600 Base Reads on the Ion S5™ Next-Generation Sequencing System Enables Accurate HLA Typing of 96 Samples on One 530™ Chip

Longer read lengths simplify genome assembly, haplotyping, metagenomics, and the design of library primers for targeted resequencing. Several new technologies were developed to enable the sequencing of templates with inserts over 600 bases: a fast isothermal templating technology, an ISP™ that is optimized for maximum template density, a new long-read sequencing polymerase, and instrument scripts that consume less reagents. We demonstrate the combination of these technologies to sequence 600 base long DNAs on an Ion 530 Chip™ with an average AQ20 mean read length over 500 bp. The protocol was used to type human leukocyte antigen (HLA) alleles, a haplotyping application that is greatly simplified by long read length sequence data. 96 HLA samples were typed with 99.7% concordance to truth on one Ion 530 chip.