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1,417 results on '"Luthra, Rajyalakshmi"'

1. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial.

Author

Parra, Edwin, Zhang, Jiexin, Duose, Dzifa, Gonzalez-Kozlova, Edgar, Redman, Mary, Chen, Hong, Manyam, Ganiraju, Kumar, Gayatri, Zhang, Jianhua, Song, Xingzhi, Lazcano, Rossana, Marques-Piubelli, Mario, Laberiano-Fernandez, Caddie, Rojas, Frank, Zhang, Baili, Taing, Len, Jhaveri, Aashna, Geisberg, Jacob, Altreuter, Jennifer, Michor, Franziska, Provencher, James, Yu, Joyce, Cerami, Ethan, Moravec, Radim, Kannan, Kasthuri, Luthra, Rajyalakshmi, Alatrash, Gheath, Huang, Hsin-Hui, Xie, Hui, Patel, Manishkumar, Nie, Kai, Harris, Jocelyn, Argueta, Kimberly, Lindsay, James, Biswas, Roshni, Van Nostrand, Stephen, Kim-Schulze, Seunghee, Gray, Jhanelle, Herbst, Roy, Wistuba, Ignacio, Gettinger, Scott, Kelly, Karen, Bazhenova, Lyudmila, Gnjatic, Sacha, Lee, J, Zhang, Jianjun, and Haymaker, Cara

Subjects
Humans, Nivolumab, Lung Neoplasms, Multiomics, Antineoplastic Combined Chemotherapy Protocols, Carcinoma, Non-Small-Cell Lung, Carcinoma, Squamous Cell, Immunotherapy, Lung, Epithelial Cells, Ipilimumab, Tumor Microenvironment
Abstract

PURPOSE: Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN: Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS: Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS: The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.

Published
2024

3. Evolutionary Action Score of TP53 Analysis in Pathologically High-Risk Human Papillomavirus-Negative Head and Neck Cancer From a Phase 2 Clinical Trial: NRG Oncology Radiation Therapy Oncology Group 0234

Author

Michikawa, Chieko, Torres-Saavedra, Pedro A, Silver, Natalie L, Harari, Paul M, Kies, Merrill S, Rosenthal, David I, Le, Quynh-Thu, Jordan, Richard C, Duose, Dzifa Y, Mallampati, Saradhi, Trivedi, Sanchit, Luthra, Rajyalakshmi, Wistuba, Ignacio I, Osman, Abdullah A, Lichtarge, Olivier, Foote, Robert L, Parvathaneni, Upendra, Hayes, D Neil, Pickering, Curtis R, and Myers, Jeffrey N

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Cancer, Clinical Research, Dental/Oral and Craniofacial Disease, Radiation Oncology, Rare Diseases, Clinical Trials and Supportive Activities, Orphan Drug, Digestive Diseases, 4.2 Evaluation of markers and technologies, 6.1 Pharmaceuticals, Detection, screening and diagnosis, Evaluation of treatments and therapeutic interventions, AMP Exception, Oncology and carcinogenesis
Abstract

PurposeAn evolutionary action scoring algorithm (EAp53) based on phylogenetic sequence variations stratifies patients with head and neck squamous cell carcinoma (HNSCC) bearing TP53 missense mutations as high-risk, associated with poor outcomes, or low-risk, with similar outcomes as TP53 wild-type, and has been validated as a reliable prognostic marker. We performed this study to further validate prior findings demonstrating that EAp53 is a prognostic marker for patients with locally advanced HNSCC and explored its predictive value for treatment outcomes to adjuvant bio-chemoradiotherapy.Methods and materialsEighty-one resection samples from patients treated surgically for stage III or IV human papillomavirus-negative HNSCC with high-risk pathologic features, who received either radiation therapy + cetuximab + cisplatin (cisplatin) or radiation therapy + cetuximab + docetaxel (docetaxel) as adjuvant treatment in a phase 2 study were subjected to TP53 targeted sequencing and EAp53 scoring to correlate with clinical outcomes. Due to the limited sample size, patients were combined into 2 EAp53 groups: (1) wild-type or low-risk; and (2) high-risk or other.ResultsAt a median follow-up of 9.8 years, there was a significant interaction between EAp53 group and treatment for overall survival (P = .008), disease-free survival (P = .05), and distant metastasis (DM; P = .004). In wild-type or low-risk group, the docetaxel arm showed significantly better overall survival (hazard ratio [HR] 0.11, [0.03-0.36]), disease-free survival (HR 0.24, [0.09-0.61]), and less DM (HR 0.04, [0.01-0.31]) than the cisplatin arm. In high-risk or other group, differences between treatments were not statistically significant.ConclusionsThe docetaxel arm was associated with better survival than the cisplatin arm for patients with wild-type or low-risk EAp53. These benefits appear to be largely driven by a reduction in DM.

