Abstract:
:We present a new method for fine-mapping a disease susceptibility locus using a case-control design. The new method, termed the weighted average (WA) statistic, averages the Cochran-Armitage (CA) trend test statistic and the difference between the Hardy-Weinberg disequilibrium test statistic for cases and controls (the HWD trend). The main characteristics of the WA statistic are that it improves on the weaknesses, and maintains the strengths, of both the CA trend test and the HWD trend test. Data from three different populations in the Genetic Analysis Workshop 14 (GAW14) simulated dataset (Aipotu, Karangar, and Danacaa) were first subjected to model-free linkage analysis to find regions exhibiting linkage. Then, for fine-scale mapping, 140 SNPs within the significant linkage regions were analyzed with the WA test statistic on replicates of the three populations, both separately and combined. The regions that were significant in the multipoint linkage analysis were also significant in this fine-scale mapping. The most significant regions that were obtained using the WA statistic were regions in chromosome 3 (B03T3056-B03T3058, p-value < 1 x 10(-10)) and chromosome 9 (B09T8332-B09T8334, p-value 1 x 10(-6)). Based on the results of the simulated GAW14 data, the WA test statistic showed good performance and could narrow down the region containing the susceptibility locus. However, the strength of the signal depends on both the strength of the linkage disequilibrium and the heterozygosity of the linked marker.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Song K,Orloff MS,Lu Q,Elston RCdoi
10.1186/1471-2156-6-S1-S67keywords:
subject
Has Abstractpub_date
2005-12-30 00:00:00pages
S67issn
1471-2156pii
1471-2156-6-S1-S67journal_volume
6 Suppl 1pub_type
杂志文章相关文献
BMC GENETICS文献大全abstract:BACKGROUND:The Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types and subtypes of the Drosophila CNS is frequently achieved by employing the binary Gal4/UAS system...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00895-7
更新日期:2020-10-22 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: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:The human Prader-Willi syndrome (PWS) domain and its mouse orthologue include a cluster of paternally expressed genes which imprinted expression is co-ordinately regulated by an imprinting center (IC) closely associated to the Snurf-Snrpn gene. Besides their co-regulated imprinted expression, two observation...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-1
更新日期:2005-01-05 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::We estimated the crossover frequency in 1,232 gametes from 356 subjects in pedigrees from the Collaborative Study on the Genetics on Alcoholism. We examined the effect of covariates including age, ethnicity, and years with ALDX1 on recombination rate, and found a positive correlation between recombination rate and yea...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S58
更新日期:2005-12-30 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: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:We analyzed 143 pedigrees (364 nuclear families) in the Collaborative Study on the Genetics of Alcoholism (COGA) data provided to the participants in the Genetic Analysis Workshop 14 (GAW14) with the goal of comparing results obtained from genome linkage analysis using microsatellite and with results obtaine...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-6-S1-S4
更新日期:2005-12-30 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::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: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: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: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: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:Infectious disease of livestock continues to be a cause of substantial economic loss and has adverse welfare consequences in both the developing and developed world. New solutions to control disease are needed and research focused on the genetic loci determining variation in immune-related traits has the pot...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-107
更新日期:2010-12-07 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:This study was designed to investigate epidermal growth factor receptor (EGFR) mutation types affecting lung cancer treatment in patients in Xinjiang, China. We detected and analyzed differences in the EGFR mutation points of Uighur and Han patients with lung adenocarcinoma. We examined 181 specimens of lung...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-015-0181-4
更新日期:2015-02-28 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:Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. RESULTS:We report new data on 155 i...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-9-86
更新日期:2008-12-12 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:Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, T...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-017-0553-z
更新日期:2017-10-23 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:Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research. RESULTS:We have developed 25 new microsatellite mark...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-11-41
更新日期:2010-05-18 00:00:00
abstract:BACKGROUND:Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595-9940 ) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn with various congenital defects as reflected in the name of the disease, as well as short stature, ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00913-8
更新日期:2020-09-15 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:Despite the emergence of stereotactic body radiotherapy (SBRT) for treatment of medically inoperable early-stage non-small-cell lung cancer patients, the molecular effects of focal exposure of limited lung volumes to high-dose radiation have not been fully characterized. This study was designed to identify m...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0338-9
更新日期:2016-01-27 00:00:00
abstract:BACKGROUND:The aim of this study was to determine if variable number of tandem repeats (VNTR) in the second intron (STin2) of the serotonin transporter (SLC6A4) gene was associated with tobacco use disorder, successful smoking cessation, or smoking characteristics. In this case-control study, patients with current toba...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/1471-2156-15-78
更新日期:2014-06-27 00:00:00
abstract:BACKGROUND:South African (SA) Black women have a high prevalence of preeclampsia and HIV, both conditions associated with increased inflammation. miR-146a is an inflammatory-associated miR and a common single nucleotide polymorphism (rs2910164) has been associated with several disease conditions. To date, this SNP has ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-016-0469-z
更新日期:2017-01-19 00:00:00
abstract:BACKGROUND:The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type ...
journal_title:BMC genetics
pub_type: 杂志文章
doi:10.1186/s12863-020-00889-5
更新日期:2020-07-29 00:00:00