RBCeq: A robust and scalable algorithm for accurate genetic blood typing

Abstract

Background While blood transfusion is an essential cornerstone of hematological care, patients requiring repetitive transfusion remain at persistent risk of alloimmunization due to the diversity of human blood group polymorphisms. Despite the promise, user friendly methods to accurately identify blood types from next-generation sequencing data are currently lacking. To address this unmet need, we have developed RBCeq, a novel genetic blood typing algorithm to accurately identify 36 blood group systems.Methods RBCeq can predict complex blood groups such as RH, and ABO that require identification of small indels and copy number variants. RBCeq also reports clinically significant, rare, and novel variants with potential clinical relevance that may lead to the identification of novel blood group alleles.Findings The RBCeq algorithm demonstrated 99¢07% concordance when validated on 402 samples which included 29 antigens with serology and 9 antigens with SNP-array validation in 14 blood group systems and 59 antigens validation on manual predicted phenotype from variant call files. We have also developed a user-friendly web server that generates detailed blood typing reports with advanced visualization (https://www.rbceq.org/). Interpretation RBCeq will assist blood banks and immunohematology laboratories by overcoming existing methodological limitations like scalability, reproducibility, and accuracy when genotyping and phenotyping in multi-ethnic populations. This Amazon Web Services (AWS) cloud based platform has the potential to reduce pre-transfusion testing time and to increase sample processing throughput, ultimately improving quality of patient care.

The genomic landscape of blood groups in Indigenous Australians in remote communities

“…We predicted the blood group antigen profiles for the Tiwi (457) and 1KGP3 (2504) cohort individuals using RBCeq (https://www.rbceq.org/). 5 The genomic variant call format (gvcf) of each sample was given as input with the blood group gene coverage calculated using the BAMTrimmer tool within RBCeq. RBCeq considers SNV, indels from 45 genes and calculates CNV to profile 36 blood groups and two transcription factors (Table S1).…”

“…The score helps to select allele pair which considers most of the known present variants from the input vcf file. The detailed method is described in Jadhao et al, 2022 5 …”

“…The detailed method is described in Jadhao et al, 2022. 5 The RBCeq output included the prediction of International Society of Blood Transfusion (ISBT) known blood group antigen alleles and phenotype. RBCeq also classified the filtered high-quality deleterious variants which are not mapped to known ISBT alleles.…”

“…While these technologies are powerful, there is currently a lack of comprehensive software packages with the storage and processing capability necessary to handle large volumes of NGS data and to accurately predict blood group phenotypes. Recently, our group developed RBCeq, a web server‐based blood group genotyping software designed to improve blood type compatibility testing, and to facilitate the accurate mass screening of blood groups in diverse populations with distinctive and complex blood group profiles 5 …”

“…Recently, our group developed RBCeq, a web server-based blood group genotyping software designed to improve blood type compatibility testing, and to facilitate the accurate mass screening of blood groups in diverse populations with distinctive and complex blood group profiles. 5 Australia is a multiethnic nation, with roughly onethird of the population having been born overseas. However, most Australian blood donors are Caucasian.…”