Extended Data Fig. 4: Candidate cHET filtering strategy and patient with LRBA variants.
From: Whole-genome sequencing of a sporadic primary immunodeficiency cohort
a, Filtering strategy to identify cHET pathogenic variants that consist of a rare coding variant in a PID-associated gene and a deletion of a CRE for the same gene. b, Regional plot of the cHET variants. Gene annotations are taken from Ensembl release 75, and the transcripts shown are those with mRNA identifiers in RefSeq (ENST00000357115 and ENST00000510413). The position of each variant relative to the gene transcript is shown by a red bar, with the longer bar indicating the extent of the deleted region. Variant coordinates are shown for the GRCh37 genome build. c, Pedigree of the patient with LRBA variants, showing the phase of the causal variants. d, FACS dot plot of CTLA-4 and FOXP3 expression in the patient with LRBA cHET variants and in a healthy control individual (representative of two independent experiments). Numbers in black are the percentage in each quadrant; numbers in red are the MFI of CTLA-4 staining in FOXP-negative and FOXP3-positive cells. e, Normalized CTLA-4 expression, assessed as previously described54, in the patient with LRBA cHET variants (n = 1), in healthy control individuals (n = 8) and in patients deficient in CTLA-4 (n = 4) or LRBA (n = 3) (positive controls). Data are mean ± s.e.m.