Published
2022

7. High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance

Author

Yang, Hui, Garcia-Manero, Guillermo, Sasaki, Koji, Montalban-Bravo, Guillermo, Tang, Zhenya, Wei, Yue, Kadia, Tapan, Chien, Kelly, Rush, Diana, Nguyen, Ha, Kalia, Awdesh, Nimmakayalu, Manjunath, Bueso-Ramos, Carlos, Kantarjian, Hagop, Medeiros, L. Jeffrey, Luthra, Rajyalakshmi, and Kanagal-Shamanna, Rashmi

Published
2022
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8. Poziotinib for EGFR exon 20-mutant NSCLC: Clinical efficacy, resistance mechanisms, and impact of insertion location on drug sensitivity

Author

Elamin, Yasir Y., Robichaux, Jacqulyne P., Carter, Brett W., Altan, Mehmet, Tran, Hai, Gibbons, Don L., Heeke, Simon, Fossella, Frank V., Lam, Vincent K., Le, Xiuning, Negrao, Marcelo V., Nilsson, Monique B., Patel, Anisha, Vijayan, R.S.K., Cross, Jason B., Zhang, Jianjun, Byers, Lauren A., Lu, Charles, Cascone, Tina, Feng, Lei, Luthra, Rajyalakshmi, San Lucas, Francis A., Mantha, Geeta, Routbort, Mark, Blumenschein, George, Jr., Tsao, Anne S., and Heymach, John V.

Published
2022
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10. The absolute percent deviation of IGHV mutation rather than a 98% cut‐off predicts survival of chronic lymphocytic leukaemia patients treated with fludarabine, cyclophosphamide and rituximab

Author

Jain, Preetesh, González, Graciela M Nogueras, Kanagal‐Shamanna, Rashmi, Rozovski, Uri, Sarwari, Nawid, Tam, Constantine, Wierda, William G, Thompson, Philip A, Jain, Nitin, Luthra, Rajyalakshmi, Quesada, Andres, Sanchez‐Petitto, Gabriela, Ferrajoli, Alessandra, Burger, Jan, Kantarjian, Hagop, Cortes, Jorge, O'Brien, Susan, Keating, Michael J, and Estrov, Zeev

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Oncology and Carcinogenesis, Cancer, Rare Diseases, Hematology, Clinical Research, Lymphoma, Adolescent, Adult, Aged, Aged, 80 and over, Antineoplastic Combined Chemotherapy Protocols, Biomarkers, Cyclophosphamide, Female, Humans, Immunoglobulin Heavy Chains, Immunoglobulin Variable Region, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, Male, Middle Aged, Mutation, Neoplasm Staging, Prognosis, Proportional Hazards Models, Rituximab, Treatment Outcome, Vidarabine, Young Adult, CLL, FCR, IGHV gene, immunoglobulin heavy chain gene, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

The degree of somatic hypermutation, determined as percent deviation of immunoglobulin heavy chain gene variable region sequence from the germline (IGHV%), is an important prognostic factor in chronic lymphocytic leukaemia (CLL). Currently, a cut-off of 2% deviation or 98% sequence identity to germline in IGHV sequence is routinely used to dichotomize CLL patients into mutated and unmutated groups. Because dissimilar IGHV% cut-offs of 1-5% were identified in different studies, we wondered whether no cut-off should be applied and IGHV% treated as a continuous variable. We analysed the significance of IGHV% in 203 CLL patients enrolled on the original frontline fludarabine, cyclophosphamide and rituximab (FCR) trial with a median of 10 years follow-up. Using the Cox Proportional Hazard model, IGHV% was identified as a continuous variable that is significantly associated with progression-free (PFS) and overall survival (OS) (P

Published
2018

11. Supplementary Table 6 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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12. Supplementary Figure 6 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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13. Supplementary Figure 8 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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14. Supplementary Table 3 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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15. Supplementary Figure 1 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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16. Supplementary Table 1 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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17. Supplementary Figure 7 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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18. Data from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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19. Supplementary Figure 2 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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20. Supplementary Table 7 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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21. Supplementary Table 4 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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22. Supplementary Figure 5 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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23. Supplementary Table 2 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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24. Supplementary Figure 3 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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25. Supplementary Figure 4 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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26. Supplementary Table 5 from Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial

