A general quantitative genetic model for haplotyping a complex trait in humans.

Abstract:

:Uncertainty about linkage phases of multiple single nucleotide polymorphisms (SNPs) in heterozygous diploids challenges the identification of specific DNA sequence variants that encode a complex trait. A statistical technique implemented with the EM algorithm has been developed to infer the effects of SNP haplotypes from genotypic data by assuming that one haplotype (called the risk haplotype) performs differently from the rest (called the non-risk haplotype). This assumption simplifies the definition and estimation of genotypic values of diplotypes for a complex trait, but will reduce the power to detect the risk haplotype when non-risk haplotypes contain substantial diversity. In this article, we incorporate general quantitative genetic theory to specify the differentiation of different haplotypes in terms of their genetic control of a complex trait. A model selection procedure is deployed to test the best number and combination of risk haplotypes, thus providing a precise and powerful test of genetic determination in association studies. Our method is derived on the maximum likelihood theory and has been shown through simulation studies to be powerful for the characterization of the genetic architecture of complex quantitative traits.

journal_name

Curr Genomics

journal_title

Current genomics

authors

Wu S,Yang J,Wang C,Wu R

doi

10.2174/138920207782446179

subject

Has Abstract

pub_date

2007-08-01 00:00:00

pages

343-50

issue

5

eissn

1389-2029

issn

1875-5488

journal_volume

8

pub_type

杂志文章
  • Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling.

    abstract::RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for unique insights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternative splicing events and the presence of non-coding RNAs. It has been realised non-coding R...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202911314030003

    authors: Mills JD,Kawahara Y,Janitz M

    更新日期:2013-05-01 00:00:00

  • Genomic instability and carcinogenesis: an update.

    abstract::Cancers arise as a result of stepwise accumulation of mutations which may occur at the nucleotide level and/or the gross chromosomal level. Many cancers particularly those of the colon display a form of genomic instability which may facilitate and speed up tumor initiation and development. In few instances, a "mutator...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208786847926

    authors: Abdel-Rahman WM

    更新日期:2008-12-01 00:00:00

  • A graphical weighted power improving multiplicity correction approach for SNP selections.

    abstract::Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-s...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920291505141106103959

    authors: Saunders G,Fu G,Stevens JR

    更新日期:2014-10-01 00:00:00

  • DNA instability at chromosomal fragile sites in cancer.

    abstract::Human chromosomal fragile sites are specific genomic regions which exhibit gaps or breaks on metaphase chromosomes following conditions of partial replication stress. Fragile sites often coincide with genes that are frequently rearranged or deleted in human cancers, with over half of cancer-specific translocations con...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920210791616699

    authors: Dillon LW,Burrow AA,Wang YH

    更新日期:2010-08-01 00:00:00

  • A Genome-wide Association Analysis in Four Populations Reveals Strong Genetic Heterogeneity For Birth Weight.

    abstract::Low or high birth weight is one of the main causes for neonatal morbidity and mortality. They are also associated with adulthood chronic illness. Birth weight is a complex trait which is affected by baby's genes, maternal environments as well as the complex interactions between them. To understand the genetic basis of...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160726152033

    authors: Luo T,Liu X,Cui Y

    更新日期:2016-10-01 00:00:00

  • CENPA a genomic marker for centromere activity and human diseases.

    abstract::Inheritance of genetic material requires that chromosomes segregate faithfully during cell division. Failure in this process can drive to aneuploidy phenomenon. Kinetochores are unique centromere macromolecular protein structures that attach chromosomes to the spindle for a proper movement and segregation. A unique ty...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209788920985

    authors: Valdivia MM,Hamdouch K,Ortiz M,Astola A

    更新日期:2009-08-01 00:00:00

  • Application of genomic tools in plant breeding.

    abstract::Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in parti...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920212800543084

    authors: Pérez-de-Castro AM,Vilanova S,Cañizares J,Pascual L,Blanca JM,Díez MJ,Prohens J,Picó B

    更新日期:2012-05-01 00:00:00

  • Remodeling of Proteostasis Upon Transition to Adulthood is Linked to Reproduction Onset.

    abstract::Protein folding and clearance networks sense and respond to misfolded and aggregation-prone proteins by activating cytoprotective cell stress responses that safeguard the proteome against damage, maintain the health of the cell, and enhance lifespan. Surprisingly, cellular proteostasis undergoes a sudden and widesprea...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202915666140221005023

    authors: Shai N,Shemesh N,Ben-Zvi A

    更新日期:2014-04-01 00:00:00

  • Engineering laccases: in search for novel catalysts.

    abstract::Laccases (p-diphenol oxidase, EC 1.10.3.2) are blue multicopper oxidases that catalyze the reduction of dioxygen to water, with a concomitant oxidation of small organic substrates. Since the description at the end of the nineteenth century of a factor catalyzing the rapid hardening of the latex of the Japanese lacquer...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211795564340

    authors: Robert V,Mekmouche Y,Pailley PR,Tron T

    更新日期:2011-04-01 00:00:00

  • Recent Advances in Understanding the Molecular Mechanisms Regulating the Root System Response to Phosphate Deficiency in Arabidopsis.

