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Shi, Qian

0000-0002-4640-8832

Mayo Clinic

Mayo Clinic

Citations 126

Tissue-Free Circulating Tumor DNA Assay and Patient Outcome in a Phase III Trial of FOLFOX-Based Adjuvant Chemotherapy (Alliance N0147)
Sinicrope, Frank A., Segovia, Diana, Sharma, Nalin , Alberts, Steven R. , Hardin, Aaron , Rich, Thereasa A. , Shi, Qian, Sinicrope, Frank A. , Shi, Qian , Sinicrope, Frank A , Rich, Thereasa , Shi, Qian , Alberts, Steven R , Hardin, Aaron

Journal of Clinical Oncology | January 30, 2026 | Volume: 44 | Issue: 15 | Pages: 1401-1415

10.1200/jco-25-02086 Get It

PURPOSE Detection of molecular residual disease using circulating tumor DNA (ctDNA) may enable postoperative risk stratification and guide adjuvant therapy. We evaluated the prognostic value of a tissue-free, epigenomic ctDNA assay in patients with stage III colon cancer (CC) enrolled in a phase III adjuvant chemotherapy trial. METHODS Plasma samples were collected after surgery and before adjuvant infusional fluorouracil, leucovorin, and oxaliplatin alone or combined with cetuximab. ctDNA was analyzed using a tissue-free assay; in ctDNA-positive patients, tumor fraction (TF) was quantified and genotyping was performed with a 739-gene panel. Associations with disease-free survival (DFS), time to recurrence (TTR), and overall survival (OS) were assessed using multivariable Cox models adjusted for covariates. RESULTS Among 2,260 evaluable patients, 461 (20.4%) were ctDNA-positive with significantly higher detection in advanced T-/N-stage, high-grade, obstruction/perforation, and BRAF V600E tumors. At a median follow-up of 6.1 years, ctDNA positivity was independently associated with shorter TTR (hazard ratio [HR], 5.96 [95% CI, 5.11 to 6.96]), DFS (HR, 5.03 [95% CI, 4.36 to 5.81]), and OS (HR, 4.45 [95% CI, 3.76 to 5.27]; all P < .0001). The 5-year DFS was 27.7% (95% CI, 23.8 to 32.2) v 77.1% (95% CI, 75.1 to 79.1) in ctDNA-positive versus ctDNA-negative patients, and adverse prognostic impact was greater in lower T/N stage, low-risk, and dMMR subsets (interaction P = .0012-.041). Among ctDNA-positive patients, TF was nearly double in those who recurred or died ( P = .0002) and stratified patients for TTR, DFS, and OS (all adjusted P < .002). Genotyping identified mutations in FLT1 (OR, 8.99) and PREX2 (OR, 7.73) genes that were most strongly associated with recurrence ( P < .03). CONCLUSION Evaluation of ctDNA in resected stage III CC using a tissue-free assay provided robust and independent prognostic value. Higher ctDNA burden, dMMR, and specific mutations defined poor prognostic groups among ctDNA-positive patients.
Multivariate zero-inflated generalised poisson data generation methods for simulating counts of adverse events
Chen, Ruizhe , Shi, Qian , Demirtas, Hakan , Shi, Qian , Chen, Ruizhe , Demirtas, Hakan

Journal of Statistical Computation and Simulation | November 17, 2025 | Volume: 96 | Issue: 6 | Pages: 1359-1389

10.1080/00949655.2025.2588606 Get It

Alliance A022106: A Phase II/III Trial of Nab-Paclitaxel and Gemcitabine ± Cisplatin as Second-Line Treatment for BRCA1/2 or PALB2 Mutant Metastatic Pancreatic Du
Shi, Qian , Collisson, Eric A. , Dixon, Jesse G. , Cusnir, Mike , Winograd, Rafael , Botta, Gregory P. , Shergill, Ardaman , Ko, Andrew , Tsang, Erica S , Shi, Qian , Olive, Kenneth P , Collisson, Eric , Dixon, Jesse G , Cusnir, Mike , Winograd, Rafael , Botta, Gregory P , Shergill, Ardaman , Meyerhardt, Jeffrey A , O'Reilly, Eileen M , Ko, Andrew H , Wadlow, Raymond Couric , Meyerhardt, Jeffrey A. , O’Reilly, Eileen M.

