Peutz-Jeghers Syndrome — a hereditary hamartoma syndrome carrying >85% cumulative cancer risk across six organ systems, with surveillance protocols that must begin in childhood.
STK11 is on the ACMG SF v3.2 secondary findings list. Whole genome sequencing provides complete STK11 characterization, including the large genomic deletions that account for approximately 30% of PJS cases and are not reliably detected by standard sequencing panels.
Peutz-Jeghers Syndrome
Peutz-Jeghers syndrome (PJS) is an autosomal dominant hereditary gastrointestinal polyposis and cancer predisposition syndrome caused by germline pathogenic variants in STK11 (serine/threonine kinase 11, also known as LKB1) on chromosome 19p13.3. STK11 encodes a tumor suppressor kinase that activates AMPK and regulates cell polarity and energy metabolism. PJS is characterized by the development of characteristic hamartomatous polyps throughout the gastrointestinal tract (most prominently the small bowel), distinctive mucocutaneous pigmentation (melanin spots on lips, oral mucosa, digits, and perianal region), and dramatically elevated cancer risks across multiple organs. PJS has a prevalence of approximately 1 in 50,000-200,000.
The cumulative lifetime cancer risk in PJS is extraordinarily high — estimated at over 85% by age 70 for any cancer. Individual cancer lifetime risks include: gastrointestinal cancers (small bowel ~13%, colorectal ~40%, gastric ~29%), pancreatic cancer (~36%), breast cancer (~54% in females), gynecological cancers (cervical adenocarcinoma ~10%, uterine ~9%, ovarian sex cord tumor with annular tubules ~21%), and lung cancer (~15%). Surveillance must begin in childhood and must encompass multiple organ systems simultaneously. Small bowel polyps cause recurrent intussusception in childhood, often requiring emergency surgery — preventable with regular small bowel surveillance and prophylactic polypectomy when large polyps are identified.
Approximately 94-96% of PJS cases meeting syndromic diagnostic criteria have an identifiable STK11 pathogenic variant. Large deletions or duplications detectable by MLPA or copy number variant analysis account for approximately 30% of STK11 pathogenic variants — these are missed by standard exon-sequencing-only panels. The remaining ~4-6% of clinical PJS cases without detectable STK11 variants may represent somatic mosaicism, deep intronic variants, or genetic heterogeneity. STK11 is included on the ACMG SF v3.2 secondary findings list, reflecting the availability of effective surveillance interventions that substantially reduce cancer mortality in confirmed carriers.
30% of STK11 pathogenic variants are large deletions missed by standard sequencing panels. In a syndrome where cancer surveillance must start in childhood, a missed diagnosis has lifelong consequences.
One in three PJS-causing STK11 variants are deletions — standard sequencing panels miss them
Approximately 30% of confirmed STK11 pathogenic variants are large genomic deletions spanning one or more exons. Standard next-generation sequencing panels that sequence STK11 coding exons do not reliably detect large deletions without dedicated copy number variant analysis. Several published PJS families with complete clinical phenotype — mucocutaneous pigmentation, multiple hamartomatous polyps, and characteristic family history — were found to have STK11 deletions that preceded negative panel results by months to years. In a syndrome where pediatric small bowel surveillance begins at age 8 (NCCN recommendation) and pancreatic surveillance at age 35, a diagnostic delay of that magnitude has direct cancer prevention consequences.
PJS surveillance spans six different cancer types simultaneously — requiring a single definitive diagnosis to initiate the full protocol
Establishing the STK11 molecular diagnosis triggers a multi-organ surveillance protocol that differs substantially from standard cancer screening recommendations. NCCN PJS guidelines recommend: upper endoscopy and colonoscopy from age 8-10; small bowel/capsule endoscopy from age 8-10; annual breast MRI from age 25 with mammography from age 30; annual pelvic ultrasound or endometrial assessment from age 18; pancreatic surveillance from age 35 (endoscopic ultrasound/MRI); and testicular examination in males from birth (SCTAT risk). No standard cancer screening program covers all of these — a confirmed PJS molecular diagnosis is the prerequisite for initiating the comprehensive protocol that makes surveillance meaningful.
