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1. Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma.

Author

Ocasio-Martinez, Nicole, Tsai, Harrison, Li, Yuting, Robichaud, Amanda, Khalid, Delan, Hatton, Charlie, Gillani, Riaz, Polonen, Petri, Dilig, Anthony, Gotti, Giacomo, Kavanagh, Julia, Adhav, Asmani, Gow, Sean, Tsai, Jonathan, Li, Yen, Ebert, Benjamin, Van Allen, Eliezer, Bledsoe, Jacob, Kim, Annette, Tasian, Sarah, Cooper, Stacy, Cooper, Todd, Hijiya, Nobuko, Sulis, Maria, Shukla, Neerav, Magee, Jeffrey, Mullighan, Charles, Burke, Michael, Luskin, Marlise, Mar, Brenton, Harris, Marian, Stegmaier, Kimberly, Place, Andrew, Pikman, Yana, Paolino, Jonathan, Dimitrov, Boris, Apsel Winger, Beth, Sandoval-Perez, Angelica, Jacobson, Matthew, and Rangarajan, Amith

Subjects
Humans, Child, Animals, Mice, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma, Receptor, Platelet-Derived Growth Factor alpha, Mutation, Receptor Protein-Tyrosine Kinases, Precursor Cell Lymphoblastic Leukemia-Lymphoma, T-Lymphocytes
Abstract

PURPOSE: Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. EXPERIMENTAL DESIGN: We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia. RESULTS: Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL. CONCLUSIONS: Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.

Published
2023

2. Somatic structural variants drive distinct modes of oncogenesis in melanoma

Author

Conway, Jake R., Gillani, Riaz, Crowdis, Jett, Reardon, Brendan, Park, Jihye, Han, Seunghun, Titchen, Breanna, Benamar, Mouadh, Haq, Rizwan, and Van Allen, Eliezer M.

Subjects
Carcinogenesis -- Analysis, Melanoma -- Diagnosis -- Care and treatment, Health care industry, Diagnosis, Care and treatment, Analysis
Abstract

The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histologic and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the impact on cancer-related genes of SVs that alter topologically associated domain (TAD) boundaries. Following our prior identification of double-stranded break repair deficiency in a subset of triple-wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARP inhibitors in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact., Introduction Cutaneous melanoma is among the most highly mutated cancers because of the impact of UV mutagenesis, which leads to many C>T transitions across the genome (1, 2). For this [...]

Published
2024
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7. Rare germline structural variants increase risk for pediatric solid tumors

Author

Gillani, Riaz, primary, Collins, Ryan L, additional, Crowdis, Jett, additional, Garza, Amanda, additional, Jones, Jill K, additional, Walker, Mark, additional, Sanchis-Juan, Alba, additional, Whelan, Christopher W., additional, Pierce-Hoffman, Emma, additional, Talkowski, Michael E, additional, Brand, Harrison, additional, Haigis, Kevin M, additional, LoPiccolo, Jaclyn, additional, AlDubayan, Saud H., additional, Gusev, Alexander H., additional, Crompton, Brian D, additional, Janeway, Katherine, additional, and Van Allen, Eliezer, additional

Published
2024
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8. Abstract P01: Impact of Germline and Somatic ATM Variants in Chronic Lymphocytic Leukemia (CLL): Clinical Implications and Response to PARP Inhibition

Author

Mashima, Kiyomi, primary, Moore, Nicholas, additional, Mikhaleva, Mariia, additional, Petráčková, Anna, additional, Shupe, Samantha, additional, Fernandes, Stacey M, additional, Taylor-Weiner, Amaro, additional, Gillani, Riaz, additional, Chu, Hoyin, additional, Han, Seunghun, additional, Camp, Sabrina, additional, Kofman, Eric, additional, Getz, Gad, additional, Wu, Catherine J., additional, Tyekucheva, Svitlana, additional, Davids, Matthew S, additional, Van Allen, Eliezer Mendel, additional, AlDubayan, Saud, additional, and Brown, Jennifer R, additional

