Genotype, haplotype and copy-number variation in worldwide human populations

By Mattias Jakobsson, Sonja W. Scholz, Paul Scheet, J. R. Gibbs, Jenna M. VanLiere, H. Fung, Zachary A. Szpiech, James H. Degnan, Kai Wang, R. Guerreiro and 14 more. Nature, 2008

881 citations recorded by the source corpus.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/5b9fc382a3ff6020abc53559639a4ad49c0368f8

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Citations in the corpus

Integrated detection and population-genetic analysis of SNPs and copy number variation (2008, background): “Thus, a recent report (based on an earlier SNP array) that human CNV consisted almost entirely of rare variants, and that CNVs were more common in populations from Oceania and the America”
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain (2010, background): “Additionally, we have limited our sampling to a population that represents only a small component of worldwide human genetic diversity [26].”
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data (2012, methodology): “Application to humans To test the performance of the TreeMix model with real data, we applied it to humans, whose genetic history has been studied extensively [7,21,52,53].”
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data (2009, background): “Future studies of more populations [57, 58, 59] will help alleviate this difficulty.”
Fast model-based estimation of ancestry in unrelated individuals. (2009, background): “Considerable thought has been exercised on accelerating EM algorithms (Jamshidian and Jennrich 1993; Lange 1995; Varadhan and Roland 2008).”
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, methodology): “First, we modiﬁed the similarity threshold, using either a ﬁxed similarity threshold in the range of 0.6 – 0.9, reasonable in light of past choices (Wang et al. 2007; Jakobsson et al. 2008), or by the default approach in which the threshold was determined dynamically.”
Acute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation (2014, methodology): “Each cluster identified in the initial STRUCTURE run was analyzed separately using the same settings to identify potential within-cluster structure since detection of fine-scale structuring can be limited with large data sets (see Jakobsson et al., 2008).”
Human genetic variation and its contribution to complex traits (2009, background): “Except for a potential skew towards lower MAFs, structural variants seem to behave similarly to SNPs in terms of both genomic and population distribution, indicating a similar evolutionary history: both types of variants are 'ancestral', having arisen once in human history and shared among individua”
Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems (2011, methodology): “The original data set of [48] included the genotypes at 525,910 single-nucleotide polymorphisms (SNPs) of 485 individuals from a worldwide sample of 29 populations.”
Genes mirror geography within Europe (2008, background): “We let s(2) take values of (1, 4, 19, 99), so that the resulting variance in the traits are approximately (2, 5, 20, 100), and the proportion of variance explained is approximately (50, 20, 5, 1) per cent.”