JCO Oncology Advances | October 31, 2025 | Volume: No volume available | Issue: 2 | Pages: No page available

10.1200/oa-25-00099 Get It

Sex differences in chemotherapy completion, toxicities, and survival in colon cancer: an analysis of 2201 patients from CALGB/SWOG 80702 (Alliance)
Cheng, En , Shi, Qian , Shields, Anthony F. , Xue, Xiaonan , Rohan, Thomas E. , Kuang, Chaoyuan , Shergill, Ardaman , Ma, Chao , Couture, Felix, Kuebler, J. Philip , Kumar, Pankaj , Krishnamurthi, Smitha , Ng, Kimmie , Meyerhardt, Jeffrey A. , Krishnamurthi, Smitha , Ng, Kimmie , O'Reilly, Eileen M , Brown, Justin C , Meyerhardt, Jeffrey A , Shi, Qian , Couture, Felix, Kumar, Pankaj , Tan, Benjamin, O’Reilly, Eileen M. , Brown, Justin C. , Cheng, En

JNCI: Journal of the National Cancer Institute | September 20, 2025 | Volume: 117 | Issue: 12 | Pages: 2643-2652

10.1093/jnci/djaf281 Get It

Abstract Background Completing adjuvant chemotherapy and reducing toxicities are critical for maximizing survival after a colon cancer diagnosis. Sex, as a biological variable, may affect colon cancer chemotherapy completion, toxicities, and survival differently. Methods From a National Cancer Institute–sponsored trial conducted among patients with stage III colon cancer (Cancer and Leukemia Group B (Alliance)/Southwest Oncology Group 80702), we included 2201 patients receiving the standard adjuvant chemotherapy regimen of fluorouracil, leucovorin, and oxaliplatin. We calculated relative dose intensity to indicate chemotherapy completion and considered reduced relative dose intensity (values &lt;85%) as a clinically significant deviation from standard fluorouracil, leucovorin, and oxaliplatin. Using National Cancer Institute’s Common Terminology Criteria for Adverse Events, we defined severe adverse events (grade ≥3) as the occurrence of any following event, including neutrophil count decrease, nausea, platelet count decrease, hypertension, peripheral neuropathy, diarrhea, fatigue, gastritis, creatinine level increase, gastric ulcer, myocardial ischemia, and cerebral ischemia. The primary survival outcome was disease-free survival (time from enrollment to colon cancer recurrence or death from any cause), and secondary survival outcomes were recurrence-free and overall survival. Results Compared with men, women were at statistically significantly higher risks of experiencing reduced relative dose intensity (adjusted odds ratio = 1.59, 95% CI = 1.29 to 1.96; P &lt; .001) and severe advance events (adjusted odds ratio = 1.72, 95% CI = 1.41 to 2.11; P &lt; .001). Yet, women had statistically significantly better disease-free survival (adjusted hazard ratio = 0.72, 95% CI = 0.59 to 0.87; P &lt; .001) as well as better recurrence-free and overall survival. Conclusions Our findings suggested that women with colon cancer are more likely to have worse chemotherapy completion rates and more severe adverse events, but they have better survival. Sex as a biological variable warrants further consideration in chemotherapy administration and survivorship management after colon cancer diagnosis.
Characteristics of Patients and Prognostic Factors Across Treatment Lines in Metastatic Colorectal Cancer: An Analysis From the Aide et Recherche en Cancérologie Digestive Database
Bachet, Jean‐Baptiste , Gramont, Aimery de , Raeisi, Morteza , Rakez, Manel , Goldberg, Richard M. , Tebbutt, Niall C. , Cutsem, Eric Van , Haller, Daniel G. , Hecht, J. Randolph , Mayer, R., Benson, Al B. , Sobrero, Alberto F. , Adams, Richard , Grothey, Axel, Chibaudel, Benoist , De Gramont, Aimery , Van Cutsem, Eric , Lichtman, Stuart M , Benson, Al , Sobrero, Alberto , Tabernero, Josep , Adams, Richard , Yoshino, Takayuki , André, Thierry , Shi, Qian , Chibaudel, Benoist , Tebbutt, Niall C , Mayer, Robert J., Lichtman, Stuart M. , Tabernero, Josep , Zalcberg, John , Yoshino, Takayuki , André, Thierry , Shi, Qian