Published
2024
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9. Data from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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10. Supplementary Table 4 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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11. Supplementary Figure 2 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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12. Supplementary Table 3 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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13. Supplementary Table 1 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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14. Supplementary Table 5 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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15. Supplementary Table 6 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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16. Supplementary Table 2 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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17. Supplementary Figure 1 from Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma

Author

Paolino, Jonathan, primary, Dimitrov, Boris, primary, Apsel Winger, Beth, primary, Sandoval-Perez, Angelica, primary, Rangarajan, Amith Vikram, primary, Ocasio-Martinez, Nicole, primary, Tsai, Harrison K., primary, Li, Yuting, primary, Robichaud, Amanda L., primary, Khalid, Delan, primary, Hatton, Charlie, primary, Gillani, Riaz, primary, Polonen, Petri, primary, Dilig, Anthony, primary, Gotti, Giacomo, primary, Kavanagh, Julia, primary, Adhav, Asmani A., primary, Gow, Sean, primary, Tsai, Jonathan, primary, Li, Yen Der, primary, Ebert, Benjamin L., primary, Van Allen, Eliezer M., primary, Bledsoe, Jacob, primary, Kim, Annette S., primary, Tasian, Sarah K., primary, Cooper, Stacy L., primary, Cooper, Todd M., primary, Hijiya, Nobuko, primary, Sulis, Maria Luisa, primary, Shukla, Neerav N., primary, Magee, Jeffrey A., primary, Mullighan, Charles G., primary, Burke, Michael J., primary, Luskin, Marlise R., primary, Mar, Brenton G., primary, Jacobson, Matthew P., primary, Harris, Marian H., primary, Stegmaier, Kimberly, primary, Place, Andrew E., primary, and Pikman, Yana, primary

Published
2023
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18. Integration of genomic sequencing drives therapeutic targeting of PDGFRA in T-cell acute lymphoblastic leukemia/lymphoblastic lymphoma.

Author

Paolino, Jonathan, primary, Dimitrov, Boris, additional, Apsel Winger, Beth, additional, Sandoval-Perez, Angelica, additional, Rangarajan, Amith Vikram., additional, Ocasio-Martinez, Nicole, additional, Tsai, Harrison K., additional, Li, Yuting, additional, Robichaud, Amanda L., additional, Khalid, Delan, additional, Hatton, Charlie, additional, Gillani, Riaz, additional, Polonen, Petri, additional, Dilig, Anthony, additional, Gotti, Giacomo, additional, Kavanagh, Julia, additional, Adhav, Asmani A., additional, Gow, Sean, additional, Tsai, Jonathan, additional, Li, Yen Der, additional, Ebert, Benjamin L., additional, Van Allen, Eliezer M., additional, Bledsoe, Jacob, additional, Kim, Annette S., additional, Tasian, Sarah K., additional, Cooper, Stacy L., additional, Cooper, Todd M., additional, Hijiya, Nobuko, additional, Sulis, Maria Luisa, additional, Shukla, Neerav N., additional, Magee, Jeffrey A., additional, Mullighan, Charles G., additional, Burke, Michael J., additional, Luskin, Marlise R., additional, Mar, Brenton G., additional, Jacobson, Matthew P., additional, Harris, Marian H., additional, Stegmaier, Kimberly, additional, Place, Andrew E., additional, and Pikman, Yana, additional

Published
2023
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20. Supplementary Data from Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., primary, Crowdis, Jett, primary, Conway, Jake R., primary, Dharia, Neekesh V., primary, Alimohamed, Saif, primary, Haas, Brian J., primary, Han, Kyuho, primary, Park, Jihye, primary, Dietlein, Felix, primary, He, Meng Xiao, primary, Imamovic, Alma, primary, Ma, Clement, primary, Bassik, Michael C., primary, Boehm, Jesse S., primary, Vazquez, Francisca, primary, Gusev, Alexander, primary, Liu, David, primary, Janeway, Katherine A., primary, McFarland, James M., primary, Stegmaier, Kimberly, primary, and Van Allen, Eliezer M., primary

Published
2023
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21. SUPPLEMENTARY DATA from ESR1 Mutations in Circulating Plasma Tumor DNA from Metastatic Breast Cancer Patients

