Beverly Jiali Fu

All Publications

• Differences in Survival Following Surgery Versus Chemoradiotherapy for Clinical Stage T4a Laryngeal Squamous Cell Carcinoma: A Propensity Score-Matched Analysis. Head & neck Fu, B. J., Potter, A. L., Pipkorn, P., Kraimer, K. L., Chen, M. M., Rajasekaran, K., Yang, C. J., Lee, J. J. 2025

  Abstract

  Although laryngeal cancer incidence has declined in the United States, case fatality has risen. The survival equivalence of surgery versus chemoradiotherapy (CRT) for cT4a laryngeal squamous cell carcinoma (LSCC) remains uncertain.We conducted a retrospective cohort study of cT4a LSCC patients treated with curative-intent surgery or CRT using the National Cancer Database (2010-2021). Those receiving neoadjuvant or palliative therapy, or with distant metastases were excluded. Survival was assessed using Kaplan-Meier and Cox models after 1:1 propensity score matching.Among 3569 patients (mean age 61.0, 708 female), 2437 (68.3%) underwent surgery while 1132 (31.7%) received CRT. In the matched cohort (n = 452 per arm), median survival was 52.8 (95% CI: 45.6-62.4) versus 37.6 (95% CI: 29.2-45.4) months for surgery versus CRT. Adjusted HR for CRT relative to surgery was 1.26 (95% CI: 1.02-1.57).Surgery was associated with improved overall survival compared with definitive CRT in patients with T4a LSCC.

  View details for DOI 10.1002/hed.70114

  View details for PubMedID 41403196

• A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection. bioRxiv : the preprint server for biology Fu, B. J., Viswanadham, V. V., Maziec, D., Jin, H., Park, P. J. 2025

  Abstract

  Background: The sequencing-by-synthesis technology by Illumina, Inc. enables efficient and scalable readouts of mutations from genomic data. To enhance sequencing speed and efficiency, Illumina has shifted from the four-color base calling chemistry of the HiSeq series to a two-color fluorescent dye chemistry in the NovaSeq series. Benchmarking sequencing artifacts due to biases in the newer chemistry is important to evaluate the quality of identified mutations.Results: We re-analyzed a series of whole-genome sequencing experiments in which the same samples were sequenced on the NovaSeq 6000 (two-color) and HiSeq X10 (four-color) platforms by independent groups. In several samples, we observed a higher frequency of T-to-G and A-to-C substitutions ("T>G") at the read level for NovaSeq 6000 versus HiSeq X10. As the per-base error rate is still low, the artifactual substitutions have a negligible effect in identifying germline or high variant allele frequency (VAF) somatic mutations. However, such errors can confound the detection of low-VAF somatic variants in high-depth sequencing samples, particularly in studies of mosaic mutations in normal tissues, where variants have low read support and are called without a matched normal. The artifactual T>G variant calls disproportionately occur at NT[TG] trinucleotides, and we leveraged this observation to bioinformatically reduce the T>G excess in somatic mutation callsets.Conclusions: We identified a recurrent artifact specific to the Illumina two-color chemistry platform on the NovaSeq 6000 with the potential to contaminate low-VAF somatic mutation calls. Thus, an unexpected enrichment of T>G mutations in mosaicism studies warrants caution.

  View details for DOI 10.1101/2025.09.27.678978

  View details for PubMedID 41256534

• Association Between Subclavian Vein Patency and Health-Related Quality of Life Outcomes Among Patients with Venous Thoracic Outlet Syndrome. The Journal of thoracic and cardiovascular surgery Corvi, M. E., Panda, N., Fu, B. J., Hurd, J. C., Yang, M. E., Anderson, J. N., Kuhan, S., Jeffery Yang, C. F., Donahue, D. M. 2025

  Abstract

  To evaluate the association between subclavian vein patency and health-related quality of life following supraclavicular thoracic outlet decompression among patients with venous thoracic outlet syndrome.Patients who underwent supraclavicular thoracic outlet decompression (i.e. first thoracic rib resection, scalenectomy, and subclavian venolysis) were identified from a prospectively maintained database. Demography, perioperative venography, and catheter-directed interventions were recorded. The primary endpoints were subclavian vein patency and health-related quality of life following decompression. The association between subclavian vein patency and health-related quality of life was evaluated in unadjusted and logistic regression analyses.Among 1,032 patients with TOS who underwent surgery (2007-2021), 275 patients presented with venous thoracic outlet syndrome. Two-hundred and twenty-five patients (81.8%) underwent preoperative venography; 221 (98.2%) had completely or partially stenosed subclavian veins. Preoperative catheter-based interventions were performed among 166 patients (60.4%); stenosis remained in 130 patients (78.3%). Postoperatively, 216 patients (78.5%) underwent routine venography; improvement in stenosis was observed in 54 (25.0%). Additional catheter-based interventions were performed in 155 patients (56.4%) with improvement in stenosis observed in 131 patients (84.5%). At a median follow up of 279 days [IQR 95, 674], 94.0% of patients reported improvement in health-related quality of life. Improvement in subclavian vein patency was associated with improved health-related quality of life (adjusted odds ratio 2.19 [95%CI 1.12-4.28], p=0.021).Subclavian vein patency is associated with improved health-related quality of life among patients with venous thoracic outlet syndrome. Effective venolysis during thoracic outlet decompression with perioperative catheter-directed intervention contributes most significantly to vein patency.

  View details for DOI 10.1016/j.jtcvs.2025.08.035

  View details for PubMedID 40912633

• Open, Video- and Robot-Assisted Thoracoscopic Lobectomy for Stage II-IIIA Non-Small Cell Lung Cancer. The Annals of thoracic surgery Shagabayeva, L., Fu, B., Panda, N., Potter, A. L., Auchincloss, H. G., Mansur, A., Jeffrey Yang, C. F., Schumacher, L. 2023; 115 (1): 184-190

  Abstract

  This study compares the short- and long-term outcomes of open vs robotic vs video-assisted thoracoscopic surgery (VATS) lobectomy for stage II-IIIA non-small-cell lung cancer (NSCLC).Outcomes of patients with stage II-IIIA NSCLC (excluding T4 tumors) who received open and minimally invasive surgery (MIS) lobectomy in the National Cancer Database from 2010 to 2017 were assessed using propensity score-matched analysis.A propensity score-matched analysis of 4652 open and 4652 MIS patients demonstrated a decreased median length of stay associated with MIS compared with open lobectomy (5 vs 6 days; P < .001). There were no significant differences in 30-day mortality, 30-day readmission, or overall survival between the open and MIS groups. A propensity score-matched analysis of 1186 VATS and 1186 robotic patients showed that compared with VATS, the robotic approach was associated with no significant differences in 30-day mortality, 30-day readmission, and overall survival. However, the robotic group had a decreased median length of stay compared with VATS (4 vs 5 days; P < .001). The conversion rate was also significantly lower for robotic compared with VATS lobectomy (8.9% vs 15.9%, P < .001).No significant differences were found in long-term survival between open and MIS lobectomy and between VATS and robotic lobectomy for stage II-IIIA NSCLC. However, the MIS approach was associated with a decreased length of stay compared with the open approach. The robotic approach was associated with decreased length of stay and decreased conversion rate compared with the VATS approach.

  View details for DOI 10.1016/j.athoracsur.2022.01.026

  View details for PubMedID 35149049