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Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice.

Cancer treatment communications

Rangachari D, VanderLaan PA, Le X, Folch E, Kent MS, Gangadharan SP, Majid A, Haspel RL, Joseph LJ, Huberman MS, Costa DB.
PMID: 26601054
Cancer Treat Commun. 2015;4:174-181. doi: 10.1016/j.ctrc.2015.10.004.

INTRODUCTION: Tumor genotyping using single gene assays (SGAs) is standard practice in advanced non-small-cell lung cancer (NSCLC). We evaluated how the introduction of next generation sequencing (NGS) into day-to-day clinical practice altered therapeutic decision-making.METHODS: Clinicopathologic data, tumor genotype, and...

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Rangachari D, VanderLaan PA, Le X, et al. Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice. Cancer Treat Commun. 2015;4:174-181doi: 10.1016/j.ctrc.2015.10.004.
Rangachari, D., VanderLaan, P. A., Le, X., Folch, E., Kent, M. S., Gangadharan, S. P., Majid, A., Haspel, R. L., Joseph, L. J., Huberman, M. S., & Costa, D. B. (2015). Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice. Cancer treatment communications, 4174-181. https://doi.org/10.1016/j.ctrc.2015.10.004
Rangachari, Deepa, et al. "Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice." Cancer treatment communications vol. 4 (2015): 174-181. doi: https://doi.org/10.1016/j.ctrc.2015.10.004
Rangachari D, VanderLaan PA, Le X, Folch E, Kent MS, Gangadharan SP, Majid A, Haspel RL, Joseph LJ, Huberman MS, Costa DB. Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice. Cancer Treat Commun. 2015;4:174-181. doi: 10.1016/j.ctrc.2015.10.004. PMID: 26601054; PMCID: PMC4653729.
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Epidermal growth factor receptor gene amplification in atypical adenomatous hyperplasia of the lung.

American journal of translational research

McIntire MG, Santagata S, Ligon K, Chirieac LR.
PMID: 20589169
Am J Transl Res. 2010 May 16;2(3):309-15.

Atypical adenomatous hyperplasia (AAH) is postulated to be the earliest morphologic precursor lesion in lung carcinogenesis. The epidermal growth factor receptor (EGFR), one of the members of the Erb-2 family of receptors, is commonly expressed in non-small cell lung...

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McIntire MG, Santagata S, Ligon K, et al. Epidermal growth factor receptor gene amplification in atypical adenomatous hyperplasia of the lung. Am J Transl Res. 2010;2(3):309-15
McIntire, M. G., Santagata, S., Ligon, K., & Chirieac, L. R. (2010). Epidermal growth factor receptor gene amplification in atypical adenomatous hyperplasia of the lung. American journal of translational research, 2(3), 309-15.
McIntire, Maria G, et al. "Epidermal growth factor receptor gene amplification in atypical adenomatous hyperplasia of the lung." American journal of translational research vol. 2,3 (2010): 309-15.
McIntire MG, Santagata S, Ligon K, Chirieac LR. Epidermal growth factor receptor gene amplification in atypical adenomatous hyperplasia of the lung. Am J Transl Res. 2010 May 16;2(3):309-15. PMID: 20589169; PMCID: PMC2892406.
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Moving the mountain in advanced non-small-cell lung cancer: evolving immunotherapies for a dire disease.

Translational cancer research

Rangachari D, Costa DB.
PMID: 30613479
Transl Cancer Res. 2017 Feb;6:S151-S157. doi: 10.21037/tcr.2017.02.28.

No abstract available.

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Rangachari D, Costa DB. Moving the mountain in advanced non-small-cell lung cancer: evolving immunotherapies for a dire disease. Transl Cancer Res. 2017;6:S151-S157doi: 10.21037/tcr.2017.02.28.
Rangachari, D., & Costa, D. B. (2017). Moving the mountain in advanced non-small-cell lung cancer: evolving immunotherapies for a dire disease. Translational cancer research, 6S151-S157. https://doi.org/10.21037/tcr.2017.02.28
Rangachari, Deepa, and Costa, Daniel B. "Moving the mountain in advanced non-small-cell lung cancer: evolving immunotherapies for a dire disease." Translational cancer research vol. 6 (2017): S151-S157. doi: https://doi.org/10.21037/tcr.2017.02.28
Rangachari D, Costa DB. Moving the mountain in advanced non-small-cell lung cancer: evolving immunotherapies for a dire disease. Transl Cancer Res. 2017 Feb;6:S151-S157. doi: 10.21037/tcr.2017.02.28. PMID: 30613479; PMCID: PMC6319878.
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Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival.