Author

Chu, David, primary, Paoletti, Costanza, primary, Gersch, Christina, primary, VanDenBerg, Dustin A., primary, Zabransky, Daniel J., primary, Cochran, Rory L., primary, Wong, Hong Yuen, primary, Toro, Patricia Valda, primary, Cidado, Justin, primary, Croessmann, Sarah, primary, Erlanger, Bracha, primary, Cravero, Karen, primary, Kyker-Snowman, Kelly, primary, Button, Berry, primary, Parsons, Heather A., primary, Dalton, W. Brian, primary, Gillani, Riaz, primary, Medford, Arielle, primary, Aung, Kimberly, primary, Tokudome, Nahomi, primary, Chinnaiyan, Arul M., primary, Schott, Anne, primary, Robinson, Dan, primary, Jacks, Karen S., primary, Lauring, Josh, primary, Hurley, Paula J., primary, Hayes, Daniel F., primary, Rae, James M., primary, and Park, Ben Ho, primary

Published
2023
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22. Data from ESR1 Mutations in Circulating Plasma Tumor DNA from Metastatic Breast Cancer Patients

Author

Chu, David, primary, Paoletti, Costanza, primary, Gersch, Christina, primary, VanDenBerg, Dustin A., primary, Zabransky, Daniel J., primary, Cochran, Rory L., primary, Wong, Hong Yuen, primary, Toro, Patricia Valda, primary, Cidado, Justin, primary, Croessmann, Sarah, primary, Erlanger, Bracha, primary, Cravero, Karen, primary, Kyker-Snowman, Kelly, primary, Button, Berry, primary, Parsons, Heather A., primary, Dalton, W. Brian, primary, Gillani, Riaz, primary, Medford, Arielle, primary, Aung, Kimberly, primary, Tokudome, Nahomi, primary, Chinnaiyan, Arul M., primary, Schott, Anne, primary, Robinson, Dan, primary, Jacks, Karen S., primary, Lauring, Josh, primary, Hurley, Paula J., primary, Hayes, Daniel F., primary, Rae, James M., primary, and Park, Ben Ho, primary

Published
2023
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23. Data from Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., primary, Crowdis, Jett, primary, Conway, Jake R., primary, Dharia, Neekesh V., primary, Alimohamed, Saif, primary, Haas, Brian J., primary, Han, Kyuho, primary, Park, Jihye, primary, Dietlein, Felix, primary, He, Meng Xiao, primary, Imamovic, Alma, primary, Ma, Clement, primary, Bassik, Michael C., primary, Boehm, Jesse S., primary, Vazquez, Francisca, primary, Gusev, Alexander, primary, Liu, David, primary, Janeway, Katherine A., primary, McFarland, James M., primary, Stegmaier, Kimberly, primary, and Van Allen, Eliezer M., primary

Published
2023
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25. Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma

Author

Han, Seunghun, primary, Camp, Sabrina Y., additional, Chu, Hoyin, additional, Collins, Ryan, additional, Gillani, Riaz, additional, Park, Jihye, additional, Bakouny, Ziad, additional, Ricker, Cora A., additional, Reardon, Brendan, additional, Moore, Nicholas, additional, Kofman, Eric, additional, Labaki, Chris, additional, Braun, David, additional, Choueiri, Toni K., additional, AlDubayan, Saud H., additional, and Van Allen, Eliezer M., additional

Published
2023
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26. Low-pass Whole Genome Imputation Enables the Characterization of Polygenic Breast Cancer Risk in the Indigenous Arab Population

Author

Al-Jumaan, Mohammed, primary, Chu, Hoyin, additional, Al-Sulaiman, Abdullah, additional, Camp, Sabrina Y., additional, Han, Seunghun, additional, Gillani, Riaz, additional, Al Marzooq, Yousef, additional, Almulhim, Fatmah, additional, Vatte, Chittibabu, additional, Al Nemer, Areej, additional, Almuhanna, Afnan, additional, Van Allen, Eliezer M, additional, Al-Ali, Amein, additional, and AlDubayan, Saud H, additional

Published
2022
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27. Patients with Deleterious Germline Variants in STXBP2 Develop Toxicity after CAR-T Cell Therapy with Axicabtagene Ciloleucel

