Nanopore Sequencing for Pancreatic Cancer Detection

Age: 18+

Sex: Any

Trial Phase: Academic

Sponsor: Mayo Clinic

Must not be taking: Perioperative antibiotics

Disqualifiers: Pregnancy, Institutionalized, Cognitive impairment, others

No Placebo Group All trial participants will receive the active study treatment (no placebo)

Compensation: Varies

Number of Visits: 2

What You Need to Know Before You Apply

What is the purpose of this trial?

This trial explores a new method to detect bacteria in bile, potentially preventing infections after pancreatic tumor surgery. It employs nanopore sequencing, developed by Oxford Nanopore Technologies, to examine bile samples for infection-causing bacteria. The aim is to identify these bacteria early, enabling doctors to prevent or treat infections more effectively. Patients undergoing surgery to remove a pancreatic tumor might qualify for this trial. As an unphased trial, this study provides a unique opportunity to contribute to innovative research that could enhance surgical outcomes for future patients.

Do I need to stop my current medications for the trial?

The trial information does not specify whether you need to stop taking your current medications. It's best to discuss this with the trial coordinators or your doctor.

What prior data suggests that nanopore sequencing is safe for detecting bacteria in bile?

Research has shown that Oxford Nanopore Sequencing is generally safe and well-tolerated. This technology quickly reads DNA and RNA sequences. Although studies have used it to detect various cancers, specific safety details for this application aren't provided in the sources. Since this trial is in the "Not Applicable" phase, the focus is on testing the method rather than a new drug, which usually indicates lower risk. This technology's use in other research settings generally supports its safety.

For those considering joining a trial using this technology, it is reassuring that related studies have not reported major side effects. However, discussing any concerns with the trial team remains important. ^{1 2 3 4 5}

Why are researchers excited about this trial?

Researchers are excited about nanopore sequencing for pancreatic cancer detection because it offers a novel approach to diagnosing this challenging condition. Unlike standard diagnostic methods, such as imaging and biopsy, nanopore sequencing analyzes genetic material in bile samples to identify cancer markers with potentially greater accuracy and speed. This technique could lead to earlier detection of pancreatic cancer, improving patient outcomes by allowing for timely interventions. Additionally, its ability to provide real-time data could streamline the diagnostic process, making it a promising tool for future cancer diagnostics.

What evidence suggests that nanopore sequencing is effective for detecting bacteriobilia in pancreatic cancer patients?

Research has shown that a new method called nanopore sequencing can detect bacteria in bile that might cause infections after pancreatic surgery. This trial will compare two approaches: one arm involves routine laboratory testing of bile samples, while the other uses nanopore sequencing in addition to routine testing. Nanopore sequencing excels at identifying genetic changes that older methods might miss, including significant genetic changes and specific gene variants that could lead to cancer. By identifying these bacteria early, doctors might prevent or treat infections more effectively after surgery, potentially improving recovery for patients undergoing surgery for pancreatic tumors. ^{2 4 6 7 8}

Who Is on the Research Team?

Marina R. Walther-Antonio, PhD

Principal Investigator

Mayo Clinic in Rochester

Mark J. Truty, MD, MS

Principal Investigator

Mayo Clinic in Rochester

Are You a Good Fit for This Trial?

This trial is for adults over 18 who are having surgery (pancreaticoduodenectomy or total pancreatectomy) for any pancreatic tumor, benign or cancerous. It's not open to pregnant women, those in institutions like prisons, people unable to consent, patients needing emergency surgery, or anyone already in a similar antibiotic study.

Inclusion Criteria

I am scheduled for surgery on my pancreas with consent.

Exclusion Criteria

I am currently pregnant.

I am unable to understand and make decisions about my treatment.

Patients who are institutionalized or incarcerated

Timeline for a Trial Participant

Screening

Participants are screened for eligibility to participate in the trial

2-4 weeks

Surgery and Sample Collection

Patients undergo standard of care surgery with bile sample collection for routine laboratory testing or nanopore sequencing

1 day

1 visit (in-person)

Post-operative Monitoring

Participants are monitored for surgical site infections and antibiotic stewardship

4 weeks

1 visit (in-person) at 2 weeks, 1 visit (in-person) at 4 weeks

Follow-up

Participants' medical records are reviewed for surgical site infections and antibiotic use

Up to 90 days

What Are the Treatments Tested in This Trial?

Interventions

• Oxford Nanopore Sequencing

Trial Overview The trial is testing nanopore sequencing—a rapid lab method—to detect bacteria in bile during pancreatic tumor surgeries. The goal is to see if this can prevent or improve treatment of surgical site infections by identifying harmful bacteria quickly.

How Is the Trial Designed?

Group I: Arm II (biospecimen, nanopore sequencing, routine testing) Experimental Treatment 3 Interventions

Patients undergo the collection of bile samples during standard of care surgery. Samples undergo nanopore sequencing and routine laboratory testing.

Group II: Arm I (biospecimen collection, routine testing) Active Control 2 Interventions

Patients undergo the collection of bile samples during standard of care surgery. Samples undergo routine laboratory testing.

Who Is Running the Clinical Trial?

Mayo Clinic

Lead Sponsor

Trials

3,427

Recruited

3,221,000+

National Cancer Institute (NCI)

Collaborator

Trials

14,080

Recruited

41,180,000+

Citations

1. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov/articles/PMC4848001/

Nanopore sequencing detects structural variants in cancer Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, ...

2. nanoporetech.com nanoporetech.com/resource-centre/accurate-identification-of-cancer-predisposing-deep-intronic-variants-in-tumour-suppressor-genes-with-oxford-nanopore-sequencing

accurate identification of cancer-predisposing deep intronic ... Nanopore sequencing effectively detected these variants that had been missed by legacy short-read sequencing methods and other conventional ...

3. nature.com nature.com/articles/s41525-024-00394-z

Assessing the efficacy of target adaptive sampling long ... Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read ...

4. onlinelibrary.wiley.com onlinelibrary.wiley.com/doi/10.1002/ijc.35100

Applications of Nanopore sequencing in precision cancer ... Nanopore sequencing is known to excel in detecting a wider range of isoforms compared to short-read NGS methods, facilitating effective ...

5. withpower.com withpower.com/trial/early-phase-1-pancreatic-neoplasms-10-2022-e3c56

Nanopore Sequencing for Pancreatic Cancer Detection This trial evaluates whether testing of bile with nanopore sequencing results in earlier detection of bacteriobilia (bacteria in bile) that may lead to ...

6. drugdiscoverynews.com drugdiscoverynews.com/abbvie-resolves-to-deal-with-pancreatic-cancer-13048

AbbVie 'RESOLVEs' to deal with pancreatic cancer At conclusion, the study did not meet its primary endpoint of improving PFS or OS benefit among the study population. Safety data collected from the study were ...

7. researchgate.net researchgate.net/publication/396709702_Long-read_RNa_sequencing_dataset_of_human_pancreatic_cancer_cell_lines

Long-read RNA sequencing dataset of human pancreatic ... In this study, we present a high-coverage long-read transcriptome dataset generated using Oxford Nanopore Technologies' PromethION platform from ...

8. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov/articles/PMC11011098/

The Application of Long-Read Sequencing to Cancer - PMC A more recent study used Oxford nanopore sequencing on cfDNA from plasma and urine to detect somatic copy-number aberrations in less than twenty-four hours, as ...