Articles

Haplotype structure and linkage disequilibrium in chemokine and chemokine receptor genes

To dissect the haplotype structure of candidate genes for disease association studies, it is important to understand the nature of genetic variation at these loci in different populations. We present a survey ...

Authors: Vanessa J. Clark and Michael Dean

The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs

Understanding the nature of evolutionary relationships among persons and populations is important for the efficient application of genome science to biomedical research. We have analysed 8,525 autosomal single...

Authors: Mark D Shriver, Giulia C. Kennedy, Esteban J. Parra, Heather A. Lawson, Vibhor Sonpar, Jing Huang, Joshua M. Akey and Keith W. Jones

Whole genome DNA copy number changes identified by high density oligonucleotide arrays

Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however,...

Authors: Jing Huang, Wen Wei, Jane Zhang, Guoying Liu, Graham R. Bignell, Michael R. Stratton, P. Andrew Futreal, Richard Wooster, Keith W. Jones and Michael H. Shapero

Further statistical analysis for genome-wide expression evolution in primate brain/liver/fibroblast tissue

In spite of only a 1-2 per cent genomic DNA sequence difference, humans and chimpanzees differ considerably in behaviour and cognition. Affymetrix microarray technology provides a novel approach to addressing ...

Authors: Jianying Gu and Xun Gu

'Frankenstein genes', or the Mad Magazineversion of the human pseudogenome

Annotation of the human genome is inching forward. Seven human chromosomes have now been fully annotated, covering 17 per cent of the genome, and at least one chromosome has been re-annotated. The enormity of ...

Authors: David R. Nelson

A survey of current software for genetic power calculations

Estimation of power is a key step in any study. This review briefly outlines the factors that affect power and the two main approaches for estimating it. There are a number of web-based tools and programs free...

Authors: Jo Knight

Characterisation of SNP haplotype structure in chemokine and chemokine receptor genes using CEPH pedigrees and statistical estimation

Chemokine signals and their cell-surface receptors are important modulators of HIV-1 disease and cancer. To aid future case/control association studies, aim to further characterise the haplotype structure of v...

Authors: Vanessa J Clark and Michael Dean

Genome-wide analysis of the human Alu Yb-lineage

The Alu Yb-lineage is a 'young' primarily human-specific group of short interspersed element (SINE) subfamilies that have integrated throughout the human genome. In this study, we have computationally screened th...

Authors: Anthony B. Carter, Abdel-Halim Salem, Dale J. Hedges, Catherine Nguyen Keegan, Beth Kimball, Jerilyn A. Walker, W. Scott Watkins, Lynn B. Jorde and Mark A. Batzer

Population genetic analysis of ascertained SNP data

The large single nucleotide polymorphism (SNP) typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified th...

Authors: Rasmus Nielsen

Update on genome completion and annotations: Protein Information Resource

The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt -- the Universal Protein Resource -- which no...

Authors: Cathy Wu and Daniel W Nebert

The impact of sample size and marker selection on the study of haplotype structures

Several studies of haplotype structures in the human genome in various populations have found that the human chromosomes are structured such that each chromosome can be divided into many blocks, within which t...

Authors: Xiao Sun, J. Claiborne Stephens and Hongyu Zhao

Single nucleotide polymorphism genotyping by two colour melting curve analysis using the MGB Eclipse™ Probe System in challenging sequence environment

Probe and primer design for single nucleotide polymorphism (SNP) detection can be very challenging for A-T DNA-rich targets, requiring long sequences with lower specificity and stability, while G-C-rich DNA ta...

Authors: Yevgeniy S. Belousov, Robert A. Welch, Silvia Sanders, Alan Mills, Alena Kulchenko, Robert Dempcy, Irina A. Afonina, David K. Walburger, Cynthia L. Glaser, Sunita Yadavalli, Nicolaas M.J. Vermeulen and Walt Mahoney

Editorial

Authors: Li Jin

Christoph W. Sensen (Editor)

Authors:

Pharmacogenetics of lipid diseases

The genetic basis for most of the rare lipid monogenic disorders have been elucidated, but the challenge remains in determining the combination of genes that contribute to the genetic variability in lipid leve...

