Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience

Comparison of sequence‐specific oligonucleotide probe vs next generation sequencing for HLA‐A, B, C, DRB1, DRB3/B4/B5, DQA1, DQB1, DPA1, and DPB1 typing: Toward single‐pass high‐resolution HLA typing in support of solid organ and hematopoietic cell transplant programs

“…A number of major transitions in technology platforms utilized for HLA typing have taken place over past decades, and the emergence of NGS for HLA surely marks the latest of these transitions. HLA typing for hematopoietic cell transplants has already seen the introduction of NGS HLA typing in clinical laboratories, and with careful attention to key metrics, provides an effective replacement of other technologies . In this context, a continuation of new alleles is discovered, in particular with respect to the ability of NGS technologies to examine most or all exon sequences over the subset of exons examined using older methods .…”

“…HLA typing for hematopoietic cell transplants has already seen the introduction of NGS HLA typing in clinical laboratories, and with careful attention to key metrics, provides an effective replacement of other technologies. [16][17][18] In this context, a continuation of new alleles is discovered, in particular with respect to the ability of NGS technologies to examine most or all exon sequences over the subset of exons examined using older methods. 18 While currently in limited use in clinical typing laboratories, these methods have been and continue to be very effectively used in establishing more comprehensive database entries for registries.…”

Identifying a newly discovered HLA‐C allele: HLA‐C*07:607

“…Indirect determination of phasing by variant pattern recognition is susceptible to being misled by rare or novel alleles. As NGS becomes more common in clinical settings, it has the opportunity not only to test more introns and exons to a greater resolution than earlier possible but also to resolve ambiguity even in cases where it was not suspected …”

HLA‐B*45:22: a novel allele that differs from HLA‐B*45:01:01 at several locations

“…In comparison, NGS generated nonambiguous results in one step that were able to explain the nonstandard results from the other methods. By using phased sequencing of all exons and introns NGS can quickly and clearly type patients with novel or rare alleles that confound other typing methods …”

“…By using phased sequencing of all exons and introns NGS can quickly and clearly type patients with novel or rare alleles that confound other typing methods. [3][4][5] NGS is currently undergoing widespread adoption as a replacement for other high resolution methods such as SBT and SSP. Low cost, low resolution methods such as SSO maintain their market because of their speed, low cost, and utility as a screening tool.…”