Author

Leick, Mark B., primary, Han, Seunghun, additional, Gallagher, Kathleen M.E., additional, Silva, Harrison, additional, Martin, Grace, additional, Camp, Sabrina, additional, Chu, Hoyin, additional, Gillani, Riaz, additional, Kann, Michael C., additional, Choi, Bryan D., additional, Larson, Rebecca, additional, Phillips, Merle, additional, Kienka, Tamina, additional, Bailey, Stefanie R., additional, Graham, Charlotte, additional, Reilly, Christopher R., additional, Jan, Max, additional, Gonzalez, Elba, additional, Horick, Nora K., additional, Budka, Justin, additional, Filosto, Simone, additional, Shen, Rhine R., additional, Van Allen, Eliezer, additional, AlDubayan, Saud H, additional, and Maus, Marcela V., additional

Published
2022
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28. Characteristics of Rare Germline ATM Variants in Chronic Lymphocytic Leukemia (CLL)

Author

Mashima, Kiyomi, primary, Lampson, Benjamin L., additional, Gupta, Aditi, additional, Moore, Nicholas, additional, Petrackova, Anna, additional, Shupe, Samantha J., additional, Fernandes, Stacey M., additional, Taylor-Weiner, Amaro, additional, Gillani, Riaz, additional, Chu, Hoyin, additional, Han, Seunghun, additional, Camp, Sabrina, additional, Kofman, Eric, additional, Getz, Gad, additional, Wu, Catherine J., additional, Van Allen, Eliezer, additional, AlDubayan, Saud H, additional, and Brown, Jennifer R., additional

Published
2022
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29. Germline predisposition to pediatric Ewing sarcoma is uniquely characterized by inherited pathogenic variants in DNA damage repair genes

Author

Gillani, Riaz, primary, Camp, Sabrina Y., additional, Han, Seunghun, additional, Jones, Jill K., additional, O’Brien, Schuyler, additional, Young, Erin L., additional, Hayes, Lucy, additional, Mitchell, Gareth, additional, Fowler, Trent, additional, Gusev, Alexander, additional, Kamihara, Junne, additional, Janeway, Katherine A., additional, Schiffman, Joshua D., additional, Crompton, Brian D., additional, AlDubayan, Saud H., additional, and Van Allen, Eliezer M., additional

Published
2022
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31. Abstract 96: Gene fusions create partner and collateral dependencies that are essential to cancer cell survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., additional, Crowdis, Jett, additional, Conway, Jake R., additional, Dharia, Neekesh V., additional, Alimohamed, Saif, additional, Haas, Brian J., additional, Han, Kyuho, additional, Park, Jihye, additional, Liu, David, additional, Dietlein, Felix, additional, He, Meng Xiao, additional, Imamovic, Alma, additional, Ma, Clement, additional, Bassik, Michael C., additional, Boehm, Jesse S., additional, Vazquez, Francisca, additional, Gusev, Alexander, additional, Janeway, Katherine A., additional, McFarland, James M., additional, Stegmaier, Kimberly, additional, and Van Allen, Eliezer M., additional

Published
2021
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32. Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival

Author

Gillani, Riaz, primary, Seong, Bo Kyung A., additional, Crowdis, Jett, additional, Conway, Jake R., additional, Dharia, Neekesh V., additional, Alimohamed, Saif, additional, Haas, Brian J., additional, Han, Kyuho, additional, Park, Jihye, additional, Dietlein, Felix, additional, He, Meng Xiao, additional, Imamovic, Alma, additional, Ma, Clement, additional, Bassik, Michael C., additional, Boehm, Jesse S., additional, Vazquez, Francisca, additional, Gusev, Alexander, additional, Liu, David, additional, Janeway, Katherine A., additional, McFarland, James M., additional, Stegmaier, Kimberly, additional, and Van Allen, Eliezer M., additional

Published
2021
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36. Student’s Perception of Their Academics and Clinical Practice on Graduation from Dental Colleges of Peshawar

Author

Afridi, Saira, Kundi, Jawad Ahmad, Gillani, Syed Imran, Ibad, Yasir, Muhammad, Rohail, Gillani, Riaz, Raza, Moiz, ., Haseeb, Afridi, Saira, Kundi, Jawad Ahmad, Gillani, Syed Imran, Ibad, Yasir, Muhammad, Rohail, Gillani, Riaz, Raza, Moiz, and ., Haseeb

