Wenjia Feng
Ph.D. student at Washington University in Saint Louis interested in ctDNA liquid biopsy field.
Research Expertise
Publications
Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study
PLOS Medicine / Aug 31, 2021
Chauhan, P. S., Chen, K., Babbra, R. K., Feng, W., Pejovic, N., Nallicheri, A., Harris, P. K., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Szymanski, J. J., Baumann, B. C., Ding, L., Cao, D., Reimers, M. A., Kim, E. H., Smith, Z. L., Arora, V. K., & Chaudhuri, A. A. (2021). Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study. PLOS Medicine, 18(8), e1003732. https://doi.org/10.1371/journal.pmed.1003732
Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: A cross-sectional study
PLOS Medicine / Aug 31, 2021
Szymanski, J. J., Sundby, R. T., Jones, P. A., Srihari, D., Earland, N., Harris, P. K., Feng, W., Qaium, F., Lei, H., Roberts, D., Landeau, M., Bell, J., Huang, Y., Hoffman, L., Spencer, M., Spraker, M. B., Ding, L., Widemann, B. C., Shern, J. F., … Chaudhuri, A. A. (2021). Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: A cross-sectional study. PLOS Medicine, 18(8), e1003734. https://doi.org/10.1371/journal.pmed.1003734
Abstract 543: ctDNA MRD detection from plasma and urine and personalized oncogenomic analysis in oligometastatic colorectal cancer
Cancer Research / Jul 01, 2021
Pellini, B., Pejovic, N., Feng, W., Earland, N., Harris, P. K., Usmani, A., Szymanski, J. J., Qaium, F., Mudd, J., Kim, H., Tan, B., Fields, R. C., & Chaudhuri, A. A. (2021). Abstract 543: ctDNA MRD detection from plasma and urine and personalized oncogenomic analysis in oligometastatic colorectal cancer. Cancer Research, 81(13_Supplement), 543–543. https://doi.org/10.1158/1538-7445.am2021-543
Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer
JCO Precision Oncology / Nov 01, 2020
Dang, H. X., Chauhan, P. S., Ellis, H., Feng, W., Harris, P. K., Smith, G., Qiao, M., Dienstbach, K., Beck, R., Atkocius, A., Qaium, F., Luo, J., Michalski, J. M., Picus, J., Pachynski, R. K., Maher, C. A., & Chaudhuri, A. A. (2020). Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer. JCO Precision Oncology, 4, 680–713. https://doi.org/10.1200/po.20.00047
Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients
Sep 23, 2022
Chaudhuri, A., Chauhan, P., Shiang, A., Alahi, I., Sundby, R., Feng, W., Gungoren, B., Nawaf, C., Babbra, R., Harris, P., Qaium, F., Hatscher, C., Antiporda, A., Brunt, L., Mayer, L., Shern, J., Baumann, B., Kim, E., Reimers, M., & Smith, Z. (2022). Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients. https://doi.org/10.21203/rs.3.rs-2019529/v1
Integrative analysis of urine cell-free DNA for the detection of residual disease in localized bladder cancer patients.
Journal of Clinical Oncology / Feb 20, 2022
Chauhan, P. S., Shiang, A., Chen, K., Babbra, R., Feng, W., Szymanski, J. J., Harris, P. K., Hatcher, C., Roussin, J., Basarabescu, F., Brunt, L., Mayer, L. R., Borkowski, A., Maguire, L., Baumann, B. C., Reimers, M. A., Kim, E. H., Arora, V. K., Smith, Z. L., & Chaudhuri, A. A. (2022). Integrative analysis of urine cell-free DNA for the detection of residual disease in localized bladder cancer patients. Journal of Clinical Oncology, 40(6_suppl), 559–559. https://doi.org/10.1200/jco.2022.40.6_suppl.559
Correction: Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study
PLOS Medicine / Dec 14, 2021
Chauhan, P. S., Chen, K., Babbra, R. K., Feng, W., Pejovic, N., Nallicheri, A., Harris, P. K., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Szymanski, J. J., Baumann, B. C., Ding, L., Cao, D., Reimers, M. A., Kim, E. H., Smith, Z. L., Arora, V. K., & Chaudhuri, A. A. (2021). Correction: Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study. PLOS Medicine, 18(12), e1003876. https://doi.org/10.1371/journal.pmed.1003876
Tracking minimal residual disease with urine tumor DNA in muscle-invasive bladder cancer after neoadjuvant chemotherapy.