Translational lung cancer research

Qian D, Liu H, Zhao L, Wang X, Luo S, Moorman PG, Patz EF, Su L, Shen S, Christiani DC, Wei Q.
PMID: 32676321
Transl Lung Cancer Res. 2020 Jun;9(3):575-586. doi: 10.21037/tlcr-19-318.

BACKGROUND: Both antibody-dependent cellular cytotoxicity and phagocytosis activate innate immunity, and the Fc gamma receptor (FCGR)-mediated phagocytosis is an integral part of the process. We assessed associations between single-nucleotide polymorphisms (SNPs) in FCGR-related genes and survival of patients with...

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Qian D, Liu H, Zhao L, et al. Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival. Transl Lung Cancer Res. 2020;9(3):575-586doi: 10.21037/tlcr-19-318.
Qian, D., Liu, H., Zhao, L., Wang, X., Luo, S., Moorman, P. G., Patz, E. F., Su, L., Shen, S., Christiani, D. C., & Wei, Q. (2020). Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival. Translational lung cancer research, 9(3), 575-586. https://doi.org/10.21037/tlcr-19-318
Qian, Danwen, et al. "Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival." Translational lung cancer research vol. 9,3 (2020): 575-586. doi: https://doi.org/10.21037/tlcr-19-318
Qian D, Liu H, Zhao L, Wang X, Luo S, Moorman PG, Patz EF, Su L, Shen S, Christiani DC, Wei Q. Novel genetic variants in genes of the Fc gamma receptor-mediated phagocytosis pathway predict non-small cell lung cancer survival. Transl Lung Cancer Res. 2020 Jun;9(3):575-586. doi: 10.21037/tlcr-19-318. PMID: 32676321; PMCID: PMC7354140.
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Palbociclib resistance confers dependence on an FGFR-MAP kinase-mTOR-driven pathway in .

Oncotarget

Haines E, Chen T, Kommajosyula N, Chen Z, Herter-Sprie GS, Cornell L, Wong KK, Shapiro GI.
PMID: 30167080
Oncotarget. 2018 Aug 03;9(60):31572-31589. doi: 10.18632/oncotarget.25803. eCollection 2018 Aug 03.

CDK4 is emerging as a target in

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Haines E, Chen T, Kommajosyula N, et al. Palbociclib resistance confers dependence on an FGFR-MAP kinase-mTOR-driven pathway in . Oncotarget. 2018;9(60):31572-31589doi: 10.18632/oncotarget.25803.
Haines, E., Chen, T., Kommajosyula, N., Chen, Z., Herter-Sprie, G. S., Cornell, L., Wong, K. K., & Shapiro, G. I. (2018). Palbociclib resistance confers dependence on an FGFR-MAP kinase-mTOR-driven pathway in . Oncotarget, 9(60), 31572-31589. https://doi.org/10.18632/oncotarget.25803
Haines, Eric, et al. "Palbociclib resistance confers dependence on an FGFR-MAP kinase-mTOR-driven pathway in ." Oncotarget vol. 9,60 (2018): 31572-31589. doi: https://doi.org/10.18632/oncotarget.25803
Haines E, Chen T, Kommajosyula N, Chen Z, Herter-Sprie GS, Cornell L, Wong KK, Shapiro GI. Palbociclib resistance confers dependence on an FGFR-MAP kinase-mTOR-driven pathway in . Oncotarget. 2018 Aug 03;9(60):31572-31589. doi: 10.18632/oncotarget.25803. eCollection 2018 Aug 03. PMID: 30167080; PMCID: PMC6114982.
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Rapidly fatal advanced .

Cancer treatment communications

Rangachari D, Drake L, Huberman MS, McDonald DC, VanderLaan PA, Folch E, Costa DB.
PMID: 28111612
Cancer Treat Commun. 2016;9:41-43. doi: 10.1016/j.ctarc.2016.07.001. Epub 2016 Jul 05.