Journal of Clinical Oncology | May 5, 2025 | Volume: 43 | Issue: 18 | Pages: 2094-2106

10.1200/jco-24-01968 Get It

PURPOSE Several lines of treatment can be used sequentially in patients with metastatic colorectal cancer. We investigated the evolution of patient/tumor characteristics and their prognostic impact across treatment lines to develop an overall prognostic score (OPS). PATIENTS AND METHODS Individual patient data from 48 randomized trials were analyzed. The end point was overall survival (from random assignment to death). Missing data were imputed. The complete data set was then separated into construction (80%) and validation sets (20%). The Cox's model was used to define risk groups for survival using the OPS. The discrimination capability was assessed in each treatment-line via bootstrapping to obtain optimism-corrected calibration and discrimination C-indices. Internal validation was done in the validation set. RESULTS A total of 37,560 patients (26,974 in first-line [1L], 7,693 in second-line [2L], and 2,893 in third-line [3L]) were analyzed. Some clinical, biological, and molecular characteristics of patients/tumors included in therapeutic trials evolve over the lines. Seven independent prognostic variables were retained in the final multivariate model common to all lines: Eastern Cooperative Oncology Group performance status, hemoglobin, platelet count, WBC/absolute neutrophil count ratio, lactate dehydrogenase, alkaline phosphatase, and the number of metastatic sites. The OPS was used to define four patient subgroups with significantly different prognoses in 1L, 2L, and 3L, separately, with adequate C-indices: 0.65, 0.66, and 0.69 in the construction set and 0.65, 0.66, and 0.68 in the validation set, respectively. The OPS was not predictive, with 3L drugs ( v placebo) or subsequent line (2L/1L or 3L/2L) extending survival in all prognostic groups. CONCLUSION The same prognostic model using practical variables can be used before all treatment lines. The OPS could better stratify patients in future clinical trials and help to therapeutic decision in routine practice.
Associations between early tumor shrinkage/depth of response and survival from the ARCAD database
Bando, Hideaki , Takeda, Yuriko , Misumi, Toshihiro , Nishikawa, Tomomi, Wakabayashi, Masashi , Yamazaki, Kentaro , Oki, Eiji , Douillard, Jean‐Yves , Punt, Cornelis J. A. , Koopman, Miriam , Bokemeyer, Carsten , Lenz, Heinz‐Josef , Maehara, Yoshihiko , Gramont, Aimery de, Yoshino, Takayuki , Van Cutsem, Eric , Venook, Alan P , Lenz, Heinz-Josef , Maehara, Yoshihiko , André, Thierry , Shi, Qian , De Gramont, Aimery , Yoshino, Takayuki , Oki, Eiji , Bando, Hideaki , Cutsem, Eric Van , Venook, Alan P. , André, Thierry , Shi, Qian , Gramont, Aimery de

JNCI Cancer Spectrum | April 26, 2025 | Volume: 9 | Issue: 3 | Pages: No page available