Journal of Clinical Oncology / May 20, 2021
Chen, K., Chauhan, P. S., Babbra, R. K., Feng, W., Pejovic, N., Nallicheri, A., Harris, P. K., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Szymanski, J. J., Baumann, B. C., Ding, L., Cao, D., Reimers, M. A., Kim, E. H., Smith, Z. L., Arora, V. K., & Chaudhuri, A. A. (2021). Tracking minimal residual disease with urine tumor DNA in muscle-invasive bladder cancer after neoadjuvant chemotherapy. Journal of Clinical Oncology, 39(15_suppl), e16514–e16514. https://doi.org/10.1200/jco.2021.39.15_suppl.e16514
Urinary Tumor DNA Detection of Muscle-Invasive Bladder Cancer May be Superior to Surgical Pathologic Complete Response Status for Predicting Survival Outcomes
International Journal of Radiation Oncology*Biology*Physics / Nov 01, 2020
Babbra, R. K., Chauhan, P. S., Pejovic, N., Feng, W., Harris, P. K., Nallicheri, A., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Smith, Z., Arora, V., & Chaudhuri, A. A. (2020). Urinary Tumor DNA Detection of Muscle-Invasive Bladder Cancer May be Superior to Surgical Pathologic Complete Response Status for Predicting Survival Outcomes. International Journal of Radiation Oncology*Biology*Physics, 108(3), e916. https://doi.org/10.1016/j.ijrobp.2020.07.551
Urinary cell-free DNA analysis for tumor mutation detection in patients with oligometastatic colorectal cancer.
Journal of Clinical Oncology / May 20, 2020
Pellini, B., Pejovic, N., Harris, P., Feng, W., Usmani, A., Qaium, F., Fields, R., & Chaudhuri, A. (2020). Urinary cell-free DNA analysis for tumor mutation detection in patients with oligometastatic colorectal cancer. Journal of Clinical Oncology, 38(15_suppl), e15545–e15545. https://doi.org/10.1200/jco.2020.38.15_suppl.e15545
PACT: a pipeline for analysis of circulating tumor DNA
Bioinformatics / Aug 01, 2023
Webster, J., Dang, H. X., Chauhan, P. S., Feng, W., Shiang, A., Harris, P. K., Pachynski, R. K., Chaudhuri, A. A., & Maher, C. A. (2023). PACT: a pipeline for analysis of circulating tumor DNA. Bioinformatics, 39(8). https://doi.org/10.1093/bioinformatics/btad489
Abstract 6698: Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures
Cancer Research / Apr 04, 2023
Alahi, I., Chauhan, P. S., Shiang, A. L., Webster, J., Dang, H. X., Greiner, L., yang, B., Ledet, E. M., Babbra, R. K., Feng, W., Harris, P. K., Jaeger, E. B., Miller, P. J., Caputo, S. A., Santos, G. C., Sartor, O., Pachynski, R. K., Maher, C. A., & Chaudhuri, A. A. (2023). Abstract 6698: Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures. Cancer Research, 83(7_Supplement), 6698–6698. https://doi.org/10.1158/1538-7445.am2023-6698
Abstract 2219: Urine cell-free DNA multi-omics to detect molecular residual disease and predict survival in bladder cancer patients
Cancer Research / Apr 04, 2023
Chauhan, P. S., Shiang, A. L., Alahi, I., Sundby, R. T., Feng, W., Gungoren, B., Nawaf, C., Chen, K., Babbra, R. K., Harris, P. K., Qaium, F., Hatscher, C., Antiporda, A., Brunt, L., Mayer, L. R., Shern, J. F., Baumann, B. C., Kim, E. H., Reimers, M. A., … Chaudhuri, A. A. (2023). Abstract 2219: Urine cell-free DNA multi-omics to detect molecular residual disease and predict survival in bladder cancer patients. Cancer Research, 83(7_Supplement), 2219–2219. https://doi.org/10.1158/1538-7445.am2023-2219