Author

Parra, Edwin Roger, primary, Zhang, Jiexin, primary, Duose, Dzifa Yawa, primary, Gonzalez-Kozlova, Edgar, primary, Redman, Mary W., primary, Chen, Hong, primary, Manyam, Ganiraju C., primary, Kumar, Gayatri, primary, Zhang, Jianhua, primary, Song, Xingzhi, primary, Lazcano, Rossana, primary, Marques-Piubelli, Mario L., primary, Laberiano-Fernandez, Caddie, primary, Rojas, Frank, primary, Zhang, Baili, primary, Taing, Len, primary, Jhaveri, Aashna, primary, Geisberg, Jacob, primary, Altreuter, Jennifer, primary, Michor, Franziska, primary, Provencher, James, primary, Yu, Joyce, primary, Cerami, Ethan, primary, Moravec, Radim, primary, Kannan, Kasthuri, primary, Luthra, Rajyalakshmi, primary, Alatrash, Gheath, primary, Huang, Hsin-Hui, primary, Xie, Hui, primary, Patel, Manishkumar, primary, Nie, Kai, primary, Harris, Jocelyn, primary, Argueta, Kimberly, primary, Lindsay, James, primary, Biswas, Roshni, primary, Van Nostrand, Stephen, primary, Kim-Schulze, Seunghee, primary, Gray, Jhanelle E., primary, Herbst, Roy S., primary, Wistuba, Ignacio I., primary, Gettinger, Scott, primary, Kelly, Karen, primary, Bazhenova, Lyudmila, primary, Gnjatic, Sacha, primary, Lee, J. Jack, primary, Zhang, Jianjun, primary, and Haymaker, Cara, primary

Published
2024
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27. Factors Impacting Clinically Relevant RNA Fusion Assays Using Next-Generation Sequencing

Author

Ramani, Nisha S., Patel, Keyur P., Routbort, Mark J., Alvarez, Hector, Broaddus, Russell, Chen, Hui, Rashid, Asif, Lazar, Alex, Lucas, Francis A. San, Yao, Hui, Manekia, Jawad, Dang, Hyvan, Barkoh, Bedia A., Medeiros, L. Jeffrey, Luthra, Rajyalakshmi, and Roy-Chowdhuri, Sinchita

Subjects
Tumors -- Diagnosis, RNA sequencing -- Methods, Molecular diagnostic techniques -- Methods, Biochemical assays -- Usage, Health
Abstract

Context.--RNA-based next-generation sequencing (NGS) assays are being used with increasing frequency for comprehensive molecular profiling of solid tumors. Objective.--To evaluate factors that might impact clinical assay performance. Design.--A 4-month retrospective review of cases analyzed by a targeted RNA-based NGS assay to detect fusions was performed. RNA extraction was performed from formalin-fixed, paraffin-embedded tissue sections and/or cytology smears of 767 cases, including 493 in-house and 274 outside referral cases. The types of samples included 422 core needle biopsy specimens (55%), 268 resection specimens (35%), and 77 cytology samples (10%). Results.--Successful NGS fusion testing was achieved in 697 specimens (90.9%) and correlated positively with RNA yield (P < .001) and negatively with specimen necrosis (P = .002), decalcification (P < .001), and paraffin block age of more than 2 years (P = .001). Of the 697 cases that were successfully sequenced, 50 (7.2%) had clinically relevant fusions. The testing success rates and fusion detection rates were similar between core needle biopsy and cytology samples. In contrast, RNA fusion testing was often less successful using resection specimens (P = .007). Testing success was independent of the tumor percentage in the specimen, given that at least 20% tumor cellularity was present. Conclusions.--The success of RNA-based NGS testing is multifactorial and is influenced by RNA quality and quantity. Identification of preanalytical factors affecting RNA quality and yield can improve NGS testing success rates. (Arch Pathol Lab Med. 2021;145:1405-1412; doi: 10.5858/arpa.2020-0415-OA), With the increasing use of targeted therapeutic agents in solid tumors, RNA-based next-generation sequencing (NGS) assays are progressively used for comprehensive molecular analysis. (1) Chromosome translocations and/or gene fusions are [...]

Published
2021
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29. TP53 mutation does not confer a poor outcome in adult patients with acute lymphoblastic leukemia who are treated with frontline hyper-CVAD-based regimens.

