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. Author manuscript; available in PMC: 2020 Dec 1.
Published in final edited form as: Nature. 2020 Aug 19;584(7821):E20–E28. doi: 10.1038/s41586-020-2522-3

Figure 3. Absence of somatic APP retrogene insertions in our single-cell WGS data.

Figure 3.

a. A germline pseudogene insertion (SKA3) in our scWGS data showing all distinctive characteristics of true retrogene insertion. b. No read-depth gain in APP exons in our AD single neurons. Each dot represents the median of exon/intron read-depth ratios across all exons of the gene in each scWGS dataset from AD patients. AD patients who have polymorphic germline retrogene insertions of SKA3 (AD3 and AD4) and a germline insertion of ZNF100 (AD2) show clear read-depth gain; no such gain for two housekeeping genes (GAPDH, ACTB). Single cells that had poor genomic coverage for a given gene due to locus dropout are excluded. n, number of single cells in each individual; center line, median; box limits, first and third quartiles.