86. Whole genome sequencing of mouse derived cell-free DNA to develop a NF1-MPNST-PDX liquid biopsy model
Cancer Genetics / Nov 01, 2022
Jones, P., Feng, W., Zhang, X., Harris, P., Sundby, T., Qaium, F., Shern, J., Chaudhuri, A., & Hirbe, A. (2022). 86. Whole genome sequencing of mouse derived cell-free DNA to develop a NF1-MPNST-PDX liquid biopsy model. Cancer Genetics, 268–269, 28. https://doi.org/10.1016/j.cancergen.2022.10.089
28. Detection of small mutations, copy number alterations and structural variations from targeted cfDNA sequencing in cancer
Cancer Genetics / Nov 01, 2022
Webster, J., Dang, H., Chauhan, P., Shiang, A., Feng, W., Harris, P., Pachynski, R., Chaudhuri, A., & Maher, C. (2022). 28. Detection of small mutations, copy number alterations and structural variations from targeted cfDNA sequencing in cancer. Cancer Genetics, 268–269, 10. https://doi.org/10.1016/j.cancergen.2022.10.031
65. AR/enhancer alterations in metastatic castrate-resistant prostate cancer patient plasma predicts worse overall survival
Cancer Genetics / Nov 01, 2022
Chauhan, P., Shiang, A., Dang, H., Webster, J., Ledet, E., Babbra, R., Feng, W., Harris, P., Qaium, F., Jaeger, E., Miller, P., Caputo, S., Santos, G., Pachynski, R., Sartor, A. O., Maher, C., & Chaudhuri, A. (2022). 65. AR/enhancer alterations in metastatic castrate-resistant prostate cancer patient plasma predicts worse overall survival. Cancer Genetics, 268–269, 21. https://doi.org/10.1016/j.cancergen.2022.10.068
Multimodal Urine Cell-Free DNA-Based Residual Disease Detection and Prognostication in Muscle-Invasive Bladder Cancer Patients
International Journal of Radiation Oncology*Biology*Physics / Nov 01, 2022
Shiang, A., Chauhan, P. S., Chen, K., Sundby, R. T., Alahi, I., Babbra, R. K., Feng, W., Harris, P. K., Hatscher, C., Roussin, J., Basarbescu, F., Brunt, L., Mayer, L., Borkowski, A., Maguire, L., Shern, J., Baumann, B. C., Arora, V., Reimers, M., … Chaudhuri, A. A. (2022). Multimodal Urine Cell-Free DNA-Based Residual Disease Detection and Prognostication in Muscle-Invasive Bladder Cancer Patients. International Journal of Radiation Oncology*Biology*Physics, 114(3), e247. https://doi.org/10.1016/j.ijrobp.2022.07.1223
Abstract B006: Development of a NF1-MPNST-PDX liquid biopsy model using whole-genome sequencing and quantitative PCR of mouse-derived cell-free DNA
Clinical Cancer Research / Sep 15, 2022
Jones, P. A., Feng, W., Zhang, X., Harris, P. K., Sundby, T., Szymanski, J. J., Srihari, D., Qaium, F., Shern, J. F., Chaudhuri, A. A., & Hirbe, A. C. (2022). Abstract B006: Development of a NF1-MPNST-PDX liquid biopsy model using whole-genome sequencing and quantitative PCR of mouse-derived cell-free DNA. Clinical Cancer Research, 28(18_Supplement), B006–B006. https://doi.org/10.1158/1557-3265.sarcomas22-b006
Liquid biopsy AR/enhancer alteration detection before AR-targeted therapy and correlation with survival in metastatic castrate-resistant prostate cancer patients.