    abstract::Phosphorus (P) is an essential macronutrient for plant growth and development. Inorganic phosphate (Pi) is the major form of P taken up from the soil by plant roots. It is well established that under Pi deficiency condition, plant roots undergo striking morphological changes; mainly a reduction in primary root length ...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160331201812

    authors: Bouain N,Doumas P,Rouached H

    更新日期:2016-08-01 00:00:00

  • High-Throughput Omics Technologies: Potential Tools for the Investigation of Influences of EMF on Biological Systems.

    abstract::The mode of action of a huge amount of agents on biological systems is still unknown. One example where more questions than answers exist is covered by the term electromagnetic fields (EMF). Use of wireless communication, e.g. mobile phones, has been escalated in the last few years. Due to this fact, a lot of discussi...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920209787847050

    authors: Blankenburg M,Haberland L,Elvers HD,Tannert C,Jandrig B

    更新日期:2009-04-01 00:00:00

  • Expression and function of bcl-2 proteins in melanoma.

    abstract::Bcl-2 proteins are critical regulators of mitochondrial membrane permeability and the proapoptotic mitochondrial pathway. The family encloses pro- and antiapoptotic factors encoded by over 15 genes, which frequently give rise to alternative splice products. Antiapoptotic, proapoptotic multidomain, and proapoptotic BH3...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208785699571

    authors: Eberle J,Hossini AM

    更新日期:2008-09-01 00:00:00

  • Mechano-regulation of alternative splicing.

    abstract::Alternative splicing contributes to the complexity of proteome by producing multiple mRNAs from a single gene. Affymetrix exon arrays and experiments in vivo or in vitro demonstrated that alternative splicing was regulated by mechanical stress. Expression of mechano-growth factor (MGF) which is the splicing isoform of...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920213804999156

    authors: Liu H,Tang L

    更新日期:2013-03-01 00:00:00

  • WITMSG: Large-scale Prediction of Human Intronic m6A RNA Methylation Sites from Sequence and Genomic Features.

    abstract:Introduction:N6-methyladenosine (m6A) is one of the most widely studied epigenetic modifications. It plays important roles in various biological processes, such as splicing, RNA localization and degradation, many of which are related to the functions of introns. Although a number of computational approaches have been p...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202921666200211104140

    authors: Liu L,Lei X,Meng J,Wei Z

    更新日期:2020-01-01 00:00:00

  • Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends.

    abstract::Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of th...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211794520187

    authors: Bolle C,Schneider A,Leister D

    更新日期:2011-03-01 00:00:00

  • Plant spliceosomal introns: not only cut and paste.

    abstract::Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carr...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920208784533629

    authors: Morello L,Breviario D

    更新日期:2008-06-01 00:00:00

  • Clinical and Rehabilitative Management of Retinitis Pigmentosa: Up-to-Date.

    abstract::The term retinitis pigmentosa (RP) indicates a heterogeneous group of genetic rare ocular diseases in which either rods or cones are prevalently damaged. RP represents the most common hereditary cause of blindness in people from 20 to 60 years old. In general, the different RP forms consist of progressive photo-recept...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211795860125

    authors: Parmeggiani F,Sato G,De Nadai K,Romano MR,Binotto A,Costagliola C

    更新日期:2011-06-01 00:00:00

  • A Systematic In-silico Analysis of Helicobacter pylori Pathogenic Islands for Identification of Novel Drug Target Candidates.

    abstract:BACKGROUND:Helicobacter pylori is associated with inflammation of different areas, such as the duodenum and stomach, causing gastritis and gastric ulcers leading to lymphoma and cancer. Pathogenic islands are a type of clustered mobile elements ranging from 10-200 Kb contributing to the virulence of the respective path...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202918666170705160615

    authors: Nammi D,Yarla NS,Chubarev VN,Tarasov VV,Barreto GE,Pasupulati AMC,Aliev G,Neelapu NRR

    更新日期:2017-10-01 00:00:00

  • Genome-scale studies of aging: challenges and opportunities.

    abstract::Whole-genome studies involving a phenotype of interest are increasingly prevalent, in part due to a dramatic increase in speed at which many high throughput technologies can be performed coupled to simultaneous decreases in cost. This type of genome-scale methodology has been applied to the phenotype of lifespan, as w...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920212803251454

    authors: McCormick MA,Kennedy BK

    更新日期:2012-11-01 00:00:00

  • Maps of cis-Regulatory Nodes in Megabase Long Genome Segments are an Inevitable Intermediate Step Toward Whole Genome Functional Mapping.

    abstract::The availability of complete human and other metazoan genome sequences has greatly facilitated positioning and analysis of various genomic functional elements, with initial emphasis on coding sequences. However, complete functional maps of sequenced eukaryotic genomes should include also positions of all non-coding re...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207780368178

    authors: Nikolaev LG,Akopov SB,Chernov IP,Sverdlov ED

    更新日期:2007-04-01 00:00:00

  • Genetic alterations in poorly differentiated and undifferentiated thyroid carcinomas.