Author

Kanagal-Shamanna, Rashmi, Jain, Preetesh, Takahashi, Koichi, Short, Nicholas, Tang, Guilin, Issa, Ghayas, Ravandi, Farhad, Garcia-Manero, Guillermo, Yin, Cameron, Luthra, Rajyalakshmi, Patel, Keyur, Khoury, Joseph, Montalban-Bravo, Guillermo, Sasaki, Koji, Kadia, Tapan, Borthakur, Gautam, Konopleva, Marina, Jain, Nitin, Garris, Rebecca, Pierce, Sherry, Wierda, William, Estrov, Zeev, Cortes, Jorge, Kantarjian, Hagop, Jabbour, Elias, and OBrien, Susan

Subjects
acute lymphoblastic leukemia (ALL), hyperfractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone (hyper-CVAD), next-generation sequencing, tumor protein 53 (TP53), Adult, Age Factors, Aged, Aged, 80 and over, Alleles, Antineoplastic Combined Chemotherapy Protocols, Cyclophosphamide, Dexamethasone, Doxorubicin, Female, Genes, p53, Humans, Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative, Male, Middle Aged, Mutation, Mutation, Missense, Precursor B-Cell Lymphoblastic Leukemia-Lymphoma, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Sequence Analysis, DNA, Treatment Outcome, Tumor Suppressor Protein p53, Vincristine
Abstract

BACKGROUND: Tumor protein 53 (TP53) mutations are uncommon in adult patients with acute lymphoblastic leukemia (ALL) and predict a poor outcome. METHODS: TP53 mutation analysis was performed in 164 newly diagnosed adult patients with ALL using a combination of targeted amplicon-based next-generation sequencing and Sanger sequencing. RESULTS: TP53 mutations were detected in 25 patients (15%), with a median allelic frequency of 42.2% (range, 5.6%-93.8%). The majority of mutations were single-nucleotide variants of missense type and involved the DNA-binding domain. TP53-mutated (TP53mut ) ALL was found to be significantly associated with older age, lower median white blood cell and platelet counts, lower frequency of Philadelphia chromosome and a higher frequency of low hypodiploid karyotype compared with ALL with wild-type TP53 (TP53wt ). To evaluate the prognostic effect of TP53 mutations, the authors selected 146 patients with B-cell immunophenotype ALL (24 with TP53mut and 122 with TP53wt ) who were uniformly treated with frontline hyperfractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone (hyper-CVAD)-based regimens; >90% of these individuals also received a monoclonal antibody. Over a median follow-up duration of 15 months, there was no significant difference in the median overall survival, event-free survival, and duration of complete remission noted between patients with TP53mut ALL and those with TP53wt ALL. CONCLUSIONS: Hyper-CVAD-based regimens appear to negate the poor prognostic impact of TP53 mutations in patients with adult B-cell immunophenotype ALL. Cancer 2017;123:3717-24. © 2017 American Cancer Society.

Published
2017

30. Clinico-pathologic characteristics and outcomes of the World Health Organization (WHO) provisional entity de novo acute myeloid leukemia with mutated RUNX1

Author

Quesada, Andrés E., Montalban-Bravo, Guillermo, Luthra, Rajyalakshmi, Patel, Keyur P., Sasaki, Koji, Bueso-Ramos, Carlos E., Khoury, Joseph D., Routbort, Mark.J., Bassett, Roland, Hidalgo-Lopez, Juliana E., Zhao, Chong, Lin, Pei, Loghavi, Sanam, Ok, Chi Y., Kadia, Tapan, DiNardo, Courtney D., Kantarjian, Hagop, Garcia-Manero, Guillermo, and Kanagal-Shamanna, Rashmi

Published
2020
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31. Long‐term durable remission by cladribine followed by rituximab in patients with hairy cell leukaemia: update of a phase II trial

Author

Chihara, Dai, Kantarjian, Hagop, O'Brien, Susan, Jorgensen, Jeffrey, Pierce, Sherry, Faderl, Stefan, Ferrajoli, Alessandra, Poku, Rebecca, Jain, Preetesh, Thompson, Phillip, Brandt, Mark, Luthra, Rajyalakshmi, Burger, Jan, Keating, Michael, and Ravandi, Farhad

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Oncology and Carcinogenesis, Clinical Trials and Supportive Activities, Clinical Research, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, 6.2 Cellular and gene therapies, Cancer, Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Cladribine, Disease-Free Survival, Drug Administration Schedule, Female, Follow-Up Studies, Humans, Leukemia, Hairy Cell, Male, Middle Aged, Neoplasm, Residual, Recurrence, Remission Induction, Rituximab, Hairy cell leukaemia, cladribine, phase II study, rituximab, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

