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Detecting Novel Associations in Large Data Sets
A measure of dependence for two-variable relationships: the maximal information coefficient (MIC), which captures a wide range of associations both functional and not, and for functional relationships provides a score that roughly equals the coefficient of determination of the data relative to the regression function.
A second generation human haplotype map of over 3.1 million SNPs
The Phase II HapMap is described, which characterizes over 3.1 million human single nucleotide polymorphisms genotyped in 270 individuals from four geographically diverse populations and includes 25–35% of common SNP variation in the populations surveyed, and increased differentiation at non-synonymous, compared to synonymous, SNPs is demonstrated.
Detecting recent positive selection in the human genome from haplotype structure
A framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations is introduced, and the core haplotypes carrying the proposed protective mutation stand out and show significant evidence of selection.
Genome-wide detection and characterization of positive selection in human populations
‘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.
Integrating common and rare genetic variation in diverse human populations
An expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.
Genetic signatures of strong recent positive selection at the lactase gene.
- Todd Bersaglieri, Pardis C Sabeti, J. Hirschhorn
- BiologyAmerican journal of human genetics
- 1 June 2004
It is estimated that strong selection occurred within the past 5,000-10,000 years, consistent with an advantage to lactase persistence in the setting of dairy farming; the signals of selection the authors observe are among the strongest yet seen for any gene in the genome.
Linkage disequilibrium in the human genome
The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000–53,000 years ago, implying that LD mapping is likely to be practical in this population.
Nucleic acid detection with CRISPR-Cas13a/C2c2
A Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), is used to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA.
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources.
Common deletion polymorphisms in the human genome
This work describes a systematic method for using dense SNP genotype data to discover deletions and its application to data from the International HapMap Consortium to characterize and catalogue segregating deletion variants across the human genome.