1
|
Vishwanath D, Shanmugam A, Sundaresh M, Hariharan A, Saraf S, Bahadur U, Veeramachaneni V, Chandrasekhar N, Pillai V V, Bushan V, Shetty V, Subramaniam N, Kuriakose MA, Shivaprasad KS, Khadilkar K, Suresh A, Sum S, Lakhsmikantha A, Rekha PR, Zaidi SN, Gupta V, Kannan S. Development of a Low-cost NGS Test for the Evaluation of Thyroid Nodules. Indian J Surg Oncol 2022; 13:17-22. [PMID: 35462651 PMCID: PMC8986928 DOI: 10.1007/s13193-019-01000-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022] Open
Abstract
Ultrasound-guided fine needle aspiration cytology (FNAC) is the preferred method of identifying malignancy in palpable thyroid nodules using the Bethesda reporting system. However, in around 30-40% of FNACs (Bethesda categories III, IV, and V), the results are indeterminate and surgery is required to confirm malignancy. Out of those who undergo surgery, only 10-40% of patients in these categories are found to have malignancies, thus proving surgery to be unnecessary for some patients or to be incomplete in others. While molecular testing on thyroid FNAC material is part of the American Thyroid Association (ATA) guidelines in evaluating thyroid nodules, it is currently unavailable in India due to cost constraints. In this study, we prospectively collected FNAC samples from sixty-nine patients who presented with palpable thyroid nodules. We designed a cost-effective next-generation sequencing (NGS) test to query multiple variants in the DNA and RNA isolated from the fine needle aspirate. The identification of oncogenic variants was considered to be indicative of malignancy, and confirmed by surgical histopathology. The panel showed an overall sensitivity of 81.25% and a specificity of 100%, while in the case of Bethesda categories III, IV, and V, the sensitivity was higher (87.5%) and the specificity was established at 100%. The panel could thereby serve as a rule-in test for the diagnosis of thyroid cancer and therefore help identify patients who require surgery, especially in the indeterminate Bethesda categories III, IV, and V.
Collapse
Affiliation(s)
- Divya Vishwanath
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Ashwini Shanmugam
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Mahima Sundaresh
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Arun Hariharan
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Shradha Saraf
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Urvashi Bahadur
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Vamsi Veeramachaneni
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Naveen Chandrasekhar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vijay Pillai V
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vidhya Bushan
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vivek Shetty
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Narayana Subramaniam
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Moni Abraham Kuriakose
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - K. S. Shivaprasad
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Kranti Khadilkar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Amritha Suresh
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Sum Sum
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Akhila Lakhsmikantha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Pobbisetty Radhakrishnagupta Rekha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Shaesta Naseem Zaidi
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vaijayanti Gupta
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Subramanian Kannan
- grid.416504.20000 0004 1796 819XDepartment of Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| |
Collapse
|
4
|
Panda A, Betigeri A, Subramanian K, Ross JS, Pavlick DC, Ali S, Markowski P, Silk A, Kaufman HL, Lattime E, Mehnert JM, Sullivan R, Lovly CM, Sosman J, Johnson DB, Bhanot G, Ganesan S. Identifying a Clinically Applicable Mutational Burden Threshold as a Potential Biomarker of Response to Immune Checkpoint Therapy in Solid Tumors. JCO Precis Oncol 2017; 2017:PO.17.00146. [PMID: 29951597 PMCID: PMC6016848 DOI: 10.1200/po.17.00146] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE An association between mutational burden and response to immune checkpoint therapy has been documented in several cancer types. The potential for such a mutational burden threshold to predict response to immune checkpoint therapy was evaluated in several clinical datasets, where mutational burden was measured either by whole-exome sequencing (WXS) or using commercially available sequencing panels. METHODS WXS and RNA-seq data of 33 solid cancer types from TCGA were analyzed to determine whether a robust immune checkpoint activating mutation (iCAM) burden threshold associated with evidence of immune checkpoint activation exists in these cancers that may serve as a biomarker for response to immune checkpoint blockade therapy. RESULTS We find that a robust iCAM threshold, associated with signatures of immune checkpoint activation, exists in 8 of 33 solid cancers: melanoma, lung adenocarcinoma, colon adenocarcinoma, endometrial cancer, stomach adenocarcinoma, cervical cancer, ER+HER2- breast cancer, and bladder-urothelial cancer. Tumors with mutational burden higher than the threshold (iCAM+) also had clear histologic evidence of lymphocytic infiltration. In published datasets of melanoma, lung adenocarcinoma and colon cancer, patients with iCAM+ tumors had significantly better response to immune checkpoint therapy compared to those with iCAM- tumors. ROC analysis using TCGA predictions as gold standard showed that iCAM+ tumors are accurately identifiable using clinical sequencing assays, such as FoundationOne or StrandAdvantage. Using the FoundationOne derived threshold, analysis of 113 melanoma tumors, showed that iCAM+ patients have significantly better response to immune checkpoint therapy. iCAM+ and iCAM- tumors have distinct mutation patterns and different immune microenvironments. CONCLUSION In 8 solid cancers, a mutational burden threshold exists that may predict response to immune checkpoint blockade. This threshold is identifiable using available clinical sequencing assays.