Nucleoside analogues are highly active in patients with hairy cell leukaemia (HCL); however, patients continue to relapse. This phase II study evaluated the efficacy and safety of cladribine followed by rituximab in patients with untreated HCL (N = 59), relapsed HCL (N = 14) and HCL variant (HCLv, N = 7). Cladribine 5·6 mg/m(2) was given intravenously (IV) daily for 5 d and was followed approximately 1 month later with rituximab 375 mg/m(2) IV weekly for 8 weeks. Complete response rate in patients with untreated HCL, relapsed HCL and HCLv was 100%, 100% and 86%, respectively. With a median follow up of 60 months, 5-year failure-free survival (FFS) in patients with untreated HCL, relapsed HCL and HCLv was 95%, 100% and 64%, respectively. Median duration of response to the cladribine followed by rituximab was significantly longer than the first-line cladribine single agent in patients who received this treatment as second-line treatment (72 months vs not reached, P = 0·004). Almost all patients (94%) achieved negative minimal residual disease (MRD) after the treatment. Positive MRD during the follow up did not necessarily result in clinically relevant relapse. Cladribine followed by rituximab is highly effective even in patients with relapsed disease and HCLv, and can achieve durable remission.

Published
2016

32. Intragenic EGFR::EGFR.E1E8 Fusion (EGFRvIII) in 4331 Solid Tumors

Author

Zheng, Lan, primary, Luthra, Rajyalakshmi, additional, Alvarez, Hector A., additional, San Lucas, F. Anthony, additional, Duose, Dzifa Y., additional, Wistuba, Ignacio I., additional, Fuller, Gregory N., additional, Ballester, Leomar Y., additional, Roy-Chowdhuri, Sinchita, additional, Sweeney, Keith J., additional, Rashid, Asif, additional, Yang, Richard K., additional, Chen, Wei, additional, Liu, Audrey, additional, Wu, Yun, additional, Albarracin, Constance, additional, Patel, Keyur P., additional, Routbort, Mark J., additional, Sahin, Aysegul A., additional, Ding, Qingqing, additional, and Chen, Hui, additional

Published
2023
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33. Detection of EGFR T790M Mutation by Droplet Digital Polymerase Chain Reaction in Lung Carcinoma Cytology Samples

Author

Nizamaddin, Shara Kamil, Mehrotra, Meenakshi, Nadhim, Ari Sami H., Luthra, Rajyalakshmi, and Roy-Chowdhuri, Sinchita

Subjects
Lung cancer -- Genetic aspects, Polymerase chain reaction -- Genetic aspects, Osimertinib, Tyrosine -- Genetic aspects, Carcinoma -- Genetic aspects, Health, College of American Pathologists
Abstract

Context.--Advanced-stage non-small cell lung carcinoma patients on EGFR-targeted tyrosine kinase inhibitors frequently present with an acquired EGFR T790M resistance mutation. Early detection using a high-sensitivity assay is critical to allow patients to switch to third-generation tyrosine kinase inhibitors. The detection of EGFR T790M mutation is often challenging because of low tumor fraction in posttreatment specimens. Because a large fraction of non-small cell lung carcinoma patients are given a diagnosis by cytology, evaluating a high-sensitivity technique for EGFR T790M detection in these specimens is essential. Objective.--To evaluate a high-sensitivity droplet digital polymerase chain reaction (ddPCR) assay for EGFR T790M using different cytologic specimen preparations. Design.--A total of 42 cytology samples, including smears and cell block preparation, were evaluated for EGFR T790M using ddPCR. The results of the mutation assay were compared to the patient's known EGFR T790M mutation status. Results.--The ddPCR assay successfully determined the EGFR T790M mutation status in 36 of 42 samples (86%), including samples with low tumor fraction ([less than or equal to] 20%). In 4 cases the results of the ddPCR assay could not be compared because the mutation status was unknown at the time of collection of the cytology sample. There was 1 false-positive result, with borderline positivity, and 1 false-negative result. Overall sensitivity and specificity of the ddPCR assay were 93% and 96%, respectively. Conclusions.--Our results indicate that EGFR T790M ddPCR is a highly sensitive and specific mutational assay that can be used reliably in cytologic specimens, including samples with low tumor fraction. doi: 10.5858/arpa.2019-0411-OA, The management of non-small cell lung carcinoma (NSCLC), particularly lung adenocarcinoma, has undergone a paradigm shift, with patients harboring sensitizing somatic mutations in EGFR showing a dramatic response to targeted [...]

