genoSecretor¶

genoSecretor infers genetically determined FUT2 secretor status from VCF, BGEN, PGEN, and PLINK genotype datasets.

What is secretor status?¶

Secretor status describes whether FUT2 enables formation of soluble H antigen in saliva and other mucosal secretions. A functional FUT2 copy usually gives secretor status, reduced-activity copies can give weak-secretor status, and two complete-null copies give non-secretor status. ABO enzymes may then convert H into A or B antigen according to a person's ABO genotype—secretor status does not determine ABO blood type.

Figure. FUT2 adds fucose to a type-1 precursor to make soluble H antigen, which may become A or B antigen according to ABO genotype. genoSecretor infers secretor, weak-secretor, or non-secretor status from common FUT2 variants; it does not perform a serological test.

How genoSecretor infers it¶

FUT2 tag SNPs on chromosome 19

Figure. Three tag SNPs in FUT2 on chr19: rs1047781 (weak se385), rs601338 (complete LoF se428), and rs602662 (se428 LD proxy). See Markers and Inference methods.

pip install genosecretor
genosecretor biobank.pgen --out secretor

Research use only

genoSecretor is intended for population-genetics, epidemiology, GWAS, PheWAS, and biobank research. Genotype-inferred secretor status does not capture all rare or atypical FUT2 alleles and must not be used for clinical decision-making.

Quick start¶

genosecretor cohort.pgen --out secretor
# writes: secretor.secretor.tsv, secretor.qc.tsv, secretor.summary.txt, secretor.report.html

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

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

See Examples for VCF, PGEN, and PLINK1 demos (./examples/run_synthetic.sh), plus 1000 Genomes FUT2 slices, --assume-trans vs phase, and marker LD r².

See Update Log for release notes.

Formats and methods¶

Supported inputs: VCF/BCF, PLINK2 PGEN, PLINK1, and BGEN. Methods: two-marker, common, eas, proxy (auto selects among them, with --ancestry so East Asian files missing rs1047781 are not typed with common). Phenotypes: secretor, weak-secretor, non-secretor. See Usage for formats and flags, and Inference methods for haplotype rules.

Citation¶

If you use genoSecretor, please cite:

Yunye He. genoSecretor: genetically determined FUT2 secretor status inference from genotype datasets. Version 0.3.0. 2026. https://github.com/cloufield/genoSecretor.

Method-specific references are listed under Inference methods and printed by genosecretor --method-info NAME.

License¶

MIT.