GenDx announced NGS-Turbo, a long-read HLA sequencing product for Nanopore instruments. Although we will have to see the actual protocol in practice, HLA sequencing with Nanopore long-reads should offer significant benefits in relation to short-read technologies, including:
1) Dramatic improvement in turnaround time. Nanopore long-read protocols for lib prep and sequencing often require just hours, instead of days, to complete. Depending on the number of multiplexed samples, Nanopore runs can be finished in a single day or less, whereas Illumina protocols often need two full days or more.
2) Long-reads should improve the accuracy of haplotype phasing (haplotype estimation). The statistical models in phasing algorithms depend on the number and distribution of chromosomal SNP‘s. Long-reads should increase the number of sampled SNP’s per read and show their correct order, relative to those in short-reads. Presumably, this will help determine more accurately the linkage disequilibrium among HLA alleles, and thereby help resolve the correct haplotypes derived from sequencing data.
It will be very interesting to compare long-read and short-read HLA sequencing methods when NGS-Turbo is available.