Genetic Testing for PFIC
Guest Blog by Chunyue Yin, Phd and Wenying Zhang, MD, PhD, MBA, FACMG
Genetic testing has become a cornerstone in the diagnosis of progressive familial intrahepatic cholestasis (PFIC). Historically, and in many settings still today, PFIC has been diagnosed based on clinical features such as early-onset cholestasis, serum liver function test results, liver biopsy findings, and exclusion of other causes.
However, making a diagnosis based only on symptoms and clinical signs can be tricky, because different genetic types of PFIC can look very similar. Genetic testing helps identify the exact gene change causing the condition. This can give patients a clearer idea of what to expect over time, help doctors choose the most appropriate treatments, and provide more accurate information for family planning. By identifying specific genetic changes, healthcare providers can often reach a definitive diagnosis, which is essential for guiding treatment and long-term care. In this blog, we explain what genetic testing is, why it matters, the different types of tests available, how to understand results, and the current challenges in genetic testing.
What is genetic testing?
Genetic testing looks for changes (called “variants”) in DNA that may explain a person’s symptoms or disease. DNA can be thought of as the body’s instruction manual. Sometimes, a spelling change in that manual disrupts how cells function and leads to disease. Genetic testing helps identify these changes. However, not all diseases have a known genetic cause, and some test results remain uncertain.
How does genetic testing work?
Genetic testing may sound complicated, but the process is actually very systematic. It starts with collecting a small sample, usually a blood draw or sometimes a saliva or cheek swab, by the patient’s healthcare team. This sample is carefully labeled and sent to a specialized genetics laboratory.
At the lab, scientists first extract DNA from the sample. DNA is the body’s instruction manual that contains all of our genes. The DNA is then placed into highly sensitive sequencing machines that can “read” the genetic code letter by letter.
Powerful computers then compare the patient’s DNA sequence to a reference sequence to look for differences (called variants). Trained laboratory geneticists and clinicians review these findings carefully to determine which changes are meaningful and whether they explain the patient’s condition.
Finally, the lab generates a clinical report that is sent back to the ordering provider, who discusses the results and next steps with the patient and/or their family.
Why genetic testing matters
Early diagnosis and intervention
Genetic testing can identify PFIC early, sometimes even before severe liver damage occurs. Early diagnosis allows doctors to begin appropriate management sooner, which may slow disease progression and improve quality of life.
Family planning and genetic counseling
For families affected by PFIC, genetic testing provides important information about the chance of the condition occurring again in future pregnancies. Genetic counseling helps families understand inheritance patterns and testing options. Carrier testing may also identify relatives who carry the same genetic change, allowing earlier monitoring or intervention if needed.
Personalized treatment approaches
Identifying the exact genetic cause of PFIC can guide treatment decisions. Some genetic forms of PFIC respond better to specific medications or dietary approaches, while others may progress more quickly. In advanced cases, genetic results can help inform decisions about liver transplantation.
Advancing research
Genetic testing also benefits the broader PFIC community. While many PFIC-related genes have already been identified, there are likely additional genes and disease mechanisms that we have not yet fully discovered or understood. By identifying and studying disease-causing variants through genetic testing, researchers can uncover new genetic causes, better understand how PFIC develops, and explore new treatment strategies. This ongoing discovery is essential for improving care for current patients and expanding options for future patients.
Different types of genetic testing
Targeted gene panels
Gene panel tests look at a specific group of genes that are already known to cause cholestatic liver disease. When a person’s symptoms strongly suggest a genetic form of cholestasis, a gene panel is often the fastest and most cost-effective first test. Because the test focuses on genes that are already well studied, the results are usually easier for doctors to interpret.
However, if the disease is caused by a newly discovered gene or a gene not yet known to be related to cholestasis, a gene panel may not detect it. As new research identifies additional disease-related genes, it is important that the gene lists used in these panels are regularly updated, which helps improve the chance of finding a diagnosis.