    abstract::Thyroid gland presents a wide spectrum of tumours derived from follicular cells that range from well differentiated, papillary and follicular carcinoma (PTC and FTC, respectively), usually carrying a good prognosis, to the clinically aggressive, poorly differentiated (PDTC) and undifferentiated thyroid carcinoma (UTC)...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920211798120853

    authors: Soares P,Lima J,Preto A,Castro P,Vinagre J,Celestino R,Couto JP,Prazeres H,Eloy C,Máximo V,Sobrinho-Simões M

    更新日期:2011-12-01 00:00:00

  • Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data.

    abstract::Transcriptional regulation plays vital roles in many fundamental biological processes. Reverse engineering of genome-wide regulatory networks from high-throughput transcriptomic data provides a promising way to characterize the global scenario of regulatory relationships between regulators and their targets. In this r...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202915666141110210634

    authors: Liu ZP

    更新日期:2015-02-01 00:00:00

  • Repurposing Pathogenic Variants of DMD Gene and its Isoforms for DMD Exon Skipping Intervention.

    abstract:Background:Duchenne Muscular Dystrophy (DMD) is a progressive, fatal neuromuscular disorder caused by mutations in the DMD gene. Emerging antisense oligomer based exon skipping therapy provides hope for the restoration of the reading frame. Objectives:Population-based DMD mutation database may enable exon skipping to ...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202920666191107142754

    authors: Tyagi R,Kumar S,Dalal A,Mohammed F,Mohanty M,Kaur P,Anand A

    更新日期:2019-11-01 00:00:00

  • Post-translational Modifications are Required for Circadian Clock Regulation in Vertebrates.

    abstract::Circadian clocks are intrinsic, time-tracking systems that bestow upon organisms a survival advantage. Under natural conditions, organisms are trained to follow a 24-h cycle under environmental time cues such as light to maximize their physiological efficiency. The exact timing of this rhythm is established via cell-a...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202919666191014094349

    authors: Okamoto-Uchida Y,Izawa J,Nishimura A,Hattori A,Suzuki N,Hirayama J

    更新日期:2019-08-01 00:00:00

  • A Comprehensive Review of Dysregulated miRNAs Involved in Cervical Cancer.

    abstract::MicroRNAs(miRNAs) have become the center of interest in oncology. In recent years, various studies have demonstrated that miRNAs regulate gene expression by influencing important regulatory genes and thus are responsible for causing cervical cancer. Cervical cancer being the third most diagnosed cancer among the femal...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202915666140528003249

    authors: Sharma G,Dua P,Agarwal SM

    更新日期:2014-08-01 00:00:00

  • EGFR Intron Recombination in Human Gliomas: Inappropriate Diversion of V(D)J Recombination?

    abstract::The epidermal growth factor receptor (EGFR) is a membrane-bound, 170 kDa, protein tyrosine kinase that plays an important role in tumorigenesis. The EGFR gene, which is composed of over 168 kb of sequence, including a 123-kb first intron, is frequently amplified and rearranged in malignant gliomas leading to the expre...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/138920207780833838

    authors: Fenstermaker RA,Ciesielski MJ

    更新日期:2007-05-01 00:00:00

  • Changing Faces of Transcriptional Regulation Reflected by Zic3.

    abstract::The advent of genomics in the study of developmental mechanisms has brought a trove of information on gene datasets and regulation during development, where the Zic family of zinc-finger proteins plays an important role. Genomic analysis of the modes of action of Zic3 in pluripotent cells demonstrated its requirement ...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202916666150205124519

    authors: Winata CL,Kondrychyn I,Korzh V

    更新日期:2015-04-01 00:00:00

  • Familial Colorectal Cancer Type X.

    abstract::The genetic background is unknown for the 50-60% of the HNPCC families, who fulfill the Amsterdam criteria, but do not have a mutation in an MMR gene, and is referred to as FCCTX. This study reviews the clinical, morphological and molecular characteristics of FCCTX, and discusses the molecular genetic methods used to ...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202918666170307161643

    authors: Zetner DB,Bisgaard ML

    更新日期:2017-08-01 00:00:00

  • Epigenetic Programming of Adipose Tissue in the Progeny of Obese Dams.

    abstract::According to the Developmental Origin of Health and Disease (DOHaD) concept, maternal obesity and the resulting accelerated growth in neonates predispose offspring to obesity and associated metabolic diseases that may persist across generations. In this context, the adipose tissue has emerged as an important player du...

    journal_title:Current genomics

    pub_type: 杂志文章,评审

    doi:10.2174/1389202920666191118092852

    authors: Lecoutre S,Kwok KHM,Petrus P,Lambert M,Breton C

    更新日期:2019-09-01 00:00:00

  • Analytical Models For Genetics of Human Traits Influenced By Sex.

    abstract::Analytical models usually assume an additive sex effect by treating it as a covariate to identify genetic associations with sex-influenced traits. Their underlying assumptions are violated by ignoring interactions of sex with genetic factors and heterogeneous genetic effects by sex. Methods to deal with the problems a...

    journal_title:Current genomics

    pub_type: 杂志文章

    doi:10.2174/1389202917666160420142601

    authors: Lee C

    更新日期:2015-10-01 00:00:00