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genoABO

genoABO infers genetically determined ABO blood group from VCF, BGEN, PGEN, and PLINK genotype datasets.

How ABO type arises

How ABO blood-group antigens are formed

Figure. The ABO gene controls glycosyltransferase activity on the shared H-antigen precursor. A and B transferases add different terminal sugars, AB expresses both antigen types, and common O alleles encode inactive transferase, leaving H unchanged. Rare H-deficient phenotypes are not shown.

pip install genoabo
genoabo biobank.pgen --out bloodgroup

Research use only

genoABO is intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research. Genotype-inferred ABO groups do not capture all rare, weak, cis-AB, structural, or otherwise atypical ABO alleles and must not be used for transfusion or clinical decision-making.

Quick start

genoabo cohort.pgen --out abo
# writes: abo.abo.tsv, abo.qc.tsv, abo.summary.txt, abo.report.html

From genotype to inferred type

ABO tag SNPs on chromosome 9

Figure. Four tag SNPs in ABO on chr9: rs8176719 (O-defining c.261delG), rs8176746 and rs8176747 (A vs B), and rs505922 (O LD proxy). See Markers and Inference methods.

See Usage for install, CLI flags, outputs, and the Python API.

See Workflow for the full load-to-output pipeline.

See Examples for VCF (unphased and phased), PGEN, and PLINK1 demos across builds and marker notations, a 1000 Genomes EAS four-marker example, a multi-ancestry --assume-bo check, and marker LD r².

See Update Log for release notes.

Formats and methods

Supported inputs: VCF/BCF, PLINK2 PGEN, PLINK1, and BGEN. Methods: common, three-marker, ukb, extended (auto selects among three-marker, common, and ukb). Phenotypes: A, B, AB, O. See Usage for formats and flags, and Inference methods for haplotype rules.

Citations

Full records are printed by genoabo --method-info NAME and in the Citations section of each HTML run report.

  • software — Yunye He. genoABO: genetically determined ABO blood group inference from genotype datasets. Version 0.3.1. 2026. https://github.com/cloufield/genoABO.
  • common — Melzer D, Perry JRB, Hernandez D, Corsi AM, Stevens K, Rafferty I, et al. A genome-wide association study identifies protein quantitative trait loci (pQTLs). PLoS Genet. 2008;4:e1000072. DOI: 10.1371/journal.pgen.1000072. PMID: 18464913.
  • three-marker — Fry AE, Griffiths MJ, Auburn S, Diakite M, Forton JT, Green A, et al. Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria. Hum Mol Genet. 2008;17:567–576. DOI: 10.1093/hmg/ddm331. PMID: 18003641.
  • ukb — UK Biobank. Data-Field 23165: Blood-type haplotype. https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=23165.
  • extended — Daniels GL, Fletcher A, Garratty G, Henry S, Jørgensen J, Judd WJ, et al. Blood group terminology 2004: from the International Society of Blood Transfusion committee on terminology for red cell surface antigens. Vox Sang. 2004;87:304–316. DOI: 10.1111/j.1423-0410.2004.00564.x. PMID: 15585029.

See Inference methods for used-in and molecular-basis notes.