Whole-exome sequencing (WES)
If gene panel testing is negative, doctors may recommend whole-exome sequencing (WES). WES analyzes the protein-coding regions of nearly all genes—about 20,000 genes—which contain the majority of known disease-causing variants. This broader approach can identify rare or unexpected causes, but it also increases the chance of uncertain findings that require careful interpretation.
Whole-genome sequencing (WGS)
When WES does not identify a clear cause, whole-genome sequencing (WGS) may be considered. WGS examines nearly all DNA, including non-coding regions and large structural changes. Non-coding regions act like switches that control when and where genes are turned on and how genes are processed and expressed. Structural changes involve missing, duplicated, or rearranged DNA segments. WGS provides the most comprehensive view of the genome but is more expensive, time-consuming, and complex to interpret.
Other important considerations
It is common to wonder: why not just start with whole genome sequencing (WGS) for everyone?
The answer is that different genetic tests each have advantages and trade-offs. Targeted gene panels are usually faster, less expensive, and generate fewer uncertain findings, making them a practical first step when a condition like PFIC is strongly suspected. More comprehensive tests such as WES or WGS analyze far more genetic information but are typically more costly, more resource-intensive to interpret, and more likely to uncover unexpected or uncertain results that may not be immediately helpful.
For many patients, a stepwise approach, starting with focused testing and moving to broader testing if needed, provides the most efficient and clinically useful path. Importantly, in complex or unclear cases, WES or WGS can be extremely valuable because they allow us to look beyond known PFIC genes and potentially discover new or rare genetic causes.
Singleton versus trio testing
Testing the patient alone is called “singleton testing”. Testing both parents and the child together is called “trio testing”. Trio testing increases the chance of finding a diagnosis by about 10–15%. Comparing the child’s DNA with both parents helps doctors see exactly where each genetic change came from. For example, parents may each silently carry one PFIC-related variant without being affected themselves; if the child inherits one changed copy from each parent in the same gene, the two changes together can cause disease. This is called compound heterozygosity: in simple terms, the child has two different “spelling changes” in the same gene, one from each parent.
Trio testing also makes it easier to identify de novo variants, which are new genetic changes that arise for the first time in the child and are not present in either parent. In this case, the risk of having another child with the same disease is extremely low. Knowing whether a variant was inherited or occurred de novo helps clarify the diagnosis, improves confidence in the results, and provides more accurate information about recurrence risk for the family.
Reanalysis of results
As new genes and variants not previously known to be related to cholestatic liver disease are discovered, data from previously negative tests may become informative. We recommend reanalyzing WES or WGS data at least every three years for patients who did not initially receive a diagnosis.
Understanding genetic test results
When a patient has genetic testing done and the results show a genetic variant (a change in your DNA), the next important step is to determine what that variant means.
Each variant is carefully reviewed by experts and classified based on how strongly the scientific evidence supports that it causes disease. Laboratories use standard categories for this process:
- Pathogenic – Strong evidence shows the variant causes disease
- Likely pathogenic– Evidence strongly suggests the variant causes disease
- Variant of Uncertain Significance (VUS) – Not enough information to determine whether the variant is harmful or harmless
- Likely benign – Evidence suggests the variant does not cause disease
- Benign– Strong evidence shows this genetic change is harmless. It means the variant does not cause liver disease.
The word “benign” here has a different meaning than in benign recurrent intrahepatic cholestasis (BRIC). In BRIC, the word “benign” describes the disease, not the DNA change. BRIC is called “benign” because the symptoms are usually milder and the liver often recovers between episodes, compared with PFIC. However, the genetic variants that cause BRIC are still disease-causing.
Most laboratories report only pathogenic, likely pathogenic, or VUS results. Clinicians then interpret these findings alongside clinical symptoms, laboratory results, imaging, biopsy findings, and family history to determine whether a diagnosis has been made. Over time, as more patients are studied and more research is done, a variant’s classification can sometimes change, especially for VUS results.