Abstract

OBJECTIVE:The objective of the current study was to know the perception of students regarding dental curriculum in clinical practice and academics after their graduation in three dental colleges of Peshawar.MATERIAL AND METHODS:It was a cross-sectional study design, carried out at three dental colleges of Peshawar namely Khyber College of Dentistry, Sardar Begum Dental College and Peshawar Dental College. A total number of 193 house officers were there out of which93 participated in the study. A pilot study was conducted to assess the reliability of questionnaire. The study was conducted through a self-administered questionnaire. The questionnaire consisted questions about academics and clinical practice.RESULTS:Our sample consisted of 93 subjects. There were 79% females and 21% males. The results revealed an overall positive learning experience in undergraduate academics and clinical practice. Over 86% of the graduates were satisfied with their academics and about 69% were satisfied with clinical practice. Almost 90% of the subjects were confident in carrying out specific clinical procedures.CONCLUSION:The major conclusions were that academics and clinical practice was satisfactory to the majority of subjects, although some areas of concern were identified that need improvement.

Published
2016

38. ESR1 Mutations in Circulating Plasma Tumor DNA from Metastatic Breast Cancer Patients

Author

Chu, David, primary, Paoletti, Costanza, additional, Gersch, Christina, additional, VanDenBerg, Dustin A., additional, Zabransky, Daniel J., additional, Cochran, Rory L., additional, Wong, Hong Yuen, additional, Toro, Patricia Valda, additional, Cidado, Justin, additional, Croessmann, Sarah, additional, Erlanger, Bracha, additional, Cravero, Karen, additional, Kyker-Snowman, Kelly, additional, Button, Berry, additional, Parsons, Heather A., additional, Dalton, W. Brian, additional, Gillani, Riaz, additional, Medford, Arielle, additional, Aung, Kimberly, additional, Tokudome, Nahomi, additional, Chinnaiyan, Arul M., additional, Schott, Anne, additional, Robinson, Dan, additional, Jacks, Karen S., additional, Lauring, Josh, additional, Hurley, Paula J., additional, Hayes, Daniel F., additional, Rae, James M., additional, and Park, Ben Ho, additional

Published
2016
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40. Patients with Deleterious Germline Variants in STXBP2Develop Toxicity after CAR-T Cell Therapy with Axicabtagene Ciloleucel

Author

Leick, Mark B., Han, Seunghun, Gallagher, Kathleen M.E., Silva, Harrison, Martin, Grace, Camp, Sabrina, Chu, Hoyin, Gillani, Riaz, Kann, Michael C., Choi, Bryan D., Larson, Rebecca, Phillips, Merle, Kienka, Tamina, Bailey, Stefanie R., Graham, Charlotte, Reilly, Christopher R., Jan, Max, Gonzalez, Elba, Horick, Nora K., Budka, Justin, Filosto, Simone, Shen, Rhine R., Van Allen, Eliezer, AlDubayan, Saud H, and Maus, Marcela V.

Published
2022
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41. Nanofunctionalized zirconia and barium sulfate particles as bone cement additives

Author

Gillani,Riaz, Ercan,Batur, Qiao,Alex, Webster,Thomas, Gillani,Riaz, Ercan,Batur, Qiao,Alex, and Webster,Thomas

