Genes associated with several neurological disorders have been shown to be highly polymorphic. Targeted sequencing of these genes using NGS technologies is a powerful way to increase the cost-effectiveness of variant discovery and detection. However, for a comprehensive view of these target genes, it is necessary to have complete and uniform coverage across regions of interest. Unfortunately, short-read sequencing technologies are not ideal for these types of studies as they are prone to mis-mapping and often fail to span repetitive regions. Targeted sequencing with PacBio long reads provides the unique advantage of single-molecule observations of complex genomic regions. PacBio long reads not only provide continuous sequence data though polymorphic or repetitive regions, but also have no GC bias. Here we describe the characterization of the poly-T locus in TOMM40, a gene known to be associated with progression to Alzheimer’s, using PacBio long reads. Probes were designed to capture a 20 kb region comprising the TOMM40 and ApoE genes. Target regions were captured in multiple cell lines and sequencing libraries made using standard sample preparation methods. We will present our results on the poly-T structural variants that we observed in TOMM40 in these cell lines. We will also present our results on probe design optimization and barcoding strategies for a cost-effective solution.