The GBA gene and GBAP1 pseudogene are located on chromosome 1. Pathogenic variants in GBA cause Gaucher disease and lead to an increased risk of Parkinson’s disease. GBA has sequence homology with its pseudogene GBAP1 particularly in the last three exons, where gene conversion can bring pseudogene-like variants into GBA. Unequal crossing overs can result in fusion genes between GBA and GBAP1.
Fields shared across all genes are defined in the general json file. The GBA locus does not include unique fields.
To visualize phased haplotypes, load the output bam file in IGV, group reads by the HP tag and color alignments by YC tag.
Reads in gray are either unassigned or consistent with more than one possible haplotype. When two haplotypes are identical over a region, there can be more than one haplotype consistent with a read, and the read is randomly assigned to a haplotype and colored in gray.
- The top panel shows a sample with two copies of GBA and two copies of GBAP1. The GBAP1 copies are shorter because they can no longer align beyond the end of the homology region.
- The middle panel shows a sample with a deletion (
hap3), where the 5' end is consistent with the shorter GBAP1 and the 3' end is consistent with the longer GBA. The red arrow marks the deletion breakpoint. The other side of the breakpoint can be found in thefusions_calledfield in thejson. - The bottom panel shows a sample with a duplicaton (
hap2), where the 5' end is consistent with the longer GBA and the 3' end is consistent with the shorter GBAP1. The red arrow marks the duplication breakpoint. The other side of the breakpoint can be found in thefusions_calledfield in thejson.