Abstract

Riaz Gillani1, Batur Ercan1, Alex Qiao3, Thomas J Webster1,21Division of Engineering, 2Department of Orthopaedics, Brown University, Providence, RI, USA; 3G3 Technology Innovations, LLC, Pittsford, NY, USAAbstract: Zirconia (ZrO2) and barium sulfate (BaSO4) particles were introduced into a methyl methacrylate monomer (MMA) solution with polymethyl methacrylate (PMMA) beads during polymerization to develop the following novel bone cements: bone cements with unfunctionalized ZrO2 micron particles, bone cements with unfunctionalized ZrO2 nanoparticles, bone cements with ZrO2 nanoparticles functionalized with 3-(trimethoxysilyl)propyl methacrylate (TMS), bone cements with unfunctionalized BaSO4 micron particles, bone cements with unfunctionalized BaSO4 nanoparticles, and bone cements with BaSO4 nanoparticles functionalized with TMS. Results demonstrated that in vitro osteoblast (bone-forming cell) densities were greater on bone cements containing BaSO4 ceramic particles after four hours compared to control unmodified bone cements. Osteoblast densities were also greater on bone cements containing all of the ceramic particles after 24 hours compared to unmodified bone cements, particularly those bone cements containing nanofunctionalized ceramic particles. Bone cements containing ceramic particles demonstrated significantly altered mechanical properties; specifically, under tensile loading, plain bone cements and bone cements containing unfunctionalized ceramic particles exhibited brittle failure modes whereas bone cements containing nanofunctionalized ceramic particles exhibited plastic failure modes. Finally, all bone cements containing ceramic particles possessed greater radio-opacity than unmodified bone cements. In summary, the results of this study demonstrated a positive impact on the properties of traditional bone cements for orthopedic applications with the addition of unfunctionalized and TMS functionalized ceramic nanoparticles.Keywords: orthopedic, nanotechnol

Published
2009

42. Targeted in silicocharacterization of fusion transcripts in tumor and normal tissues via FusionInspector

Author

Haas, Brian J., Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James T., Gillani, Riaz, Kasif, Simon, and Regev, Aviv

Abstract

Here, we present FusionInspector for in silicocharacterization and interpretation of candidate fusion transcripts from RNA sequencing (RNA-seq) and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of tumor and normal transcriptomes and identified statistical and experimental features enriched among biologically impactful fusions. Through clustering and machine learning, we identified large collections of fusions potentially relevant to tumor and normal biological processes. We show that biologically relevant fusions are enriched for relatively high expression of the fusion transcript, imbalanced fusion allelic ratios, and canonical splicing patterns, and are deficient in sequence microhomologies between partner genes. We demonstrate that FusionInspector accurately validates fusion transcripts in silicoand helps characterize numerous understudied fusions in tumor and normal tissue samples. FusionInspector is freely available as open source for screening, characterization, and visualization of candidate fusions via RNA-seq, and facilitates transparent explanation and interpretation of machine-learning predictions and their experimental sources.

Published
2023
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45. Rare germline structural variants increase risk for pediatric solid tumors.

Author

Gillani R, Collins RL, Crowdis J, Garza A, Jones JK, Walker M, Sanchis-Juan A, Whelan C, Pierce-Hoffman E, Talkowski M, Brand H, Haigis K, LoPiccolo J, AlDubayan SH, Gusev A, Crompton BD, Janeway KA, and Van Allen EM

Abstract

Pediatric solid tumors are rare malignancies that represent a leading cause of death by disease among children in developed countries. The early age-of-onset of these tumors suggests that germline genetic factors are involved, yet conventional germline testing for short coding variants in established predisposition genes only identifies pathogenic events in 10-15% of patients. Here, we examined the role of germline structural variants (SVs)-an underexplored form of germline variation-in pediatric extracranial solid tumors using germline genome sequencing of 1,766 affected children, their 943 unaffected relatives, and 6,665 adult controls. We discovered a sex-biased association between very large (>1 megabase) germline chromosomal abnormalities and a four-fold increased risk of solid tumors in male children. The overall impact of germline SVs was greatest in neuroblastoma, where we revealed burdens of ultra-rare SVs that cause loss-of-function of highly expressed, mutationally intolerant, neurodevelopmental genes, as well as noncoding SVs predicted to disrupt three-dimensional chromatin domains in neural crest-derived tissues. Collectively, our results implicate rare germline SVs as a predisposing factor to pediatric solid tumors that may guide future studies and clinical practice.

Published
2024
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46. Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma.