Published
2020
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34. BRAF mutation testing with a rapid, fully integrated molecular diagnostics system

Author

Janku, Filip, Claes, Bart, Huang, Helen J, Falchook, Gerald S, Devogelaere, Benoit, Kockx, Mark, Bempt, Isabelle Vanden, Reijans, Martin, Naing, Aung, Fu, Siqing, Piha-Paul, Sarina A, Hong, David S, Holley, Veronica R, Tsimberidou, Apostolia M, Stepanek, Vanda M, Patel, Sapna P, Kopetz, E Scott, Subbiah, Vivek, Wheler, Jennifer J, Zinner, Ralph G, Karp, Daniel D, Luthra, Rajyalakshmi, Roy-Chowdhuri, Sinchita, Sablon, Erwin, Meric-Bernstam, Funda, Maertens, Geert, and Kurzrock, Razelle

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Cancer, Human Genome, Genetics, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Good Health and Well Being, DNA Mutational Analysis, Formaldehyde, High-Throughput Nucleotide Sequencing, Humans, Melanoma, Mutation, Neoplasms, Paraffin Embedding, Pathology, Molecular, Proto-Oncogene Proteins B-raf, Real-Time Polymerase Chain Reaction, Reproducibility of Results, Skin Neoplasms, BRAF, rapid, integrated, qPCR, Oncology and carcinogenesis
Abstract

Fast and accurate diagnostic systems are needed for further implementation of precision therapy of BRAF-mutant and other cancers. The novel IdyllaTMBRAF Mutation Test has high sensitivity and shorter turnaround times compared to other methods. We used Idylla to detect BRAF V600 mutations in archived formalin-fixed paraffin-embedded (FFPE) tumor samples and compared these results with those obtained using the cobas 4800 BRAF V600 Mutation Test or MiSeq deep sequencing system and with those obtained by a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory employing polymerase chain reaction-based sequencing, mass spectrometric detection, or next-generation sequencing. In one set of 60 FFPE tumor samples (15 with BRAF mutations per Idylla), the Idylla and cobas results had an agreement of 97%. Idylla detected BRAF V600 mutations in two additional samples. The Idylla and MiSeq results had 100% concordance. In a separate set of 100 FFPE tumor samples (64 with BRAF mutation per Idylla), the Idylla and CLIA-certified laboratory results demonstrated an agreement of 96% even though the tests were not performed simultaneously and different FFPE blocks had to be used for 9 cases. The IdyllaTMBRAF Mutation Test produced results quickly (sample to results time was about 90 minutes with about 2 minutes of hands on time) and the closed nature of the cartridge eliminates the risk of PCR contamination. In conclusion, our observations demonstrate that the Idylla test is rapid and has high concordance with other routinely used but more complex BRAF mutation-detecting tests.

Published
2015

35. Erratum: Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies

Author

Janku, Filip, Angenendt, Philipp, Tsimberidou, Apostolia M, Fu, Siqing, Naing, Aung, Falchook, Gerald S, Hong, David S, Holley, Veronica R, Cabrilo, Goran, Wheler, Jennifer J, Piha-Paul, Sarina A, Zinner, Ralph G, Bedikian, Agop Y, Overman, Michael J, Kee, Bryan K, Kim, Kevin B, Kopetz, E Scott, Luthra, Rajyalakshmi, Diehl, Frank, Meric-Bernstam, Funda, and Kurzrock, Razelle

Subjects
Oncology and Carcinogenesis
Abstract

The Abstract is incorrect in PubMed. The corrected Abstract is provided here.

Published
2015

36. Actionable mutations in plasma cell-free DNA in patients with advanced cancers referred for experimental targeted therapies

Author

Janku, Filip, Angenendt, Philipp, Tsimberidou, Apostolia M, Fu, Siqing, Naing, Aung, Falchook, Gerald S, Hong, David S, Holley, Veronica R, Cabrilo, Goran, Wheler, Jennifer J, Piha-Paul, Sarina A, Zinner, Ralph G, Bedikian, Agop Y, Overman, Michael J, Kee, Bryan K, Kim, Kevin B, Kopetz, E Scott, Luthra, Rajyalakshmi, Diehl, Frank, Meric-Bernstam, Funda, and Kurzrock, Razelle

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Genetics, Clinical Research, Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Class I Phosphatidylinositol 3-Kinases, DNA Mutational Analysis, DNA, Neoplasm, Female, Genes, erbB-1, Humans, Kaplan-Meier Estimate, Male, Middle Aged, Neoplasms, Phosphatidylinositol 3-Kinases, Proto-Oncogene Proteins B-raf, Proto-Oncogene Proteins p21(ras), Young Adult, EGFR, BRAF, KRAS, PIK3CA, cell-free DNA, Oncology and carcinogenesis
Abstract

