Skip to main content

Table 2 Breakpoint impact on genes

From: Detecting non-allelic homologous recombination from high-throughput sequencing data

Impact Number of NAHR calls
Fusions: gene–gene 16
Fusions: gene–pseudogene 3
Fusions: pseudogene–pseudogene 1
Deleted genes 39
Deleted pseudogenes 14
Duplicated genes 381
Duplicated pseudogenes 12
Expanded genes 251
Expanded pseudogenes 46
Contracted genes 52
Contracted pseudogenes 3
Unaffected genes on LCRs 403
Unaffected pseudogenes on LCRs 10
  1. Of our 1,043 positive NAHR calls across the 44 individuals, 512 had highly confident breakpoints (log-odds ratio ≥6). Checking these 512 breakpoints against databases of genes and pseudogenes, we determined the impact of each breakpoint on various genes and pseudogenes. Note that one NAHR event may affect multiple genes (see Additional file 1: Table S4 and Figure S11 for examples), and so the total number of genes affected may not be equal to the number of called breakpoints passing the log-odds ratio threshold. NAHR, non-allelic homologous recombination.