The roles of genetic counselor
A genetic counselor is a healthcare professional with specialized training in medical genetics and patient communication who helps individuals and families understand and navigate genetic testing. Their role is to guide patients through the testing process in a way that is medically accurate, emotionally supportive, and tailored to each family’s situation.
Before testing, the genetic counselor reviews the patient’s medical and family history to assess whether genetic testing is appropriate and which test is most likely to be helpful. They explain what the test can and cannot tell us, discuss possible types of results, and help families weigh the benefits, limitations, and potential costs. This step is important for setting expectations and ensuring informed decision-making.
After results are available, the genetic counselor helps interpret what the findings mean in practical terms. They translate complex genetic information into clear language, clarify whether a variant explains the patient’s condition, and discuss implications for medical management. They also help families understand inheritance patterns, including whether other relatives may be at risk and what the chances are for future children. When results are uncertain—such as a variant of uncertain significance—the counselor provides context and helps families cope with the ambiguity while outlining possible next steps.
In conditions like PFIC and other genetic cholestatic liver diseases, where testing and interpretation can be complex and knowledge is still evolving, genetic counselors play an important role in bridging advanced genomic data with real-world clinical care and family planning. Their goal is to ensure that families not only receive results but truly understand what those results mean for their health and their future.
Challenges in genetic testing
Although exome and genome sequencing have greatly improved diagnosis, more than half of patients with chronic cholestasis still do not receive a clear genetic answer. One major challenge is the high number of VUS results, which lack enough evidence for clear interpretation. Mislabeling these variants can lead to unnecessary worry or missed treatment opportunities.
Resolving a VUS often requires additional family testing, specialized laboratory experiments, or identification of other patients with similar variants. In routine clinical care, however, these steps can be challenging to complete. Additional testing of parents or relatives may not be covered by insurance, family members may be unavailable or live far away, and coordinating testing takes time. Functional laboratory studies—which can help determine whether a variant disrupts gene function—are typically performed only in research settings and are not widely available in clinical laboratories. In addition, many hospitals and clinics do not have the infrastructure or resources to systematically reanalyze variants as new knowledge emerges.
Because of these practical barriers, many VUS results remain unresolved for years. This may contribute to the reality that a substantial proportion of patients who ultimately require liver transplantation for cholestatic liver disease never receive a definitive molecular diagnosis. For families currently navigating a VUS result, understanding these limitations can be helpful: lack of resolution often reflects gaps in available data and resources rather than anything unusual about the patient or the quality of their care.
Sometimes a person has symptoms that seem genetic, but they are actually caused by things in their environment or by many genes working together. Also, today’s genetic tests cannot find every kind of DNA change. Some conditions are caused by changes in how genes are turned on or off (called epigenetic changes), and these do not show up on regular genetic tests. Finally, different labs may look at the same DNA change and come to different conclusions, which can lead to different results.
A hopeful outlook
Despite these challenges, there is strong reason for optimism. Researchers are always working to make genetic testing better. They are improving the tools used to read DNA (sequencing technologies) and using artificial intelligence to study genetic information more quickly. In the laboratory, they introduce newly discovered variants into cells, zebrafish, and mice and use special test systems to figure out if and how they cause disease. These advances are helping uncover answers that were not possible just a few years ago.
Progress in rare disease research depends on support from funding agencies, industry partners, and philanthropy. Because rare diseases affect relatively few patients, this work is often overlooked. Equally important is the partnership with patients and their families—through participation in research studies, sharing blood or liver samples that allow scientists to study disease in the lab, and, when possible, philanthropic support. Together, scientific innovation and family involvement bring us closer to earlier diagnoses, better treatments, and lasting hope for the future.
About the authors
Chunyue Yin, Phd.
Chunyue Yin, Ph.D, is a liver researcher and Associate Professor at the University of Cincinnati. She co-directs the Center for Undiagnosed and Rare Liver Disease and leads the Yin Research Lab.
MD, PhD, MBA, FACMG
- Director, Genetics and Genomics Diagnostic Laboratory, Division of Human Genetics, CCHMC
- Professor, University of Cincinnati Department of Pediatrics