Use of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) is associated with dramatic, durable, and tolerable responses and side effect profiles when applied for palliation of advanced

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Rangachari D, Drake L, Huberman MS, et al. Rapidly fatal advanced . Cancer Treat Commun. 2016;9:41-43doi: 10.1016/j.ctarc.2016.07.001.
Rangachari, D., Drake, L., Huberman, M. S., McDonald, D. C., VanderLaan, P. A., Folch, E., & Costa, D. B. (2016). Rapidly fatal advanced . Cancer treatment communications, 941-43. https://doi.org/10.1016/j.ctarc.2016.07.001
Rangachari, Deepa, et al. "Rapidly fatal advanced ." Cancer treatment communications vol. 9 (2016): 41-43. doi: https://doi.org/10.1016/j.ctarc.2016.07.001
Rangachari D, Drake L, Huberman MS, McDonald DC, VanderLaan PA, Folch E, Costa DB. Rapidly fatal advanced . Cancer Treat Commun. 2016;9:41-43. doi: 10.1016/j.ctarc.2016.07.001. Epub 2016 Jul 05. PMID: 28111612; PMCID: PMC5241076.
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Kinase inhibitor-responsive genotypes in EGFR mutated lung adenocarcinomas: moving past common point mutations or indels into uncommon kinase domain duplications and rearrangements.

Translational lung cancer research

Costa DB.
PMID: 27413714
Transl Lung Cancer Res. 2016 Jun;5(3):331-7. doi: 10.21037/tlcr.2016.06.04.

The most frequent epidermal growth factor receptor (EGFR) mutations found by traditional or comprehensive molecular profiling of lung adenocarcinomas include indels of exon 19 (the exon 19 deletion delE746_A750 being the most common) and the exon 21 L858R point...

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Costa DB. Kinase inhibitor-responsive genotypes in EGFR mutated lung adenocarcinomas: moving past common point mutations or indels into uncommon kinase domain duplications and rearrangements. Transl Lung Cancer Res. 2016;5(3):331-7doi: 10.21037/tlcr.2016.06.04.
Costa, D. B. (2016). Kinase inhibitor-responsive genotypes in EGFR mutated lung adenocarcinomas: moving past common point mutations or indels into uncommon kinase domain duplications and rearrangements. Translational lung cancer research, 5(3), 331-7. https://doi.org/10.21037/tlcr.2016.06.04
Costa, Daniel B. "Kinase inhibitor-responsive genotypes in EGFR mutated lung adenocarcinomas: moving past common point mutations or indels into uncommon kinase domain duplications and rearrangements." Translational lung cancer research vol. 5,3 (2016): 331-7. doi: https://doi.org/10.21037/tlcr.2016.06.04
Costa DB. Kinase inhibitor-responsive genotypes in EGFR mutated lung adenocarcinomas: moving past common point mutations or indels into uncommon kinase domain duplications and rearrangements. Transl Lung Cancer Res. 2016 Jun;5(3):331-7. doi: 10.21037/tlcr.2016.06.04. PMID: 27413714; PMCID: PMC4931120.
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Novel genetic variants of .

American journal of cancer research

Liu L, Liu H, Luo S, Patz EF, Glass C, Su L, Lin L, Christiani DC, Wei Q.
PMID: 32905494
Am J Cancer Res. 2020 Aug 01;10(8):2603-2616. eCollection 2020.

Although lymphangiogenesis is a vital step in lung cancer metastasis, the association between lymphangiogenesis and non-small cell lung cancer (NSCLC) survival remains unclear. Since single-nucleotide polymorphisms (SNPs) have been reported to predict NSCLC survival, we investigated associations between SNPs...

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Liu L, Liu H, Luo S, et al. Novel genetic variants of . Am J Cancer Res. 2020;10(8):2603-2616
Liu, L., Liu, H., Luo, S., Patz, E. F., Glass, C., Su, L., Lin, L., Christiani, D. C., & Wei, Q. (2020). Novel genetic variants of . American journal of cancer research, 10(8), 2603-2616.
Liu, Lihua, et al. "Novel genetic variants of ." American journal of cancer research vol. 10,8 (2020): 2603-2616.
Liu L, Liu H, Luo S, Patz EF, Glass C, Su L, Lin L, Christiani DC, Wei Q. Novel genetic variants of . Am J Cancer Res. 2020 Aug 01;10(8):2603-2616. eCollection 2020. PMID: 32905494; PMCID: PMC7471352.
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Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival.

Cancer informatics

Wang Z, Choi S, Lee J, Huang YT, Chen F, Zhao Y, Lin X, Neuberg D, Kim J, Christiani DC.
PMID: 25657573
Cancer Inform. 2015 Jan 27;14:1-9. doi: 10.4137/CIN.S13976. eCollection 2015.

Mutations in the mtDNA genome have long been suspected to play an important role in cancer. Although most cancer cells harbor mtDNA mutations, the question of whether such mutations are associated with clinical prognosis of lung cancer remains unclear....

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Wang Z, