Abstract 630: Directly engaging participants in rare cancer research is feasible: the osteosarcoma and leiomyosarcoma projects
Bibliographic record
Abstract
Abstract Background and Purpose: Osteosarcoma (OS) and Leiomyosarcoma (LMS) are sarcomas with complex genomes for which there has been limited progress in identifying new treatments and improving outcomes. While slow progress is partially due to insufficient genomic characterization, generating large genomic datasets has been challenging because these are rare cancers. The OS and LMS Projects use various approaches to directly engage pediatric and adult participants with OS and LMS in genomics research. Methods: Working with patients and advocates at the design stage, we created websites (OSProject.org and LMSProject.org) where patients register and consent to participation. Any patient with OS or LMS living in the United States or Canada is eligible. Participant outreach approaches include partnership with advocacy organizations, webinars, social media posts, meeting presentations, stakeholder and physician engagement committees, and direct mailings. Blood and saliva are collected directly from consented participants by mail, archival FFPE tumor samples are obtained from pathology departments and medical records are requested from treating institutions. WES, WGS, DNA panel sequencing and RNASeq of tumor and germline (T/N) is performed. Results are shared with patient, advocacy, physician, and research communities in several ways. Individual participants receive a shared learning report describing the somatic variants identified in their tumor from T/N clinical WES and are offered clinical germline genetic testing and genetic counseling. Results: The study outreach team has participated in or led a total of 33 online and in person events not including social media posts or stakeholder meetings. So far, in 26 months 515 LMS patients (ages 16-83y; median 55) and 145 OS patients (ages 7-74y; median 20) have consented. Thus far, 274 and 76 tumor samples and 555 and 127 germline samples have been obtained from LMS and OS consented participants, respectively. Analysis of the first 20 LMS participants with T/N WGS showed widespread alteration of TP53 (11 pts), RB1 (8 pts), and PTEN (16 pts), concordant with findings in past studies. Likewise, the first 7 OS pts with T/N WGS demonstrated inactivation of TP53 (4 pts) and RB1 (2 pts), as expected from past OS cohorts. Conclusions: Using community partnerships and direct outreach to connect and engage with participants and a virtual consenting process for genomics research in rare cancers is feasible. It is possible to obtain germline samples directly from about half of participants and archival tumor samples from treating pathology departments for about one third of participants consented in direct-to-patient online genomics studies. We have been able to utilize archival tumor samples to identify, with T/N WES/WGS, expected genomic events in complex genome cancers. Recruitment and sequencing are ongoing. Citation Format: Julia M. Wong, David Merrell, Eirian Siegal-Botti, Noorshifa Arssath, Carrie Cibulskis, Evelina Ceca, Alanna Church, Alex Wilson, Lorena Lazo De La Vega, Jill Stopfer, Ellen Sukharevsky, Nia Daley, Anusha Sharma, Sidney Benich, Zachary Kahn, Lauren Fisher, Parker Chastain, Brendan Reardon, Taisha Hendrickson, Colleen Nguyen, Melissa Chiumiento, Melissa Mirick, Noriela Elia, Priscilla Merriam, Eliezer Van Allen, Judy Garber, Riaz Gillani, Chandrajit Raut, Stacey Gabriel, Timothy Rebbeck, Jason L. Hornick, Jennifer Mack, Suzanne George, Diane Diehl, Gad Getz, Katherine A. Janeway. Directly engaging participants in rare cancer research is feasible: the osteosarcoma and leiomyosarcoma projects [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 630.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.056 | 0.043 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.007 | 0.003 |
| Scholarly communication | 0.005 | 0.003 |
| Open science | 0.002 | 0.022 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.042 | 0.010 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".