Author

Han S, Camp SY, Chu H, Collins R, Gillani R, Park J, Bakouny Z, Ricker CA, Reardon B, Moore N, Kofman E, Labaki C, Braun D, Choueiri TK, AlDubayan SH, and Van Allen EM

Abstract

Importance: RCC encompasses a set of histologically distinct cancers with a high estimated genetic heritability, of which only a portion is currently explained. Previous rare germline variant studies in RCC have usually pooled clear and non-clear cell RCCs and have not adequately accounted for population stratification that may significantly impact the interpretation and discovery of certain candidate risk genes., Objective: To evaluate the enrichment of germline PVs in established cancer-predisposing genes (CPGs) in clear cell and non-clear cell RCC patients compared to cancer-free controls using approaches that account for population stratification and to identify unconventional types of germline RCC risk variants that confer an increased risk of developing RCC., Design Setting and Participants: In 1,436 unselected RCC patients with sufficient data quality, we systematically identified rare germline PVs, cryptic splice variants, and copy number variants (CNVs). From this unselected cohort, 1,356 patients were ancestry-matched with 16,512 cancer-free controls, and gene-level enrichment of rare germline PVs were assessed in 143 CPGs, followed by an investigation of somatic events in matching tumor samples., Main Outcomes and Measures: Gene-level burden of rare germline PVs, identification of secondary somatic events accompanying the germline PVs, and characterization of less-explored types of rare germline PVs in RCC patients., Results: In clear cell RCC (n = 976 patients), patients exhibited significantly higher prevalence of PVs in VHL compared to controls (OR: 39.1, 95% CI: 7.01-218.07, p-value:4.95e-05, q-value:0.00584). In non-clear cell RCC (n = 380 patients), patients carried enriched burden of PVs in FH (OR: 77.9, 95% CI: 18.68-324.97, p-value:1.55e-08, q-value: 1.83e-06) and MET (OR: 1.98e11, 95% CI: 0-inf, p-value: 2.07e-05, q-value: 3.50e-07). In a CHEK2 -focused analysis with European cases and controls, clear cell RCC patients (n=906 European patients) harbored nominal enrichment of the previously reported low-penetrance CHEK2 variants, p.Ile157Thr (OR:1.84, 95% CI: 1.00-3.36, p-value:0.049) and p.Ser428Phe (OR:5.20, 95% CI: 1.00-26.40, p-value:0.045) while non-clear cell RCC patients (n=295 European patients) exhibited nominal enrichment of CHEK2 LOF germline PVs (OR: 3.51, 95% CI: 1.10-11.10, p-value: 0.033). RCC patients with germline PVs in FH, MET, and VHL exhibited significantly earlier age of cancer onset compared to patients without any germline PVs in CPGs (Mean: 46.0 vs 60.2 years old, Tukey adjusted p-value < 0.0001), and more than half had secondary somatic events affecting the same gene (n=10/15, 66.7%, 95% CI: 38.7-87.0%). Conversely, patients with rare germline PVs in CHEK2 exhibited a similar age of disease onset to patients without any identified germline PVs in CPGs (Mean: 60.1 vs 60.2 years old, Tukey adjusted p-value: 0.99), and only 30.4% of the patients carried secondary somatic events in CHEK2 (n=7/23, 95% CI: 14.1-53.0%). Finally, rare pathogenic germline cryptic splice variants underexplored in RCC were identified in SDHA and TSC1, and rare pathogenic germline CNVs were found in 18 patients, including CNVs in FH , SDHA , and VHL ., Conclusions and Relevance: This systematic analysis supports the existing link between several RCC risk genes and elevated RCC risk manifesting in earlier age of RCC onset. Our analysis calls for caution when assessing the role of germline PVs in CHEK2 due to the burden of founder variants with varying population frequency in different ancestry groups. It also broadens the definition of the RCC germline landscape of pathogenicity to incorporate previously understudied types of germline variants, such as cryptic splice variants and CNVs., Competing Interests: COMPETING INTERESTS E.M.V.A. holds consulting roles with Tango Therapeutics, Genome Medical, Genomic Life, Enara Bio, Manifold Bio, Monte Rosa, Novartis Institute for Biomedical Research, Riva Therapeutics and Serinus Bio; he receives research support from Novartis, Bristol-Myers Squibb and Sanofi; he has equity in Tango Therapeutics, Genome Medical, Genomic Life, Syapse, Enara Bio, Manifold Bio, Microsoft, Monte Rosa, Riva Therapeutics and Serinus Bio; he has filed institutional patents on chromatin mutations, immunotherapy response, and methods for clinical interpretation. T.K.C. reports institutional and personal, paid and/or unpaid support for research, advisory boards, consultancy, and honoraria from: Alkermes, AstraZeneca, Aravive, Aveo, Bayer, Bristol Myers-Squibb, Calithera, Circle Pharma, Eisai, EMD Serono, Exelixis, GlaxoSmithKline, IQVA, Infinity, Ipsen, Jansen, Kanaph, Lilly, Merck, Nikang, Nuscan, Novartis, Pfizer, Roche, Sanofi/Aventis, Surface Oncology, Takeda, Tempest, Up-To-Date, CME events (Peerview, OncLive, MJH and others), outside the submitted work. Institutional patents filed on molecular alterations and immunotherapy response/toxicity, and ctDNA. Equity: Tempest, Pionyr, Osel, Precede Bio. CureResponse. Committees: NCCN, GU Steering Committee, ASCO/ESMO, ACCRU, KidneyCan. Medical writing and editorial assistance support may have been funded by Communications companies in part. No speaker’s bureau. Mentored several non-US citizens on research projects with potential funding (in part) from non-US sources/Foreign Components. The institution (Dana-Farber Cancer Institute) may have received additional independent funding of drug companies or/and royalties potentially involved in research around the subject matter. T. K. C is also supported in part by the Dana-Farber/Harvard Cancer Center Kidney SPORE (2P50CA101942-16) and Program 5P30CA006516-56, the Kohlberg Chair at Harvard Medical School and the Trust Family, Michael Brigham, Pan Mass Challenge, Hinda and Arthur Marcus Fund and Loker Pinard Funds for Kidney Cancer Research at DFCI. D.A.B. reports nonfinancial support from Bristol Myers Squibb, honoraria from LM Education/Exchange Services, advisory board fees from Exelixis and AVEO, personal fees from Charles River Associates, Schlesinger Associates, Imprint Science, Insight Strategy, Trinity Group, Cancer Expert Now, Adnovate Strategies, MDedge, CancerNetwork, Catenion, OncLive, Cello Health BioConsulting, PWW Consulting, Haymarket Medical Network, Aptitude Health, ASCO Post/Harborside, Targeted Oncology, AbbVie, and research support from Exelixis and AstraZeneca, outside of the submitted work. R.G. has equity in Google, Microsoft, Amazon, Apple, Moderna, Pfizer, and Vertex Pharmaceuticals. B.R. has filed institutional patents on methods for clinical interpretation. Z.B. receives research support from Bristol Myers Squibb and imCORE/Genentech. He also reports honoraria from UpToDate. C.L. receives research funding from imCORE/Genentech outside the submitted work. The other authors declare no competing interests.