10.1093/jncics/pkaf042 Get It

Abstract Background Early tumor shrinkage and depth of response have emerged as potential prognostic indicators in metastatic colorectal cancer (CRC). However, their associations with overall survival, progression-free survival (PFS), and postprogression survival in patients receiving anti–epidermal growth factor receptor (EGFR) antibodies or bevacizumab remain unclear. Methods We analyzed 3219 treatment-naive patients with RAS wild-type metastatic CRC from 8 randomized studies (CRYSTAL, OPUS, PRIME, CAIRO2, CALGB80405, WJOG4407G, ATOM, PARADIGM) in the Aid and Research in Digestive Cancerology database. Early tumor shrinkage was defined as a 20% or more reduction in tumor size at 8 ± 2 weeks, whereas depth of response was assessed by maximum tumor shrinkage at nadir. Cox regression models evaluated the associations of early tumor shrinkage and depth of response with overall survival, PFS, and postprogression survival, adjusting for confounders. A 2-sided test was conducted with a significance level of .05. Results Early tumor shrinkage and depth of response substantially stratified overall survival, PFS, and postprogression survival outcomes across all treatment groups. Early tumor shrinkage positivity was associated with improved overall survival, PFS, and postprogression survival in anti-EGFR and bevacizumab-based therapies, with a trend toward better outcomes in the anti-EGFR group. The depth of response analysis revealed optimal cutoff values of 0.55 for anti-EGFR–based therapy and 0.47 for bevacizumab-based therapy to achieve a median overall survival of approximately 32 months. Conclusions Early tumor shrinkage and depth of response serve as valuable prognostic markers in RAS wild-type metastatic CRC, particularly for patients treated with anti-EGFR antibodies. These findings highlight the potential role of early tumor shrinkage and depth of response in guiding treatment strategies and improving outcomes for patients with CRC.
Utilizing Patient Input in Rectal Cancer Trial Design
Alvarez, Janet , Zambare, Wini , George, Manju, Garcia, Reese , Gallagher, Phuong , Kitchens, Caleah , Bercz, Aron , Kim, Min Jung , Romesser, Paul B. , Cercek, Andrea , Sanoff, Hanna K. , Hong, Theodore S. , Baghdadi, Tareq Al, Shergill, Ardaman , Meyerhardt, Jeffrey A. , Horvat, Natally , Hall, William A., Smith, J. Joshua , Sanoff, Hanna , George, Thomas J , Hong, Theodore S , Yothers, Greg , Philip, Philip , Alese, Olatunji B , Shergill, Ardaman , O'Reilly, Eileen M , Meyerhardt, Jeffrey A , Horvat, Natally , Dasari, Arvind N , Shi, Qian , Schrag, Deborah , Smith, J Joshua , Romesser, Paul B , Baghdadi, Tareq Al , Kitchens, Caleah , García‐Aguilar, Julio , George, Thomas J. , Yothers, Greg , Philip, Philip A. , Alese, Olatunji B. , O’Reilly, Eileen M. , Dasari, Arvind , Shi, Qian

JNCI: Journal of the National Cancer Institute | March 20, 2025 | Volume: 117 | Issue: 7 | Pages: 1421-1428

10.1093/jnci/djaf074 Get It

Abstract Background The treatment of locally advanced rectal cancer now includes “watch-and-wait” (WW) management for patients who exhibit a clinical complete response (cCR) to total neoadjuvant therapy (TNT). We assessed patients’ knowledge and preferences regarding WW with the goal of incorporating patient input into clinical trial design. Methods Rectal cancer patients in advocacy groups (COLONTOWN/Rectalburgh and Fight CRC) were surveyed regarding perceptions about treatment strategies, tolerable risks of treatment failure, and preferences on clinical trial design. Surveys were initially distributed in 2019, with the shift toward WW prompting re-survey of select questions in 2023. Results All respondents preferred enrollment in trials that incorporated patient input. Most respondents (76%) preferred treatment that incorporated chemotherapy escalation over radiation escalation. Furthermore, when presented with a hypothetical patient who developed a cCR after chemoradiation (without the option for WW), 58% of patients chose surgical treatment (with 100% risk of permanent ostomy and 80% chance of cure) over omission of surgery (with &lt;80% chance of cure). In contrast, when the hypothetical patient developed a cCR after TNT (with an option for WW), 82% of patients opted for selective WW over surgery. Conclusions This work successfully integrated patient advocacy groups as a resource for obtaining patient input. Surveys revealed patients had a strong preference for chemotherapy escalation, for selective WW when offered, and for incorporation of input into future clinical trial design. These findings describe how well-informed patients approach complex medical decision-making and serve as a starting point for future studies seeking to incorporate patient voices.
Genomic Landscapes of Early-Onset Versus Average-Onset Colorectal Cancer Populations
Storandt, Michael H. , Shi, Qian , Lieu, Christopher H. , George, Thomas J. , Stoppler, Melissa C. , Mauer, Elizabeth , Teslow, Emily A. , Mahipal, Amit , Jin, Zhaohui , Lieu, Christopher , George, Thomas J , Teslow, Emily A , Mahipal, Amit , Jin, Zhaohui , Shi, Qian , Eng, Cathy , Yilma, Binyam , Fragkogianni, Stamatina

