An adaptive gene-level association test for pedigree data.


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 the null hypothesis) for the whole genome, thereby being computationally efficient. RESULTS:We applied our approach to test for association with the high-density lipoprotein (HDL) ratio of post- and pretreatments in GAW20 data. Using the LMM similar to that used by Aslibekyan et al. (PLos One, 7:48663, 2012), our method identified 2 nearly significant genes (APOA5 and ZNF259) near rs964184, whereas neither the other gene-level tests nor the standard test on each individual single-nucleotide polymorphism (SNP) detected any significant gene in a genome-wide scan. CONCLUSIONS:Gene-level association testing can be a complementary approach to the SNP-level association testing and our method is adaptive and efficient compared to several other existing gene-level association tests.


BMC Genet


BMC genetics


Park JY,Wu C,Pan W




Has Abstract


2018-09-17 00:00:00




Suppl 1








  • Mapping and validation of major quantitative trait loci for kernel length in wild barley (Hordeum vulgare ssp. spontaneum).

    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


    authors: Zhou H,Liu S,Liu Y,Liu Y,You J,Deng M,Ma J,Chen G,Wei Y,Liu C,Zheng Y

    更新日期:2016-09-13 00:00:00

  • GWAS of habitual coffee consumption reveals a sex difference in the genetic effect of the 12q24 locus in the Japanese population.

    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


    authors: Jia H,Nogawa S,Kawafune K,Hachiya T,Takahashi S,Igarashi M,Saito K,Kato H

    更新日期:2019-07-26 00:00:00

  • Freeze-thaw Caenorhabditis elegans freeze-thaw stress response is regulated by the insulin/IGF-1 receptor daf-2.

    abstract:BACKGROUND:Adaption to cold temperatures, especially those below freezing, is essential for animal survival in cold environments. Freezing is also used for many medical, scientific, and industrial purposes. Natural freezing survival in animals has been extensively studied. However, the underlying mechanisms remain uncl...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Hu JP,Xu XY,Huang LY,Wang LS,Fang NY

    更新日期:2015-12-03 00:00:00

  • Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

    abstract:BACKGROUND:DGAT2 is a promising candidate gene for obesity because of its function as a key enzyme in fat metabolism and because of its localization on chromosome 11q13, a linkage region for extreme early onset obesity detected in our sample. We performed a mutation screen in 93 extremely obese children and adolescents...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Friedel S,Reichwald K,Scherag A,Brumm H,Wermter AK,Fries HR,Koberwitz K,Wabitsch M,Meitinger T,Platzer M,Biebermann H,Hinney A,Hebebrand J

    更新日期:2007-05-03 00:00:00

  • Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.

    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


    authors: Magwanga RO,Lu P,Kirungu JN,Lu H,Wang X,Cai X,Zhou Z,Zhang Z,Salih H,Wang K,Liu F

    更新日期:2018-01-15 00:00:00

  • Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums.

    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


    authors: Li X,Jin F,Jin L,Jackson A,Huang C,Li K,Shu X

    更新日期:2014-12-05 00:00:00

  • Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies.

    abstract:BACKGROUND:Phenotype error causes reduction in power to detect genetic association. We present a quantification of phenotype error, also known as diagnostic error, on power and sample size calculations for case-control genetic association studies between a marker locus and a disease phenotype. We consider the classic P...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Edwards BJ,Haynes C,Levenstien MA,Finch SJ,Gordon D

    更新日期:2005-04-08 00:00:00

  • Association of dopaminergic pathway gene polymorphisms with chronic renal insufficiency among Asian Indians with type-2 diabetes.

    abstract:BACKGROUND:Genetic markers conferring susceptibility to diabetes specific renal disease remains to be identified for early prediction and development of effective drugs and therapies. Inconsistent results obtained from analysis of genes from classical pathways generate need for examination of unconventional genetic mar...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Prasad P,Kumar KM,Ammini AC,Gupta A,Gupta R,Thelma BK

    更新日期:2008-03-22 00:00:00

  • Polymorphisms of two loci at the oxytocin receptor gene in populations of Africa, Asia and South Europe.

