Non-invasive fetal HLA and KIR genotyping of cell-free DNA from maternal blood

The National Institute of Child Health and Human Development awarded $436,100 to the University of North Carolina at Charlotte on September 1, 2026, under the Child Health and Human Development Extramural Research program (CFDA 93.865) to develop and validate non-invasive high-resolution fetal HLA and KIR genotyping protocols using cell-free DNA from maternal blood.

The project addresses preeclampsia risk stratification in early pregnancy by developing a high-resolution HLA genotyping protocol for cell-free fetal DNA and a corresponding bioinformatics pipeline to distinguish maternal and fetal genotypes from sequencing reads. The recipient will develop and validate a non-invasive method for fetal HLA genotyping from maternal blood cell-free DNA collected at 10–20 weeks of pregnancy using probe panel hybrid capture enrichment and sequencing on the Illumina platform, validated with maternal, paternal, and fetal samples. Additionally, the project will develop and validate a high-resolution fetal KIR genotyping protocol from maternal cell-free DNA, addressing structural variation and sequence homology challenges in the KIR region and validating results with maternal-fetal dyads and trios. Upon completion, the recipient expects to have a validated high-resolution fetal KIR-HLA genotyping protocol that facilitates development of a prognostic tool for preeclampsia.

Performance occurs in Charlotte, NC 28223. The award covers the period of performance from September 1, 2026, through August 31, 2028.

Abstract

Hypertensive disorders in gestational stages, particularly preeclampsia, are a leading cause of maternal mortality globally, accounting for approximately 14% of maternal deaths and affecting 62,000 to 77,000 women annually. In the US, afican american mothers face a 60% higher prevalence and a threefold higher mortality rate compared to others. This study focuses on the immune-related gene families KIR (killer-cell immunoglobulin-like receptor) and HLA (human leukocyte antigen), whose maternal-fetal genotype interactions significantly influence preeclampsia risk. A specific KIR-HLA combination increases preeclampsia risk twofold, but the clinical application has been limited by technical challenges in fetal genotyping. Our project aims to develop a non-invasive test for early gestational risk stratification of preeclampsia using cell-free fetal DNA (cfdna) from maternal blood. This proposal aligns with the white house executive order to advance research and the notice of special interest for high priority areas in placental research. Our team will develop a high-resolution HLA genotyping protocol for cfdna and bioinformatics pipeline to distinguish maternal and fetal genotypes from cfdna sequencing reads. We aim to develop and validate a non-invasive method for fetal HLA genotyping from maternal blood cfdna collected at 10-20 weeks of pregnancy using a probe panel for hybrid capture enrichment and sequencing on the illumina platform, validated with maternal, paternal, and fetal samples. In addition, we propose to develop and validate a high-resolution fetal KIR genotyping protocol from maternal cfdna, addressing the challenges of structural variation and sequence homology in the KIR region and validating IT with maternal-fetal dyads and trios. Upon completion, we expect to have a validated high-resolution fetal KIR-HLA genotyping protocol, facilitating the development of a prognostic biomarker for fetal-maternal health.