Journal of Clinical Oncology / Feb 20, 2022
Shiang, A., Chauhan, P. S., Dang, H. X., Webster, J., Ledet, E. M., Babbra, R. K., Feng, W., Harris, P. K., Jaeger, E. B., Miller, P., Caputo, S., Cittolin Santos, G. F., Pachynski, R. K., Sartor, A. O., Maher, C., & Chaudhuri, A. A. (2022). Liquid biopsy AR/enhancer alteration detection before AR-targeted therapy and correlation with survival in metastatic castrate-resistant prostate cancer patients. Journal of Clinical Oncology, 40(6_suppl), 171–171. https://doi.org/10.1200/jco.2022.40.6_suppl.171
Urine- and Plasma-Based Detection of Minimal Residual Disease in Localized Bladder Cancer Patients
International Journal of Radiation Oncology*Biology*Physics / Nov 01, 2021
Chen, K., Chauhan, P. S., Babbra, R. K., Feng, W., Pejovic, N., Harris, P. K., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Huang, Y., Szymanski, J., Baumann, B. C., Ding, L., Cao, D., Reimers, M., Kim, E., Smith, Z., Arora, V., & Chaudhuri, A. A. (2021). Urine- and Plasma-Based Detection of Minimal Residual Disease in Localized Bladder Cancer Patients. International Journal of Radiation Oncology*Biology*Physics, 111(3), e258–e259. https://doi.org/10.1016/j.ijrobp.2021.07.854
Abstract 550: Cell-free DNA alterations in the AR/enhancer locus measured before AR signaling inhibition portend poor overall survival in metastatic castration resistant prostate cancer patients
Cancer Research / Jul 01, 2021
Chauhan, P. S., Hartman, S. H., Dang, H. X., Webster, J., Ellis, H., Feng, W., Harris, P. K., Ledet, E. M., Jaeger, E. B., Miller, P. J., Caputo, S. A., Pachynski, R. K., Sartor, O., Maher, C. A., & Chaudhuri, A. A. (2021). Abstract 550: Cell-free DNA alterations in the AR/enhancer locus measured before AR signaling inhibition portend poor overall survival in metastatic castration resistant prostate cancer patients. Cancer Research, 81(13_Supplement), 550–550. https://doi.org/10.1158/1538-7445.am2021-550
Abstract 577: A unified pipeline to detect small mutations, structural variations and copy number alterations from targeted cell-free DNA sequencing in cancer
Cancer Research / Jul 01, 2021
Dang, H. X., Webster, J., Chauhan, P. S., Hartman, S. H., Feng, W., Ledet, E. M., Ellis, H., Miller, P. J., Jaeger, E. B., Caputo, S. A., Harris, P. K., Sartor, A. O., Pachynski, R. K., Chaudhuri, A. A., & Maher, C. A. (2021). Abstract 577: A unified pipeline to detect small mutations, structural variations and copy number alterations from targeted cell-free DNA sequencing in cancer. Cancer Research, 81(13_Supplement), 577–577. https://doi.org/10.1158/1538-7445.am2021-577
Abstract 547: Urine tumor DNA MRD detection and correlation with pathologic complete response in muscle-invasive bladder cancer treated with curative-intent radical cystectomy
Cancer Research / Jul 01, 2021
Chen, K., Chauhan, P. S., Babbra, R. K., Feng, W., Harris, P. K., Dienstbach, K., Atkocius, A., Maguire, L., Qaium, F., Nallicheri, A., Baumann, B. C., Reimers, M. A., Kim, E. H., Smith, Z. L., Arora, V. K., & Chaudhuri, A. A. (2021). Abstract 547: Urine tumor DNA MRD detection and correlation with pathologic complete response in muscle-invasive bladder cancer treated with curative-intent radical cystectomy. Cancer Research, 81(13_Supplement), 547–547. https://doi.org/10.1158/1538-7445.am2021-547
00005 Urine tumor DNA detects minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy
Journal of Clinical and Translational Science / Mar 01, 2021
Chen, K., Chauhan, P. S., Babbra, R. K., Feng, W., Kim, E. H., Smith, Z. L., Arora, V. K., & Chaudhuri, A. A. (2021). 00005 Urine tumor DNA detects minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy. Journal of Clinical and Translational Science, 5(s1), 113–114. https://doi.org/10.1017/cts.2021.690
Size-based Enrichment Of Urinary Cell-free DNA Compared To Plasma Cell-free DNA For Liquid Biopsy Analysis Of Oligometastatic Colorectal Cancer
International Journal of Radiation Oncology*Biology*Physics / Nov 01, 2020
Pellini, B., Pejovic, N., Harris, P. K., Feng, W., Usmani, A., Qaium, F., Fields, R. C., & Chaudhuri, A. A. (2020). Size-based Enrichment Of Urinary Cell-free DNA Compared To Plasma Cell-free DNA For Liquid Biopsy Analysis Of Oligometastatic Colorectal Cancer. International Journal of Radiation Oncology*Biology*Physics, 108(3), e552. https://doi.org/10.1016/j.ijrobp.2020.07.1714
Can Ultra-low-pass Whole Genome Sequencing from Blood Plasma Detect Transformation to Malignant Peripheral Nerve Sheath Tumor in Patients with Neurofibromatosis Type I?