    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


    authors: Butovskaya PR,Lazebny OE,Sukhodolskaya EM,Vasiliev VA,Dronova DA,Fedenok JN,Rosa A,Peletskaya EN,Ryskov AP,Butovskaya ML

    更新日期:2016-01-06 00:00:00

  • Cytoplasm affects grain weight and filled-grain ratio in indica rice.

    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


    authors: Tao D,Xu P,Zhou J,Deng X,Li J,Deng W,Yang J,Yang G,Li Q,Hu F

    更新日期:2011-06-01 00:00:00

  • Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds.

    abstract:BACKGROUND:The extent of linkage disequilibrium (LD) is of critical importance for genomic selection and marker assisted selection. The primary purpose of this study is to examine patterns of LD in three Danish pig breeds (Duroc, Landrace and Yorkshire); we also examine patterns of persistence of phase between the bree...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Wang L,Sørensen P,Janss L,Ostersen T,Edwards D

    更新日期:2013-12-05 00:00:00

  • The prognostic value of IL10 and TNF alpha functional polymorphisms in premenopausal early-stage breast cancer patients.

    abstract:BACKGROUND:Interleukin-10 and tumor necrosis factor α play an important role in breast carcinogenesis. Genes, encoding those two cytokines, contain single nucleotide polymorphisms, which are associated with differential levels of gene transcription. This study analyzes single nucleotide polymorphisms in interleukin 10 ...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Korobeinikova E,Myrzaliyeva D,Ugenskiene R,Raulinaityte D,Gedminaite J,Smigelskas K,Juozaityte E

    更新日期:2015-06-26 00:00:00

  • Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene.

    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


    authors: Yang M,Yang B,Yan X,Ouyang J,Zeng W,Ai H,Ren J,Huang L

    更新日期:2012-07-13 00:00:00

  • Fusion of the NUP98 gene with the LEDGF/p52 gene defines a recurrent acute myeloid leukemia translocation.

    abstract:BACKGROUND:The NUP98 gene is involved in multiple rearrangements in haematological malignancy. The leukemic cells in an acute myeloid leukemia (AML) patient with a t(9;11)(p22;p15) were recently shown to have a fusion between the NUP98 gene and the LEDGF gene but it was not demonstrated that this fusion was recurrent i...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Hussey DJ,Moore S,Nicola M,Dobrovic A

    更新日期:2001-01-01 00:00:00

  • Interval estimation of disease loci: development and applications of new linkage methods.

    abstract::Three variants of the confidence set inference (CSI) procedure were proposed and applied to both the simulated and the Collaborative Study on the Genetics of Alcoholism (COGA) data. For each of the two applications, we first performed a preliminary genome scan study based on the microsatellite markers using the GENEHU...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Papachristou C,Lin S

    更新日期:2005-12-30 00:00:00

  • Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.

    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


    authors: Dunn G,Hinrichs AL,Bertelsen S,Jin CH,Kauwe JS,Suarez BK,Bierut LJ

    更新日期:2005-12-30 00:00:00

  • A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism.

    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


    authors: Velie BD,Fegraeus KJ,Solé M,Rosengren MK,Røed KH,Ihler CF,Strand E,Lindgren G

    更新日期:2018-08-29 00:00:00

  • GM and KM immunoglobulin allotypes in the Galician population: new insights into the peopling of the Iberian Peninsula.

    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


    authors: Calderón R,Lodeiro R,Varela TA,Fariña J,Ambrosio B,Guitard E,González-Martín A,Dugoujon JM

    更新日期:2007-06-27 00:00:00

  • Genome-wide survey indicates involvement of loci on canine chromosomes 7 and 31 in patellar luxation in Flat-Coated Retrievers.

    abstract:BACKGROUND:Patellar luxation is an orthopedic disorder in which the patella moves out of its normal location within the femoral trochlea of the knee and it can lead to osteoarthritis, lameness, and pain. In dogs it is a heritable trait, with both environmental and genetic factors contributing to the phenotype. The prev...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Lavrijsen IC,Leegwater PA,Wangdee C,van Steenbeek FG,Schwencke M,Breur GJ,Meutstege FJ,Nijman IJ,Cuppen E,Heuven HC,Hazewinkel HA

