Is Your Immune System Fighting You? The Hidden Genetic Link to Autoimmune Diseases
So, how do autoimmune diseases begin? Basically, autoimmune diseases occur when the immune system attacks the body’s own tissues and organs. There are more than 100 distinct conditions in the category, affecting areas such as joints, skin, thyroid, pancreas, and the nervous system. Plus, over 80 autoimmune disorders are officially recognized in medical classifications.
Symptoms can range from chronic fatigue and muscle aches to organ-specific inflammation, making diagnosis challenging because different conditions can present with similar signs.
The Genetic Connection in Autoimmune Diseases
Genetics can determine an individual’s risk. Twin research has shown that identical twins have a much higher concordance for specific autoimmune diseases than fraternal twins, pointing to inherited factors as a major driver. Some genetic regions, especially the human leukocyte antigen (HLA) complex, are strongly associated with conditions such as type 1 diabetes, ankylosing spondylitis, and multiple sclerosis.
Autoimmune diseases also show a marked gender difference, with around 80% of cases occurring in women. Such patterns may be influenced by differences in sex hormones, immune gene expression, and chromosomal factors.
What genetic testing can uncover
Genetic testing identifies DNA variants that influence immune system function and susceptibility to disease. There are three main approaches:
- Targeted panel testing that screens a specific set of genes linked to immune conditions. The composition of these panels differs by laboratory, both in the genes included and the types of variants detected.
- Whole exome sequencing (WES) that examines the coding regions of more than 20,000 genes, offering a broader scope for complex or unclear presentations.
- Whole genome sequencing (WGS) that includes both coding and non-coding DNA, capturing regulatory variants and enabling future reanalysis as scientific understanding grows.
Results are typically reported as pathogenic, likely pathogenic, or variants of uncertain significance. Some labs also include secondary findings (clinically actionable variants unrelated to the original reason for testing) based on professional guidelines such as those from the American College of Medical Genetics and Genomics.
A Clinical Example of Autoimmune Genetic Testing
The Autoinflammatory and Autoimmunity Syndromes Panel from Invitae examines 156 genes associated with immune-mediated conditions. It achieves more than 99% analytical sensitivity and specificity for small DNA variants, with an average turnaround time of 14 days.
Such a test is important for patients whose symptoms overlap across multiple autoimmune diseases, as it helps narrow the list of possible diagnoses.
The progression from risk to disease
In autoimmune diseases, genetic susceptibility remains silent until immune regulation shifts and a trigger initiates inflammation. The three-step process can unfold over months or years, eventually leading to chronic tissue damage.
Some people experience multiple autoimmune diseases, a phenomenon that reflects shared genetic pathways. Genetic testing can uncover these connections, which may help clinicians design treatment plans that address the root immune dysfunction rather than only its most obvious symptoms.
When Genetic Testing is Valuable for Autoimmune Diseases
Strong family history – multiple relatives with autoimmune conditions
A comprehensive family history can be one of the clearest indicators for moving forward with genetic testing in autoimmune diseases. When multiple relatives across the same or different generations are affected by conditions such as rheumatoid arthritis, type 1 diabetes, or lupus, it suggests the possibility of inherited immune system variants.
These patterns can reveal shared risk genes and may also show clustering of related autoimmune conditions, even when they present differently in each person. Documenting at least three generations of health history, with details on age of onset and specific diagnoses, gives clinicians a stronger foundation to select the right testing approach.
Symptoms appearing early in life (in childhood or adolescence)
Early onset of symptoms is a red flag for a stronger genetic influence. Many autoimmune diseases present in adulthood, but when they emerge in childhood or adolescence, there is a higher likelihood that an inherited variant is playing a big role.
Early genetic testing in these cases can prevent years of doubt, reduce unnecessary investigations, and guide earlier treatment to protect organs from long-term damage. It can also help identify related immune system issues before they fully develop, allowing for preventive monitoring in both the patient and close family members.
Clinical presentation that is complex or spans multiple systems
When symptoms involve multiple organ systems, such as joint inflammation alongside neurological changes, skin rashes, or gastrointestinal problems, diagnosing based on traditional methods alone can be challenging. In such cases, genetic testing can uncover a single genetic explanation for a wide spectrum of symptoms.
It can shorten the path to an accurate diagnosis, ensure that treatment addresses the underlying immune dysfunction rather than isolated symptoms, and help avoid delays caused by misdirected referrals. Multi-system involvement is also a strong signal that the disease mechanism may overlap with other autoimmune conditions, which can influence the choice of therapy.
Suspicion of HLA-linked risks
Some autoimmune diseases are associated with HLA markers, making their detection a major part of the diagnostic process. For example, HLA-B27 is strongly linked to ankylosing spondylitis and related forms of inflammatory arthritis, while HLA-B51 is associated with Behçet’s disease. Finding these markers through genetic testing can back up a doctor’s diagnosis and help shape both current care and future plans.
It can also matter for relatives, who might choose to get screened if a high-risk HLA variant shows up. Including HLA analysis as part of a broader genetic panel can provide a more complete picture of immune system risk factors and their potential impact over time.
How Genetic Test Results Influence Autoimmune Disease Care
- Early monitoring of individuals with high-risk genetic profiles, even before symptoms appear.
- Selection of therapies that target specific immune pathways identified through testing.
- Family planning guidance through carrier testing and genetic counseling.
- Designing personalized screening schedules for associated complications.
- Genetic findings can also improve medication selection, avoiding trial-and-error in treatment and focusing on options most likely to control disease activity.
Move Forward with Lifecode’s Genetic Testing Kit
Genetic testing can reveal how inherited factors shape autoimmune disease risk. It helps doctors confirm or clarify a diagnosis, choose treatments that match the way a person’s immune system works, and decide which screenings might benefit relatives.
It also gives families clearer options for prevention and ongoing monitoring.
Lifecode’s easy-to-use genetic testing kit provides a practical way to take this step. You can also talk to one of our certified counselors to better understand the results.
Then, pair your test results with a detailed family history and symptom record, then work with your clinician to integrate the findings into a proactive care strategy.
Education: Bachelor of Pharmacy (B.Pharm) from the Tata Institute of Social Sciences (TISS), Mumbai Experience: Agarwal is a seasoned pharmacist with over 7 years of experience in the pharmaceutical field. She has worked in various settings, including hospital pharmacies and community clinics, where she has excelled in medication management, patient counseling, and clinical support. Agarwal is known for her expertise in drug therapy optimization and patient safety. In addition to her practical experience, she contributes to health journalism, focusing on pharmaceutical advancements and health policy, and is involved in research projects aimed at improving medication practices and health outcomes. is known for her expertise in drug therapy optimization and patient safety. In addition to her practical experience, she contributes to health journalism, focusing on pharmaceutical advancements and health policy, and is involved in research projects aimed at improving medication practices and health outcomes.