ARPKD affects roughly one in 20,000 children. The disease causes liquid-filled cysts to form in the kidney, and those cysts can appear even before a child is born. For newborns, they can be life-threatening, and for some patients the damage accumulates until the kidneys fail before adulthood. The segment of the kidney primarily affected is the collecting duct, the network of tubules responsible for draining urine from the organ. Because the disease is rare and its cellular origins are difficult to access in living patients, researchers have long lacked the experimental systems needed to watch the disease unfold at the cellular level, let alone to screen potential therapies against it. Li’s project is designed to close that gap.

The strategy rests on two complementary types of lab-grown biological systems, both derived from human stem cells. The first is the organoid, a three-dimensional structure grown from a type of progenitor cell that gives rise to the collecting duct system. In a Petri dish, these organoids self-organize into elongated tubules that closely mimic the architecture and function of human collecting duct tissue. The second is the assembloid, a more complex construct grown by combining collecting duct progenitor cells with cells that develop into the kidney’s filtering units, allowing two distinct compartments of the organ to be modeled together. With success, the project’s organizers say, these systems could become a major enabling factor for basic, translational and clinical research tackling ARPKD.

The power of the organoid approach lies in scale and speed. Because the structures are grown from human cells in culture, researchers can manufacture hundreds of thousands of them cost-effectively, according to Li. That opens the door to high-throughput drug screening, in which vast libraries of candidate compounds can be evaluated simultaneously against diseased tissue. Instead of testing one drug at a time in slow and expensive animal studies, scientists can rapidly identify the most promising molecules in vitro and then advance only the strongest candidates. For a disease as rare as ARPKD, where commercial incentives for drug development are limited, such a screening platform could dramatically lower the barriers to discovering new therapies.

The assembloid arm of the project addresses a different and equally stubborn problem in drug development: the failure of treatments that looked promising in the lab but collapsed in clinical trials. Li points to two major reasons such failures occur, kidney toxicity and the biological differences between animal models and human patients. His team’s plan is to grow diseased human kidney tissue in the form of assembloids and transplant it into mice, creating what researchers describe as a humanized model of the disease living inside an animal host. Drugs tested against that tissue would, in principle, yield far more accurate predictions of both efficacy and safety in human patients than conventional animal models can provide, because the target tissue itself would be human.

The project does not begin from scratch. Li’s research group has already developed a collecting duct organoid that closely mimics the structure and function of human tissue, and the team has shown that it can effectively model a related, more common condition: autosomal dominant polycystic kidney disease, or ADPKD. ADPKD accounts for about 90 percent of all polycystic kidney disease cases and is generally a milder illness that tends to emerge during adulthood rather than before birth. Having modeled ADPKD both in Petri dishes with collecting duct organoids and in mice with assembloids, the researchers now plan to apply the same principles to ARPKD, adapting systems they have already validated to a rarer and more severe form of the disease.

International collaboration supplies another key ingredient. Cell lines carrying ARPKD-related mutations were provided by the two researchers who developed them: Yun Xia, PhD, of Singapore’s Agency for Science, Technology and Research, and Ryuji Morizane, MD, PhD, of Harvard Medical School. These mutated cell lines serve as the starting material from which the diseased organoids and assembloids will be grown, embedding the genetic defects that drive cyst formation into the lab-grown tissue itself. Li has described the generosity of these colleagues as a perfect example of how the research community works together to help patients, a reminder that progress on rare diseases often depends on scientists sharing hard-won tools across institutions and continents.

The grant also reflects a deliberate strategic bet by the funder. The PKD Foundation, founded in 1982, is the only organization in the United States solely dedicated to finding treatments and a cure for polycystic kidney disease, and it is the largest private funder of research into the illness. Susan Bushnell, the foundation’s president and CEO, said that the field is seeing unprecedented momentum in PKD research and that the organization believes this is the right time to invest boldly in the scientists working to change the future of the disease. Because of the generosity of donors, she noted, the foundation is able to increase its investment in promising research that represents hope for the millions of people and families living with PKD.