Published
2023
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47. Detection of Cancer DNA in Early Stage and Metastatic Breast Cancer Patients.

Author

Medford AJ, Gillani RN, and Park BH

Subjects
Biomarkers, Tumor genetics, Breast Neoplasms blood, Breast Neoplasms pathology, Circulating Tumor DNA genetics, Female, Humans, Neoplasm Staging, Polymerase Chain Reaction instrumentation, Specimen Handling instrumentation, Specimen Handling methods, Biomarkers, Tumor isolation & purification, Breast pathology, Breast Neoplasms genetics, Circulating Tumor DNA isolation & purification, Polymerase Chain Reaction methods
Abstract

Breast cancer is the leading cause of cancer in women and the second leading cause of cancer-related death. There are many subtypes of breast cancer, which can be identified through the process of molecular and genetic profiling. While the current standard of care utilizes tumor tissue biopsy to subclassify breast cancer, plasma tumor DNA (ptDNA) can be detected through droplet digital PCR (ddPCR) of plasma obtained from a simple blood draw. Tissue biopsy is not only more invasive but because tumors exhibit heterogeneity it can be less accurate. Blood collects DNA shed from normal and cancerous cells alike, thus ddPCR of plasma offers a broader picture of a cancer's genetic makeup. This chapter summarizes how patients with breast cancer can be screened for specific cancerous mutations in both tissue and plasma through the use of ddPCR.

Published
2018
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