Cell-free (cf) DNA in the plasma of cancer patients offers an easily obtainable source of biologic material for mutation analysis. Plasma samples from 157 patients with advanced cancers who progressed on systemic therapy were tested for 21 mutations in BRAF, EGFR, KRAS, and PIK3CA using the BEAMing method and results were compared to mutation analysis of archival tumor tissue from a CLIA-certified laboratory obtained as standard of care from diagnostic or therapeutic procedures. Results were concordant for archival tissue and plasma cfDNA in 91% cases for BRAF mutations (kappa = 0.75, 95% confidence interval [CI] 0.63 - 0.88), in 99% cases for EGFR mutations (kappa = 0.90, 95% CI 0.71- 1.00), in 83% cases for KRAS mutations (kappa = 0.67, 95% CI 0.54 - 0.80) and in 91% cases for PIK3CA mutations (kappa = 0.65, 95% CI 0.46 - 0.85). Patients (n = 41) with > 1% of KRAS mutant cfDNA had a shorter median survival compared to 20 patients with 1% of mutant cfDNA (BRAF, EGFR, KRAS, or PIK3CA) had a shorter median survival compared to 33 patients with

Published
2015

41. Gemtuzumab ozogamicin with fludarabine, cytarabine, and granulocyte colony stimulating factor (FLAG‐GO) as front‐line regimen in patients with core binding factor acute myelogenous leukemia

Author

Borthakur, Gautam, Cortes, Jorge E, Estey, Elihu E, Jabbour, Elias, Faderl, Stefan, O'Brien, Susan, Garcia‐Manero, Guillermo, Kadia, Tapan Mahendra, Wang, Xuemei, Patel, Keyur, Luthra, Rajyalakshmi, Koller, Charles, Brandt, Mark, Ravandi, Farhad, and Kantarjian, Hagop

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Oncology and Carcinogenesis, Hematology, Cancer, Pediatric Cancer, Pediatric Research Initiative, Childhood Leukemia, Clinical Research, Rare Diseases, Pediatric, Adult, Aged, Aminoglycosides, Antibodies, Monoclonal, Humanized, Antineoplastic Combined Chemotherapy Protocols, Core Binding Factors, Cytarabine, Disease-Free Survival, Female, Gemtuzumab, Granulocyte-Macrophage Colony-Stimulating Factor, Humans, Leukemia, Myeloid, Acute, Male, Middle Aged, Survival Rate, Vidarabine, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

Despite being considered "good-risk" acute myelogenous leukemia (AML), long term outcomes in core binding factor (CBF) AML suggest room for improvement. We report on a regimen consisting of fludarabine, cytarabine, granulocyte colony stimulating factor, and low dose gemtuzumab ozogamicin (FLAG-GO) as front-line therapy of patients with CBF AML. Forty-five patients were enrolled (median age 48 years). Remission rate was 95% with 5% induction deaths. The overall survival (OS) and relapse free survival (RFS) probability at 3 years are 78% and 85%, respectively. FLAG-GO regimen results in high rates of RFS and OS in CBF AML. Our data along with recent data from several large groups strongly argues in favor of incorporation of gemtuzumab ozogamicin in frontline regimens for CBF AML.

Published
2014

42. Phase II trial of HyperCVAD and Dasatinib in patients with relapsed Philadelphia chromosome positive acute lymphoblastic leukemia or blast phase chronic myeloid leukemia

Author

Benjamini, Ohad, Dumlao, Theresa Liu, Kantarjian, Hagop, O'Brien, Susan, Garcia‐Manero, Guillermo, Faderl, Stefan, Jorgensen, Jeffrey, Luthra, Rajyalakshmi, Garris, Rebecca, Thomas, Deborah, Kebriaei, Partow, Champlin, Richard, Jabbour, Elias, Burger, Jan, Cortes, Jorge, and Ravandi, Farhad

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Oncology and Carcinogenesis, Orphan Drug, Clinical Research, Cancer, Pediatric Cancer, Childhood Leukemia, Hematology, Pediatric, Rare Diseases, Genetics, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Adult, Aged, Antineoplastic Combined Chemotherapy Protocols, Cyclophosphamide, Dasatinib, Dexamethasone, Doxorubicin, Humans, Leukemia, Myelogenous, Chronic, BCR-ABL Positive, Middle Aged, Philadelphia Chromosome, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Pyrimidines, Recurrence, Thiazoles, Vincristine, Young Adult, Cardiorespiratory Medicine and Haematology, Immunology, Cardiovascular medicine and haematology
Abstract