Cancers | February 28, 2025 | Volume: 17 | Issue: 5 | Pages: 836

10.3390/cancers17050836 Get It

Background: Rates of early-onset colorectal cancer (eoCRC), defined as disease diagnosed at <50 years of age, are increasing. The incidence and spectrum of somatic and pathogenic germline variants (PGV) in this population are not well understood. Methods: This cross-sectional study leveraged Tempus’ clinicogenomic database, including de-identified records of patients diagnosed with CRC between 2000–2022, to analyze and compare eoCRC and average-onset colorectal cancer (aoCRC, disease diagnosed ≥50 years of age) patients. The frequency and spectrum of somatic mutations and PGVs in patients with eoCRC and aoCRC were evaluated and compared. Results: Among 11,006 participants in this study, 57% were male, 76% were white, and 80% had stage 4 disease. Within the total cohort, 2379 had eoCRC and 8627 had aoCRC. Among patients with eoCRC, 4.2% had a tumor with high microsatellite instability and/or deficient mismatch repair (MSI-H/dMMR) and 6.8% with aoCRC had an MSI-H/dMMR tumor (p < 0.001). The most frequent somatic mutations involved TP53, APC, and KRAS, with the most significant difference in BRAF, which was more frequently mutated in aoCRC (9.8% vs. 4.7%, p < 0.0001). In total, 1413 (59.4%) eoCRC and 4898 (56.8%) aoCRC patients had matched normal specimen (blood or saliva) sequencing and a PGV was identified in 6.9% of eoCRC and 5.0% of aoCRC patients. Conclusions: Somatic and germline mutation profiles were similar for eoCRC and aoCRC patients and may not adequately explain differences in tumor behavior and age of disease onset.
Minimal Residual Disease–Based End Point for Accelerated Assessment of Clinical Trials in Multiple Myeloma: A Pooled Analysis of Individual Patient Data From Multiple Randomized Trials
Shi, Qian , Paiva, Bruno , Pederson, Levi , Dimier, Natalie , Talpes, Ela, Prior, Thomas J. , Órfão, Alberto , Sonneveld, Pieter , Kumar, Shaji , Patel, Reshma, Bartlett, Blake, Schecter, Jordan M. , Seckinger, Anja , D’Agostino, Mattia , Goldschmidt, Hartmut , Owen, Roger G., Durie, Brian G.M. , Munshi, Nikhil C. , Group, on behalf of the International Independent Team for Endpoint Approval of Myeloma Minimal Residual Disease (i2TEAMM), Pederson, Levi D , Moreau, Philippe , Sonneveld, Pieter , Kumar, Shaji K , Dixon, Jesse G. , McCarthy, Phillip , Hose, Dirk , Seckinger, Anja , Mattia, D'Agostino , Goldschmidt, Hartmut , Oliva, Stefania , Anderson, Kenneth C , San-Miguel, Jesus , Munshi, Nikhil C , Shi, Qian , Paiva, Bruno , Orfao, Alberto , Moreau, Philippe , Patel, Reshma, McCarthy, Philip L. , Hose, Dirk , Oliva, Stefania , Anderson, Kenneth C. , Miguel, Jesús F. San , Group, on behalf of the International Independent Team for Endpoint Approval of Myeloma Minimal Residual Disease (i2TEAMM)