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A patient had spent decades in the UK healthcare system without a diagnosis. Dante data, accepted by NHS clinical teams at Queen Elizabeth University Hospital Glasgow, identified Noonan Syndrome and a RUNX1 leukemia-associated variant that had gone undetected. After 40 years, they finally had an answer.
A complete read delivers a complete picture.
A patient came to Dante to investigate periodic paralysis. Reading the complete genome identified a concurrent hereditary cardiac finding — Brugada syndrome — that their doctor confirmed with an ECG. The result also explained a family member's unresolved cardiac history. One test. Every answer in it.
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Jennifer sequenced her genome with Dante two years before her breast cancer diagnosis. When treatment began, Dante's pharmacogenomics data showed her prescribed chemotherapy would cause serious adverse effects. Her doctor selected an alternative — and she started effective treatment from day one.
Every genetic question deserves a complete answer.
Whether you are searching for answers today or protecting your health for tomorrow, a complete read of your entire genome is the only place to start.
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Your genome contains inherited variants associated with medical conditions like cardiac, cancer, and neurological. We read all of them — with the clinical depth to give the result meaning.
Learn more →When traditional lab tests say you're fine. And you know you're not.
Standard diagnostic tests check for a pre-selected set of answers. We sequence your full DNA — including parts that no test was designed to check. If the answer is in your genome, we will help you find it.
Learn more →Your diagnosis may be right. Your treatment plan may be incomplete.
Your genes determine which treatments are most likely to work — and which are not. We give your doctor the tools and insights to inform your treatment plan.
Learn more →You want to know before something forces the question.
Some people don't wait for a diagnosis or a family history to act. Whole genome sequencing gives you the complete genetic picture now — so you and your doctor can make informed decisions before anything becomes urgent.
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Common questions about whole genome sequencing.
What is the difference between whole genome sequencing and a targeted genetic test?
Targeted genetic tests — including standard hereditary cancer panels — read a pre-defined list of known variants in a specific set of genes. They are designed to find what they already know to look for. Whole genome sequencing reads your entire genome: all 6 billion base pairs, every gene, every region between genes. A Mayo Clinic study published in JAMA Oncology found that standard testing guidelines missed more than half of patients with inherited cancer mutations. Genome Test does not have a fixed list.
What will I receive when my results are ready?
Your Dante Genome delivers 200+ physician-ready reports organized by clinical category — hereditary cancer, cardiac conditions, rare diseases, pharmacogenomics, carrier status, and more. Reports are delivered to your secure Genome Manager and are formatted for direct clinical use. Your genome data is permanently retained and re-analyzed automatically as science advances.
What happens if a clinically significant variant is found?
If a pathogenic or likely-pathogenic variant is identified, it will be clearly flagged in your physician-ready report with clinical context, published evidence, and recommended next steps. We recommend sharing any clinically significant finding with your physician or a genetic counselor, who can guide decisions about surveillance, risk reduction, or cascade testing for family members.
How is this different from a consumer DNA test like 23andMe or AncestryDNA?
Consumer DNA tests use genotyping chips that read less than 0.1% of your genome — a tiny pre-selected set of common variants. They are optimized for ancestry and population-level traits, not clinical genetic findings. The Dante Genome Test sequences 100% of your genome at 30X coverage, the same standard used in clinical diagnostic settings. The two tests are not comparable in scope, methodology, or clinical utility.
How long does it take to get results, and how are they delivered?
Your collection kit ships within 48 hours of ordering. Once your sample arrives at our CLIA-certified laboratory, sequencing and analysis takes 6–8 weeks. Results are delivered securely to your Genome Manager, where you can access your reports, share them with your physician, and receive automatic updates as new findings are validated against your genome.
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Dante Labs works with patient advocacy groups of any size — for Peutz-Jeghers Syndrome and other conditions, rare and common. We support groups in any country, including virtual patient advocacy groups.
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