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

Table 2 Breakpoint impact on genes

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

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.

ISSN: 1474-760X