Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals
Fig 2
HAT-seq performance evaluation using a positive control.
(A) Representative gel image used for the identification of ACC1-specific insertions based on 3’ PCR analysis. For each site, genomic DNA from ACC1 and ACC2 was amplified using the same protocol and the PCR products were run on the gel side-by-side (left: ACC1; right: ACC2). NTC: negative control. (B) Representative gel image used for the zygosity analysis of ACC1-specific insertions based on full-length PCR. The four sites on the left were homozygous L1Hs insertions and the others were heterozygous L1Hs insertions. (C) The distributions of signal counts (reads with unique start positions) per ACC1-specific insertion closely followed Poisson distributions (chi-squared goodness-of-fit tests). (D) Representative ACC1-specific insertion (ACC1_132 at chr21:29069173) in 1%, 0.1%, and 0.01% spike-in libraries. Read coverage and supporting signal counts (unique start positions were indicated by black arrows) were positively correlated with the spike-in concentration. (E) The effectiveness of error filters. 64 ACC1-specific germline insertions in 1%, 0.1%, and 0.01% spike-in libraries were considered as “true positives”; all other signals were considered as “false positives”, which might include both background noise and some true somatic insertions present in the blood gDNA.