For Li, the ARPKD project is one milestone within a much larger scientific mission. For nearly 15 years, he has worked on coaxing stem cells to produce kidney-like structures, with the long-term goal of engineering an artificial kidney for patients awaiting an organ transplant. The scale of that unmet need is enormous: kidneys account for about 80 percent of the demand for donor organs, and more than 90,000 people are on the kidney donation waitlist in the United States alone. Engineering a transplantable kidney, Li has said, is the ultimate goal of his career, but along the way, developing kidney-like tissue in which disease can be modeled and new therapies found offers the chance to meaningfully benefit patients with kidney disease now.

The significance of the work extends beyond a single rare disease. If collecting duct organoids and kidney assembloids prove reliable models for ARPKD, the same platforms could accelerate research into ADPKD and other disorders of the kidney’s tubular and filtering systems, and could sharpen the preclinical testing pipeline for any drug destined for the kidney. The approach also illustrates a broader shift in biomedical science, as human stem cell-derived tissues increasingly replace or supplement animal models whose biology often fails to translate to patients. For the families facing ARPKD, a condition that currently offers few answers, the grant represents something concrete: a funded, technically grounded path toward the models that drug discovery requires, built from the very cells where the disease begins.

Subject of Research: Development of human stem cell-derived organoid and assembloid models for autosomal recessive polycystic kidney disease research

Article Title: PKD Foundation provides support for kidney disease research by USC Stem Cell’s Zhongwei Li

Article References: PKD Foundation provides support for kidney disease research by USC Stem Cell’s Zhongwei Li. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: polycystic kidney disease, ARPKD, organoids, assembloids, stem cells, kidney disease, PKD Foundation, drug screening, collecting duct, USC Stem Cell, genetic disease, transplantation

The central challenge the team confronted is a notorious one in human genetics. PKD1 shares extensive stretches of near-identical sequence with six pseudogenes located elsewhere on chromosome 16, remnants of duplicated DNA that have lost their protein-coding function. Any sequencing approach that reads the genome indiscriminately risks aligning true PKD1 reads to the wrong location or, worse, mistaking pseudogene sequence for genuine gene sequence, producing false calls that could mislead clinical decisions. To sidestep this interference, the researchers employed long-range PCR, a technique that selectively amplifies the functional PKD1 gene in large fragments before sequencing, effectively isolating the target from its deceptive copies.

Oxford Nanopore Technology has attracted growing interest in clinical genomics because of its accessibility. A MinION device is roughly the size of a large USB stick, requires comparatively modest capital investment, and can be run in laboratories far from major sequencing centers. The trade-off has always been accuracy: nanopore reads carry higher error rates than the short-read Illumina platforms that dominate clinical laboratories, because each DNA strand threads through a protein pore and is read base by base as electrical current fluctuations. Raw errors, however, are largely random rather than systematic, which means that reading the same molecule many times and applying sophisticated computational correction can drive the consensus error rate down to levels suitable for variant calling. The catch is that this correction demands careful bioinformatic optimization, and until now no validated, end-to-end pipeline existed specifically for PKD1 on the nanopore platform.

The Chilean team built their solution as a nine-stage bioinformatic pipeline, with each stage dedicated to a distinct computational task in the journey from raw electrical signal to final variant call. The stages encompass the standard architecture of modern long-read analysis: quality assessment of the raw data, basecalling that converts current measurements into DNA sequence, demultiplexing to sort reads by sample, adapter trimming and filtering to remove artifacts, alignment of reads to the human reference genome, post-alignment processing, variant calling, and annotation that interprets each variant’s likely biological consequence. Crucially, rather than adopting tools by default, the authors performed a systematic, criteria-based selection at every stage, comparing candidate programs against explicit performance benchmarks to choose the configuration best suited to the error profile of nanopore data derived from long-range PCR amplicons.

This structured development approach is what distinguishes the work from ad hoc bioinformatics. Nanopore pipelines are notoriously sensitive to parameter choices: the settings that work for whole-genome sequencing of bacteria may fail badly when applied to a single amplified human gene, where coverage is deep, read lengths are constrained by the PCR fragment size, and homopolymer stretches, runs of identical bases that nanopore sequencers historically struggled to measure, can distort indel calls. By evaluating tools stage by stage against defined criteria, the team produced a reproducible framework whose behavior can be understood and audited, an essential property for any pipeline intended for clinical use. The pipeline was also designed with computational efficiency in mind, so that it can run on modest hardware rather than demanding a high-performance computing cluster, although the authors acknowledged the Patagn supercomputer team for supporting their development work.