    更新日期:2014-05-28 00:00:00

  • Sucrose non-ferment 1 related protein kinase 2 (SnRK2) genes could mediate the stress responses in potato (Solanum tuberosum L.).

    abstract:BACKGROUND:The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinas...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Bai J,Mao J,Yang H,Khan A,Fan A,Liu S,Zhang J,Wang D,Gao H,Zhang J

    更新日期:2017-05-15 00:00:00

  • Analysis of an independent tumor suppressor locus telomeric to Tp53 suggested Inpp5k and Myo1c as novel tumor suppressor gene candidates in this region.

    abstract:BACKGROUND:Several reports indicate a commonly deleted chromosomal region independent from, and distal to the TP53 locus in a variety of human tumors. In a previous study, we reported a similar finding in a rat tumor model for endometrial carcinoma (EC) and through developing a deletion map, narrowed the candidate regi...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Hedberg Oldfors C,Dios DG,Linder A,Visuttijai K,Samuelson E,Karlsson S,Nilsson S,Behboudi A

    更新日期:2015-07-14 00:00:00

  • Hierarchical modeling in association studies of multiple phenotypes.

    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 ...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Liu X,Jorgenson E,Witte JS

    更新日期:2005-12-30 00:00:00

  • Comparative mapping combined with homology-based cloning of the rice genome reveals candidate genes for grain zinc and iron concentration in maize.

    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


    authors: Jin T,Chen J,Zhu L,Zhao Y,Guo J,Huang Y

    更新日期:2015-02-14 00:00:00

  • An investigation of the effects of lipid-lowering medications: genome-wide linkage analysis of lipids in the HyperGEN study.

    abstract:BACKGROUND:Use of anti-hyperlipidemic medications compromises genetic analysis because of altered lipid profiles. We propose an empirical method to adjust lipid levels for medication effects so that the adjusted lipid values substitute the unmedicated lipid values in the genetic analysis. RESULTS:Published clinical tr...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Wu J,Province MA,Coon H,Hunt SC,Eckfeldt JH,Arnett DK,Heiss G,Lewis CE,Ellison RC,Rao DC,Rice T,Kraja AT

    更新日期:2007-09-10 00:00:00

  • The use of the SLC16A1 gene as a potential marker to predict race performance in Arabian horses.

    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


    authors: Ropka-Molik K,Stefaniuk-Szmukier M,Szmatoła T,Piórkowska K,Bugno-Poniewierska M

    更新日期:2019-09-11 00:00:00

  • Hemi-nested touchdown PCR combined with primer-template mismatch PCR for rapid isolation and sequencing of low molecular weight glutenin subunit gene family from a hexaploid wheat BAC library.

    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


    authors: Huang XQ,Cloutier S

    更新日期:2007-05-04 00:00:00

  • Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.

    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


    authors: Wang Y,Li L,Tang S,Liu J,Zhang H,Zhi H,Jia G,Diao X

    更新日期:2016-04-12 00:00:00

  • Molecular organization and chromosomal localization of 5S rDNA in Amazonian Engystomops (Anura, Leiuperidae).

    abstract:BACKGROUND:For anurans, knowledge of 5S rDNA is scarce. For Engystomops species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species Engystomops freibergi and Engystomops peter...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: Rodrigues DS,Rivera M,Lourenço LB

    更新日期:2012-03-20 00:00:00

  • Characterization of the chromosomal inversion associated with the Koa mutation in the mouse revealed the cause of skeletal abnormalities.

    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


    authors: Katayama K,Miyamoto S,Furuno A,Akiyama K,Takahashi S,Suzuki H,Tsuji T,Kunieda T

    更新日期:2009-09-22 00:00:00

  • Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle.

    abstract:BACKGROUND:Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We per...

    journal_title:BMC genetics

    pub_type: 杂志文章


    authors: An B,Xu L,Xia J,Wang X,Miao J,Chang T,Song M,Ni J,Xu L,Zhang L,Li J,Gao H

    更新日期:2020-03-14 00:00:00