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs tha...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0364-7
更新日期:2016-04-12 00:00:00