International Journal of Radiation Oncology*Biology*Physics / Nov 01, 2020
Szymanski, J., Jones, P. A., Harris, P. K., Feng, W., Qaium, F., Moon, C. I., Zhou, Z., Ball, T. A., Hirbe, A., & Chaudhuri, A. A. (2020). Can Ultra-low-pass Whole Genome Sequencing from Blood Plasma Detect Transformation to Malignant Peripheral Nerve Sheath Tumor in Patients with Neurofibromatosis Type I? International Journal of Radiation Oncology*Biology*Physics, 108(3), S15. https://doi.org/10.1016/j.ijrobp.2020.07.2095
Abstract LB-269: Detection of cell-free DNA alterations in AR and its enhancer significantly outperformed CTC AR-V7 detection for identifying treatment resistance in patients with metastatic prostate cancer
Cancer Research / Aug 15, 2020
Chauhan, P. S., Dang, H. X., Ellis, H., Feng, W., Harris, P. K., Smith, G., Qiao, M., Dienstbach, K., Beck, R., Atkocius, A., Qaium, F., Luo, J., Michalski, J. M., Picus, J., Pachynski, R. K., Maher, C. A., & Chaudhuri, A. A. (2020). Abstract LB-269: Detection of cell-free DNA alterations in AR and its enhancer significantly outperformed CTC AR-V7 detection for identifying treatment resistance in patients with metastatic prostate cancer. Cancer Research, 80(16_Supplement), LB-269-LB-269. https://doi.org/10.1158/1538-7445.am2020-lb-269
AR enhancer and locus genomic alterations as cell-free DNA biomarkers of primary resistance to AR-directed treatment of metastatic prostate cancer.
Journal of Clinical Oncology / May 20, 2020
Maher, C., Dang, H. X., Chauhan, P. S., Ellis, H., Feng, W., Harris, P., Smith, G., Qiao, M., Dienstbach, K., Beck, R., Atkocius, A., Qaium, F., Luo, J., Michalski, J., Picus, J., Pachynski, R. K., & Chaudhuri, A. (2020). AR enhancer and locus genomic alterations as cell-free DNA biomarkers of primary resistance to AR-directed treatment of metastatic prostate cancer. Journal of Clinical Oncology, 38(15_suppl), 5529–5529. https://doi.org/10.1200/jco.2020.38.15_suppl.5529
Practical Evaluation of Different Omics Data Integration Methods
Precision Health and Medicine / Aug 02, 2019
Feng, W., Yu, Z., Kang, M., Gong, H., & Ahn, T.-H. (2019). Practical Evaluation of Different Omics Data Integration Methods. Studies in Computational Intelligence, 193–197. https://doi.org/10.1007/978-3-030-24409-5_20
Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: a cross-sectional study
Apr 25, 2021
Szymanski, J. J., Sundby, R. T., Jones, P. A., Srihari, D., Earland, N., Harris, P. K., Feng, W., Qaium, F., Lei, H., Roberts, D., Landeau, M., Bell, J., Huang, Y., Hoffman, L., Spencer, M., Spraker, M. B., Ding, L., Widemann, B. C., Shern, J. F., … Chaudhuri, A. A. (2021). Cell-free DNA ultra-low-pass whole genome sequencing to distinguish malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion: a cross-sectional study. https://doi.org/10.1101/2021.04.22.21255769
Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients
npj Precision Oncology / Jan 19, 2023
Chauhan, P. S., Shiang, A., Alahi, I., Sundby, R. T., Feng, W., Gungoren, B., Nawaf, C., Chen, K., Babbra, R. K., Harris, P. K., Qaium, F., Hatscher, C., Antiporda, A., Brunt, L., Mayer, L. R., Shern, J. F., Baumann, B. C., Kim, E. H., Reimers, M. A., … Chaudhuri, A. A. (2023). Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients. Npj Precision Oncology, 7(1). https://doi.org/10.1038/s41698-022-00345-w
ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine
JCO Precision Oncology / Nov 01, 2021
Pellini, B., Pejovic, N., Feng, W., Earland, N., Harris, P. K., Usmani, A., Szymanski, J. J., Qaium, F., Mudd, J., Petty, M., Jiang, Y., Singh, A., Maher, C. A., Henke, L. E., Park, H., Ciorba, M. A., Kim, H., Mutch, M. G., Pedersen, K. S., … Chaudhuri, A. A. (2021). ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine. JCO Precision Oncology, 5, 378–388. https://doi.org/10.1200/po.20.00276
Education
Saint Louis University
Master of Science, Bioinformatics & Computational Biology / May, 2018
Washington University in St. Louis
Ph.D., Computational and System Biology / May, 2028 (anticipated)
Experience
Washington University in Saint Louis
Bioinformatician / July, 2018 — July, 2023
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