Approximately independent linkage disequilibrium blocks in human populations

By Tomaz Berisa, Joseph K. Pickrell. bioRxiv, 2015

536 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/afbb4916bd1de07f6c1baa614b1d3c57451cadfd

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In Genetics

In Molecular Biology

Citations in the corpus

The GTEx Consortium atlas of genetic regulatory effects across human tissues (2019, background): “Thus, to provide functional interpretation of the 5,385 significant GWAS associations in 1,167 loci from approximately independent LD blocks (46) across the 87 complex traits, we”
A more accurate method for colocalisation analysis allowing for multiple causal variants (2021, methodology): “We used lddetect[9] to divide the genome into approximately LD-independent blocks, and extracted haplotypes from the EUR samples in 1000 Genomes phase 3 data, consisting of 1000 contiguous SNPs with MAF > 0.01.”
The Polygenic and Monogenic Basis of Blood Traits and Diseases (2020, background): “Loci of colocalization were defined by the recombination regions identified by (Berisa and Pickrell, 2016).”
Genomic dissection of bipolar disorder and schizophrenia including 28 subphenotypes (2018, methodology): “The genome was split into 1,703 previously defined approximately LD-independent regions (Berisa and Pickrell, 2016).”
Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies (2018, unknown): “671 [30] Berisa T, Pickrell JK.”
Probabilistic fine-mapping of transcriptome-wide association studies (2017, methodology): “To sim336 ulate genotype samples, we first partitioned genotype data for 489 individuals of European ancestry in 337 1000Genomes(40) into independent LD blocks as defined by LDetect.(28) We annotated LD-blocks with all 338 genes in RefSeq(27) whose transcription start site was flanked by region boun”
Polygenic prediction via Bayesian regression and continuous shrinkage priors (2018, methodology): “In practice, we partition the genome into 1,703 largely independent genomic regions estimated using data from the 1000 Genomes Project European samples [Berisa and Pickrell, 2016], and conduct multivariate updating of the effect sizes within each LD block (see Appendix A).”
Polygenic scores via penalized regression on summary statistics (2016, background): “…of twin studies as well as recent genome-wide association studies have demonstrated that a large proportion of the variance in liability to common diseases and human traits is due to genetic diﬀerences between individuals (Polderman et al. , 2015; Yang et al. , 2011; Bulik-Sullivan et al. , 2015).”
Reduced signal for polygenic adaptation of height in UK Biobank (2018, methodology): “To evaluate this signal for each dataset, we independently ascertained the SNP with the smallest p-value within each of 1700 approximately independent LD blocks [25, 7] (subject to the constraint that MAF > 0.”
Dissecting the genetics of complex traits using summary association statistics (2016, methodology): “A simple approach to regularization is to set all correlations between distal SNPs to zero, based on a fixed distance threshold 7 or approximately independent LD blocks inferred from the data 20 .”