Sentence examples for by using reference panels from inspiring English sources
As an alternative, Jostins et al. (2011) suggested balancing accuracy and computation by using reference panels that "approximately cluster" with the study individuals on a plot of principal components (PC) that capture genetic ancestry.
We found similar patterns when using reference panels from other European populations (see Additional file 1).
The most frequently used reference panels are HapMap [ 74, 75] and 1000 Genomes [ 76– 76].
Imputation accuracy for common SNPs may be further increased by using larger reference panels with data on denser sets of variants.
Using Adapt-Mix, we estimated Σ using 1KG reference panels by optimizing over each chromosome (1KG-Chrom), over the whole genome (1KG-Genome) and per window (1KG-Window).
While these approaches mainly utilize reference panels, imputation accuracy of rare variants can also be increased by using exome chips containing rare variants.
To improve imputation accuracy of rare variants, various approaches have been suggested, including increasing the sample size of the reference panel, using sequencing data from study-specific samples (i.e., specific populations), and using local reference panels by genotyping or sequencing a subset of study samples.
Hence, most investigators will use statistical imputation from SNP arrays in GWAS using dense reference panels.
This advantage may be offset to some degree by using a smaller reference panel than is available for independent study populations, although this effect is likely to be small because the reference panel used here is approximately 90% of the full 1000 Genomes phase 1 reference panel.
However, in the case that there is no best guess panel available, we have shown that there is a potential for increased false positives by using the wrong reference panel.