Validation proceeded in two independent cohorts with distinct purposes. The first consisted of eight samples in which PKD1 variants had already been confirmed by Sanger sequencing, the decades-old method that reads DNA through chain-termination chemistry and remains the reference standard in many clinical laboratories. The optimized nanopore pipeline achieved complete concordance with Sanger across all eight samples, correctly recovering every previously known variant without introducing false positives. This head-to-head agreement is the critical benchmark for any platform aspiring to clinical deployment, because it demonstrates that the computational corrections have neutralized the platform’s raw error rate to the point where the two technologies deliver identical answers on real patient material.

The second cohort provided the true test of diagnostic utility: 26 ADPKD patients who had never received a molecular diagnosis. When the pipeline was applied to their sequenced samples, it identified pathogenic or likely pathogenic PKD1 variants in 69 percent of cases, a detection rate consistent with the known genetics of ADPKD, in which PKD1 accounts for the large majority of cases with an identifiable cause and roughly a tenth of patients carry variants in PKD2 or other genes instead. Among the prioritized findings were six variants never before reported, expanding the catalog of known disease-causing mutations in the gene. To confirm these new calls, the researchers sent 18 prioritized variants for independent Sanger verification, and 17 were confirmed, a validation rate that underscores both the sensitivity of the pipeline and the value of orthogonal confirmation for novel discoveries.

The implications reach well beyond a single gene. ADPKD is one of the most common inherited kidney diseases worldwide, and targeted therapies now exist that can slow disease progression, making early molecular diagnosis clinically meaningful rather than merely informative. Yet in many countries, including Chile where this study was conducted, patients may wait years for genetic testing or never receive it, because sending samples to commercial laboratories abroad is costly and short-read sequencing of PKD1 requires careful strategies to handle the pseudogene problem. A pipeline that runs on a benchtop nanopore device, uses long-range PCR to guarantee specificity, and delivers Sanger-concordant results changes the calculus for public health systems, allowing regional hospitals and university laboratories to perform the analysis in-house at low infrastructure cost.

The work also offers a template for tackling other clinically important genes haunted by pseudogenes or other architectural complexities. Many disease genes share this burden, and the authors argue that their structured, criteria-based development approach, demonstrated diagnostic performance, and computational optimization make the framework applicable to genomic research and clinical settings requiring high-sensitivity analysis of large, complex genes. Because the pipeline is described as reproducible and its development logic is documented stage by stage, other groups can adapt it rather than rebuilding the analysis from scratch, accelerating the spread of long-read diagnostics into low-resource environments.

The study, conducted under ethical approval from the Research Ethics Committee of the Health Service of Valdivia and with informed consent from all participants recruited across Chilean health centers, was supported by Chile’s National Agency for Research and Development through FONDECYT Regular projects and by Innovation Fund for Competitiveness grants from the Regional Government of Los Ros. The authors credit collaboration among the Nephrology Laboratory of Universidad Austral de Chile, the Valdivia Base Hospital, the Centro de Investigacin Clnica Avanzada, and nephrologists across the country who connected patients with the research. As nanopore sequencing matures from a promising technology into a validated clinical tool, this pipeline stands as evidence that careful bioinformatics, not expensive hardware, can be the decisive factor in bringing precision diagnosis to patients who have historically been left waiting.

Subject of Research: Development and clinical validation of an Oxford Nanopore bioinformatic pipeline for detecting PKD1 variants in autosomal dominant polycystic kidney disease

Article Title: An optimized nanopore-based bioinformatic pipeline for PKD1 variant detection: development and validation with clinical samples

Article References: Millar, D., Gajardo, M., Poblete, B., Ubilla, R., Izquierdo, M., Medina, A., Lehmann, P., Flores, C., Krall, P., & Maturana, J. (2026). An optimized nanopore-based bioinformatic pipeline for PKD1 variant detection: development and validation with clinical samples. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06644-4

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06644-4

Keywords: Oxford Nanopore Technology, PKD1, ADPKD, long-read sequencing, bioinformatic pipeline, variant detection, pseudogene, long-range PCR, Sanger sequencing, polycystic kidney disease, low-resource sequencing, clinical genomics