Detecting recent positive selection in the human genome from haplotype structure

@article{Sabeti2002DetectingRP,
  title={Detecting recent positive selection in the human genome from haplotype structure},
  author={Pardis C Sabeti and David Reich and John M. Higgins and Haninah Levine and Daniel J. Richter and Stephen F. Schaffner and S. Gabriel and Jill V. Platko and Nick J. Patterson and Gavin J. McDonald and Hans C. Ackerman and Sarah J. Campbell and David Altshuler and Richard Cooper and Dominic P. Kwiatkowski and Ryk H Ward and Eric S. Lander},
  journal={Nature},
  year={2002},
  volume={419},
  pages={832-837}
}
The ability to detect recent natural selection in the human population would have profound implications for the study of human history and for medicine. Here, we introduce a framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations. We first identify haplotypes at a locus of interest (core haplotypes). We then assess the age of each core haplotype by the decay of its association to alleles at various distances from the locus… 
Genome-wide detection and characterization of positive selection in human populations
TLDR
‘Long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are developed.
Genome-wide detection and characterization of positive selection in human populations
TLDR
‘long-range haplotype’ methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population are used.
Screening for recently selected alleles by analysis of human haplotype similarity.
TLDR
A method that uses a sliding window to estimate similarity among the haplotypes associated with any given single-nucleotide polymorphism (SNP) allele is described and found to be comparable in power to the popular long-range haplotype test and more powerful than methods based on nucleotide diversity.
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TLDR
The haplotype entropy method is powerful for detecting population-specific LD embedded in short regions and should contribute to further studies aiming to decipher the evolutionary histories of modern humans.
A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations
TLDR
Combining the haplotype test and the flipped SNPs determination, the WGLRH test serves as an unbiased genome-wide screen for regions under putative selection, and is potentially applicable to the study of other human populations.
A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation
TLDR
This study confirms strong positive selection on genes previously reported to be associated with specific phenotypes, and identifies other candidates that are likely to contribute to phenotypic differences between human populations.
Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.
Genomic landscape of positive natural selection in Northern European populations
TLDR
The potential of genome-wide data sets to discover loci that lie behind evolutionary adaptation in different human populations, including Great Britain, Northern Germany, Eastern and Western Finland, and Sweden is demonstrated.
Focusing on human haplotype diversity in numerous individual genomes demonstrates an evolutional feature of each locus
TLDR
This simple method helped clarify evolutionary events for each locus, including rare evolutionary events such as introgression, incomplete lineage sorting, selection, and haplotype recombination that may be hard to discriminate from each other.
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies
TLDR
HapFinder is presented, a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.
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