Journal of Clinical Oncology | February 12, 2025 | Volume: 43 | Issue: 11 | Pages: 1289-1301

10.1200/jco-24-02020 Get It

PURPOSE Newly approved drugs and combinations treating multiple myeloma (MM) have resulted in substantial improvements in patients' survival. To deliver rapid access to newer therapies, an earlier end point to expedite clinical trials is needed. Our objective was to evaluate the minimal residual disease–negative complete response (MRD-CR) as an intermediate end point for progression-free survival (PFS) and overall survival (OS) in newly diagnosed (ND) transplant-eligible (NDTE) patients, ND transplant-ineligible (NDTinE) patients, and patients with relapsed/refractory (RR) MM. PATIENTS AND METHODS Individual patient data from 20 randomized multicenter trials were collected. Eleven studies (4,773 patients) with sufficient data were analyzed to evaluate whether 9- or 12-month MRD-CR classified at a 10 –5 threshold could be reasonably likely to predict the clinical benefit of new agents regarding PFS and OS. Global odds ratio (OR) was estimated using the bivariate Plackett Copula model. Supportive evaluation included correlations of the treatment effects on MRD-CR end points and PFS/OS, evaluated by both linear regression ( R 2 weighted least squared ) and Copula ( R 2 Copula ) models. RESULTS The analysis demonstrated that both 9- and 12-month MRD-CR strongly correlated with PFS at patient level in NDTE patients, NDTinE patients, and patients with RRMM. Global ORs ranged from 3.06 to 16.24, all with 95% CIs excluding 1.0. Encouraging trial-level correlations ( R 2 , 0.61-0.70) were observed by pooling three populations and were stronger ( R 2 , 0.67-0.78) in the ND population. Similar results were observed for OS. CONCLUSION Our findings provided the support for use of MRD-CR classified at a 10 –5 threshold at either 9 or 12 months after starting of the treatment, as an intermediate end point to support accelerated approvals, in future trials in NDTE patients, NDTinE patients, and patients with RRMM.
Benchmarks of success in radiotherapy vs systemic therapy: National Clinical Trials Network (NCTN) randomized controlled trials sponsored by the National Cancer Institute (NCI)
Sanford, Nina N. , Shi, Qian , Hein, David , Hall, William A. , Hein, David M , Shi, Qian

JNCI: Journal of the National Cancer Institute | December 10, 2024 | Volume: 117 | Issue: 5 | Pages: 879-889

10.1093/jnci/djae313 Get It

Abstract Background The National Clinical Trials Network (NCTN) is the largest government-sponsored organization in the United States; it is tasked with funding randomized controlled trials in oncology. It is unknown whether there are differences in study design by treatment modality. We evaluated differences in methodology between trials testing radiation therapy (RT) vs systemic therapy. Methods The Clinical Trials Support Unit website was used to identify active randomized controlled trials of systemic therapy or RT across NCTN cooperative groups through December 31, 2023. Studies in disease sites with more than 5 RT trials were included. Each trial’s protocol was reviewed to obtain key design information that was descriptively compared: primary endpoint, hypothesis testing type (superiority vs noninferiority), noninferiority margin, hypothesized effect size, power, and statistical significance level. Results A total of 186 randomized controlled trials (142 systemic therapy, 44 RT) were examined. Comparing primary endpoints, 59.1% vs 26.8% of RT vs systemic therapy trials, respectively, had a primary endpoint of overall survival. Nearly one-third (31.2%) of RT trials were noninferiority vs 6.3% of systemic therapy trials. Among breast cancer trials, 75% of RT studies were noninferiority vs 11.1% systemic therapy. Target effect size, power, and statistical significance level were similar by treatment modality within tumor types and disease settings. Conclusion Among NCTN cooperative group randomized controlled trials, there were marked differences in study design between RT vs systemic therapy trials. A higher benchmark for defining success for RT interventions was observed, with greater emphasis on overall survival as the primary endpoint. This finding may reflect differences in therapeutic mechanism by modality and types of study questions posed.