Authors: Jose M. Ordovas

Development of an integrated genome informatics, data management and workflow infrastructure: A toolbox for the study of complex disease genetics

The genetic dissection of complex disease remains a significant challenge. Sample-tracking and the recording, processing and storage of high-throughput laboratory data with public domain data, require integrat...

Authors: Oliver S. Burren, Barry C. Healy, Alex C. Lam, Helen Schuilenburg, Geoffrey E. Dolman, Vincent H. Everett, Davide Laneri, Sarah Nutland, Helen E. Rance, Felicity Payne, Deborah Smyth, Chris Lowe, Bryan J. Barratt, Rebecca C.J. Twells, Daniel B. Rainbow, Linda S. Wicker…

The truth about mouse, human, worms and yeast

Genome comparisons are behind the powerful new annotation methods being developed to find all human genes, as well as genes from other genomes. Genomes are now frequently being studied in pairs to provide cros...

Authors: David R. Nelson and Daniel W. Nebert

Robustness of the inference of human population structure: A comparison of X-chromosomal and autosomal microsatellites

In this paper, data on 20 X-chromosomal microsatellite polymorphisms from the HGDP-CEPH cell line panel are used to infer human population structure. Inferences from these data are compared to those obtained f...

Authors: Sohini Ramachandran, Noah A. Rosenberg, Lev A. Zhivotovsky and Marcus W. Feldman

Genomic and proteomic approaches for studying human cancer: Prospects for true patient-tailored therapy

Global gene expression analysis is beginning to move from the laboratories of basic investigators to large-scale clinical trials. The potential of this technology to improve diagnosis and tailored treatment of...

Authors: Kristen M. Carr, Kevin Rosenblatt, Emanuel F. Petricoin and Lance A. Liotta

Chromosomal phenotypes and submicroscopic abnormalities

The finding, during the last decade, that several common, clinically delineated syndromes are caused by submicroscopic deletions or, more rarely, by duplications, has provided a powerful tool in the annotation...

Authors: Koen Devriendt and Joris R. Vermeesch

A survey of current software for haplotype phase inference

In the past two years, tracking the explosion in data due to ever-improving single nucleotide polymorphism (SNP) maps and cheaper high-throughput genotyping technologies, a bewildering array of new algorithms ...

Authors: Michael E. Weale

Stuart Brown with John Hay and Harry Ostrer

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Editorial

Authors: David D Pollock

Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps

Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this an...

Authors: William J Murphy, Guillaume Bourque, Glenn Tesler, Pavel Pevzner and Stephen J O'Brien

Integration of association statistics over genomic regions using Bayesian adaptive regression splines

In the search for genetic determinants of complex disease, two approaches to association analysis are most often employed, testing single loci or testing a small group of loci jointly via haplotypes for their ...

Authors: Xiaohua Zhang, Kathryn Roeder, Garrick Wallstrom and Bernie Devlin

Genome-wide characterisation of the binding repertoire of small molecule drugs

Most, if not all, drugs interact with multiple proteins. One or more of these interactions are responsible for carrying out the primary therapeutic effects of the drug. Others are involved in the transport or ...

Authors: Lee Makowski and Diane J Rodi

Gametic phase estimation over large genomic regions using an adaptive window approach

The authors present ELB, an easy to programme and computationally fast algorithm for inferring gametic phase in population samples of multilocus genotypes. Phase updates are made on the basis of a window of ne...

Authors: Laurent Excoffier, Guillaume Laval and David Balding

Measuring and using admixture to study the genetics of complex diseases

Admixture is an important evolutionary force that can and should be used in efforts to apply genomic data and technology to the study of complex disease genetics. Admixture linkage disequilibrium (ALD) is crea...

Authors: Indrani Halder and Mark D Shriver

Update on human genome completion and annotations: Gene nomenclature

Why is agreeing on one particular name for each gene important? As one genome after another becomes sequenced, it is imperative to consider the complexity of genes, genetic architecture, gene expression, gene-...

Authors: Daniel W Nebert and Hester M Wain

A survey of current software for linkage analysis

There is now a wide choice of software available for linkage analysis. The most well known packages are briefly reviewed here. The package with the most extensive range of analyses is GENEHUNTER, but for many ...

Authors: Frank Dudbridge

Editorial

Authors: Li Jin and David B Goldstein

Matt Ridley

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