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A linear complexity phasing method for thousands of genomes
Human-disease etiology can be better understood with phase information about diploid sequences. We present a method for estimating haplotypes, using genotype data from unrelated samples or small… Expand
Improved whole-chromosome phasing for disease and population genetic studies
SHAPEIT2 uses multithreading so that multiple cores can be used to phase whole chromosomes, allowing users to make the best use of their computational resources. We tested SHAPEIT2 on several… Expand
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses.… Expand
Haplotype estimation using sequencing reads.
- O. Delaneau, B. Howie, A. Cox, J. Zagury, J. Marchini
- Biology, Medicine
- American journal of human genetics
- 3 October 2013
High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by… Expand
New class I and II HLA alleles strongly associated with opposite patterns of progression to AIDS.
The genetics of resistance to infection by HIV-1 cohort consists of 200 slow and 75 rapid progressors to AIDS corresponding to the extremes of HIV disease outcome of 20,000 Caucasians of European… Expand
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
- S. Limou, S. Le Clerc, +20 authors J. Zagury
- Biology, Medicine
- The Journal of infectious diseases
- 1 February 2009
To elucidate the genetic factors predisposing to AIDS progression, we analyzed a unique cohort of 275 human immunodeficiency virus (HIV) type 1-seropositive nonprogressor patients in relation to a… Expand
CD39/Adenosine Pathway Is Involved in AIDS Progression
HIV-1 infection is characterized by a chronic activation of the immune system and suppressed function of T lymphocytes. Regulatory CD4+ CD25high FoxP3+CD127low T cells (Treg) play a key role in both… Expand
Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls
Multiple genome-wide association studies (GWAS) have been performed in HIV-1 infected individuals, identifying common genetic influences on viral control and disease course. Similarly, common genetic… Expand
Accurate, scalable and integrative haplotype estimation
- O. Delaneau, J. Zagury, M. R. Robinson, J. Marchini, E. Dermitzakis
- Computer Science, Medicine
- Nature Communications
- 30 October 2019
The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Expand
Antibodies to the HIV-1 Tat protein correlated with nonprogression to AIDS: a rationale for the use of Tat toxoid as an HIV-1 vaccine.
OBJECTIVES To investigate which immune parameters, such as antibodies against HIV-1 specificities, or viral parameters, such as p24 antigenemia, are predictive of disease progression. STUDY DESIGN… Expand