Dasatinib is a second generation tyrosine kinase inhibitor, with activity in imatinib resistant Ph-positive ALL.We have treated 34 patients with relapsed Philadelphia chromosome positive acute lymphoblastic leukemia(ALL) (n519) or lymphoid blast phase of chronic myelogenous leukemia (CML-LB) (n515) with the combination of dasatinib and the hyper CVAD regimen. Prior regimens included hyper CVAD plus imatinib(n511, 4 had transplant in first CR), other combination chemotherapy (n512), monotherapy with kinase inhibitors other than dasatinib (n59), and investigational agents (n52). Pretreatment ABL mutations were noted in 10 patients. The overall response rate was 91%, with 24 patients (71%) achieving complete response(CR), and 7(21%) CR with incomplete platelet recovery (CRp). Two patients died during induction and one had progressive disease. Twenty-six patients (84%) achieved complete cytogenetic remission after one cycle of therapy. Overall, 13 patients (42%) achieved complete molecular response, and 11 patients (35%) had major molecular response (BCR-ABL/ABL

Published
2014

43. 30. Chromosomal microarray analysis work-up for hypocellular MDS patients with inconclusive cytogenetics

Author

Nguyen, Ha, primary, Xu, Fangling, additional, Raju, Sherin, additional, Ahmed, Nazneen, additional, Bowman, Christopher, additional, Alvarez, Hector, additional, Dang, Hyvan, additional, Kalia, Awdhesh, additional, Hu, Peter, additional, Luthra, Rajyalakshmi, additional, Rush, Diana, additional, Tang, Guilin, additional, Kim, Kunhwa, additional, Chien, Kelly, additional, and Garcia-Manero, Guillermo, additional

Published
2023
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45. Detection of clinically actionable gene fusions by next‐generation sequencing‐based RNA sequencing of non–small cell lung cancer cytology specimens: A single‐center experience with comparison to fluorescence in situ hybridization

Author

Diks, John, primary, Tang, Zhenya, additional, Altan, Mehmet, additional, Anderson, Sarah, additional, Chen, Hui, additional, Rashid, Asif, additional, Yang, Richard Kenneth, additional, Routbort, Mark J., additional, Patel, Keyur P., additional, Toruner, Gokce A., additional, Medeiros, L. Jeffrey, additional, Tang, Guilin, additional, Luthra, Rajyalakshmi, additional, and Roy‐Chowdhuri, Sinchita, additional

Published
2023
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46. A phase 2 study of ruxolitinib in combination with azacitidine in patients with myelofibrosis

Author

Masarova, Lucia, Verstovsek, Srdan, Hidalgo-Lopez, Juliana E., Pemmaraju, Naveen, Bose, Prithviraj, Estrov, Zeev, Jabbour, Elias J., Ravandi-Kashani, Farhad, Takahashi, Koichi, Cortes, Jorge E., Ning, Jing, Ohanian, Maro, Alvarado, Yesid, Zhou, Lingsha, Pierce, Sherry, Gergis, Romany, Patel, Keyur P., Luthra, Rajyalakshmi, Kadia, Tapan M., DiNardo, Courtney D., Borthakur, Gautam, Bhalla, Kapil, Garcia-Manero, Guillermo, Bueso-Ramos, Carlos E., Kantarjian, Hagop M., and Daver, Naval

Published
2018
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49. Evolutionary action score identifies a subset of TP53 mutated myelodysplastic syndrome with favorable prognosis

Author

Kanagal-Shamanna, Rashmi, Montalban-Bravo, Guillermo, Katsonis, Panagiotis, Sasaki, Koji, Class, Caleb A., Jabbour, Elias, Sallman, David, Hunter, Anthony Michael, Benton, Christopher, Chien, Kelly S., Luthra, Rajyalakshmi, Bueso-Ramos, Carlos E., Kadia, Tapan, Andreeff, Michael, Komrokji, Rami S., Al Ali, Najla H, Short, Nicholas, Daver, Naval, Routbort, Mark J., Khoury, Joseph D., Patel, Keyur, Ganan-Gomez, Irene, Wei, Yue, Borthakur, Gautam, Ravandi, Farhad, Do, Kim-Anh, Soltysiak, Kelly A., Lichtarge, Olivier, Medeiros, L. Jeffrey, Kantarjian, Hagop, and Garcia-Manero, Guillermo

Published
2021
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