Collapse
Affiliation(s)
- Anshuman Panda
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Anil Betigeri
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Kalyanasundaram Subramanian
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Jeffrey S. Ross
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Dean C. Pavlick
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Siraj Ali
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Paul Markowski
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Ann Silk
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Howard L. Kaufman
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Edmund Lattime
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Janice M. Mehnert
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Ryan Sullivan
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Christine M. Lovly
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Jeffrey Sosman
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Douglas B. Johnson
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Gyan Bhanot
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Shridar Ganesan
- Anshuman Panda, Ann Silk, Howard L. Kaufman, Edmund Lattime, Janice M. Mehnert, Gyan Bhanot, and Shridar Ganesan, Rutgers Cancer Institute of New Jersey; Paul Markowski, Ann Silk, Howard L. Kaufman, Janice M. Mehnert, and Shridar Ganesan, Rutgers Robert Wood Johnson Medical School, New Brunswick; Anshuman Panda and Gyan Bhanot, Rutgers University, Piscataway, NJ; Anil Betigeri and Kalyanasundaram Subramanian, Strand Life Sciences, Bangalore, India; Jeffrey S. Ross, Dean C. Pavlick, and Siraj Ali, Foundation Medicine, Cambridge; Ryan Sullivan, Massachusetts General Hospital, Boston, MA; Christine M. Lovly and Douglas B. Johnson, Vanderbilt University Medical Center and Vanderbilt Ingram Cancer Center, Nashville, TN; and Jeffrey Sosman, Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL,Corresponding author: Shridar Ganesan, MD, PhD, 195 Little Albany St, New Brunswick, NJ 08903; e-mail:
| |
Collapse
|
5
|
Sen M, Katragadda S, Ravichandran A, Deshpande G, Parulekar M, Nayanala S, Vittal V, Shen W, Phooi Nee Yong M, Jacob J, Parchuru S, Dhanuskodi K, Eyring K, Agrawal P, Agarwal S, Shanmugam A, Gupta S, Vishwanath D, Kumari K, Hariharan AK, Balaji SA, Liang Q, Robolledo B, Gauribidanur Raghavendrachar V, Oomer Farooque M, Buresh CJ, Ramamoorthy P, Bahadur U, Subramanian K, Hariharan R, Veeramachaneni V, Sankaran S, Gupta V. StrandAdvantage test for early-line and advanced-stage treatment decisions in solid tumors. Cancer Med 2017; 6:883-901. [PMID: 28371134 PMCID: PMC5430095 DOI: 10.1002/cam4.1037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive genetic profiling of tumors using next‐generation sequencing (NGS) is gaining acceptance for guiding treatment decisions in cancer care. We designed a cancer profiling test combining both deep sequencing and immunohistochemistry (IHC) of relevant cancer targets to aid therapy choices in both standard‐of‐care (SOC) and advanced‐stage treatments for solid tumors. The SOC report is provided in a short turnaround time for four tumors, namely lung, breast, colon, and melanoma, followed by an investigational report. For other tumor types, an investigational report is provided. The NGS assay reports single‐nucleotide variants (SNVs), copy number variations (CNVs), and translocations in 152 cancer‐related genes. The tissue‐specific IHC tests include routine and less common markers associated with drugs used in SOC settings. We describe the standardization, validation, and clinical utility of the StrandAdvantage test (SA test) using more than 250 solid tumor formalin‐fixed paraffin‐embedded (FFPE) samples and control cell line samples. The NGS test showed high reproducibility and accuracy of >99%. The test provided relevant clinical information for SOC treatment as well as more information related to investigational options and clinical trials for >95% of advanced‐stage patients. In conclusion, the SA test comprising a robust and accurate NGS assay combined with clinically relevant IHC tests can detect somatic changes of clinical significance for strategic cancer management in all the stages.
Collapse
Affiliation(s)
- Manimala Sen
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Shanmukh Katragadda
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Aarthi Ravichandran
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Gouri Deshpande
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Minothi Parulekar
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Swetha Nayanala
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Vikram Vittal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Weiming Shen
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | | | - Jemima Jacob
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Sravanthi Parchuru
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kalpana Dhanuskodi
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kenneth Eyring
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Pooja Agrawal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Smita Agarwal
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Ashwini Shanmugam
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Satish Gupta
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Divya Vishwanath
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Kiran Kumari
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Arun K Hariharan
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Sai A Balaji
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| | - Qiaoling Liang
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Belen Robolledo
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | | | | | | | - Preveen Ramamoorthy
- Strand Life Sciences, 12635 E. Montview Blvd., Suite 360, Aurora, Colorado, 80045
| | - Urvashi Bahadur
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | | | - Ramesh Hariharan
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | | | - Satish Sankaran
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India
| | - Vaijayanti Gupta
- From Strand Life Sciences, 5th Floor, Kirloskar Business Park, Bangalore, India.,Mazumdar-Shaw Center for Translational Research (MSCTR), Mazumdar-Shaw Medical Foundation, A-Block, 8th Floor #258/A, NHHealth City, Bangalore, India
| |
Collapse
|