An analysis of strategies for discovery of single-nucleotide polymorphisms

High-density single-nucleotide polymorphism maps of the human genome

“…The frequency distributions found (Figs. 1a and 1b) approximately fit S (2,1) predictions for an expanded population [21]. Given that population structure, the prediction for an S(50,1) strategy (e.g., resequencing of 25 individuals) is that about 80% of identified SNPs will be private SNPs.…”

High-density single-nucleotide polymorphism maps of the human genome

“…The frequency distributions found (Figs. 1a and 1b) approximately fit S (2,1) predictions for an expanded population [21]. Given that population structure, the prediction for an S(50,1) strategy (e.g., resequencing of 25 individuals) is that about 80% of identified SNPs will be private SNPs.…”

The Effect of Single Nucleotide Polymorphism Identification Strategies on Estimates of Linkage Disequilibrium

“…Therefore, our finding that the magnitude of AB I is dictated by h is intuitive, as one would expect the level of sequence variation to mediate the probability of identifying informative SNPs. Previous studies have also suggested that a significant fraction of candidate SNPs identified in a small number of chromosomes will be uninformative (Eberle and Kruglyak 2000;Yang et al 2000), although to our knowledge we are the first to address this question in a subdivided population.…”

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

“…Combined with coalescent estimates of evolutionary age, it should now be possible to systematically identify associated introgressed SVs and assess them for signatures of adaptive evolution, as was recently demonstrated(62). Even though we estimate that 96% of SVs with an allele frequency above 2% have been theoretically discovered(63), a greater diversity of human genomes are required to adequately account for population differences, effects of selection, as well as archaic introgression. Our findings clearly indicate that genomes of African ancestry represent the deepest reservoir of untapped structural variation.…”

High-density single-nucleotide polymorphism maps of the human genome

“…The frequency distributions found (Figs. 1a and 1b) approximately fit S (2,1) predictions for an expanded population [21]. Given that population structure, the prediction for an S(50,1) strategy (e.g., resequencing of 25 individuals) is that about 80% of identified SNPs will be private SNPs.…”

The Effect of Single Nucleotide Polymorphism Identification Strategies on Estimates of Linkage Disequilibrium

“…Therefore, our finding that the magnitude of AB I is dictated by h is intuitive, as one would expect the level of sequence variation to mediate the probability of identifying informative SNPs. Previous studies have also suggested that a significant fraction of candidate SNPs identified in a small number of chromosomes will be uninformative (Eberle and Kruglyak 2000;Yang et al 2000), although to our knowledge we are the first to address this question in a subdivided population.…”

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

“…Combined with coalescent estimates of evolutionary age, it should now be possible to systematically identify associated introgressed SVs and assess them for signatures of adaptive evolution, as was recently demonstrated(62). Even though we estimate that 96% of SVs with an allele frequency above 2% have been theoretically discovered(63), a greater diversity of human genomes are required to adequately account for population differences, effects of selection, as well as archaic introgression. Our findings clearly indicate that genomes of African ancestry represent the deepest reservoir of untapped structural variation.…”

High-density single-nucleotide polymorphism maps of the human genome

“…The frequency distributions found (Figs. 1a and 1b) approximately fit S (2,1) predictions for an expanded population [21]. Given that population structure, the prediction for an S(50,1) strategy (e.g., resequencing of 25 individuals) is that about 80% of identified SNPs will be private SNPs.…”

The Effect of Single Nucleotide Polymorphism Identification Strategies on Estimates of Linkage Disequilibrium

“…Therefore, our finding that the magnitude of AB I is dictated by h is intuitive, as one would expect the level of sequence variation to mediate the probability of identifying informative SNPs. Previous studies have also suggested that a significant fraction of candidate SNPs identified in a small number of chromosomes will be uninformative (Eberle and Kruglyak 2000;Yang et al 2000), although to our knowledge we are the first to address this question in a subdivided population.…”

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

“…Combined with coalescent estimates of evolutionary age, it should now be possible to systematically identify associated introgressed SVs and assess them for signatures of adaptive evolution, as was recently demonstrated(62). Even though we estimate that 96% of SVs with an allele frequency above 2% have been theoretically discovered(63), a greater diversity of human genomes are required to adequately account for population differences, effects of selection, as well as archaic introgression. Our findings clearly indicate that genomes of African ancestry represent the deepest reservoir of untapped structural variation.…”