Yingxi Yang

Keywords IDH-mutant astrocytoma tumor heterogeneity patient stratification immune-hot glioma multi-omics spatial transcriptomics spatial proteomics gemistocytic differentiation lymphocytic infiltration GUIDE Introduction Isocitrate Dehydrogenase (IDH)-mutant astrocytoma is an aggressive, plastic brain tumor in which patients almost inevitably recur after standard treatments.

Since genotype imputation was introduced, researchers have been relying on the estimated imputation quality from imputation software to perform post-imputation quality control (QC). However, this quality estimate (denoted as Rsq) performs less well for lower-frequency variants. We recently published MagicalRsq, a machine-learning-based imputation quality calibration, which leverages additional typed markers from the same cohort and outperforms Rsq as a QC metric.

Introduction Genotype imputation is a process of estimating missing genotypes with the aid of reference panel(s). It can effectively boost power for detecting associated variants in genome-wide association studies (GWASs) and narrow down the most strongly associated variants within a genomic region. The latest TOPMed freeze 8 reference panel 1 Taliun D. Harris D.N. Kessler M.D. Carlson J. Szpiech Z.A. Torres R. Taliun S.A.G. Corvelo A. Gogarten S.M. Kang H.M. et al.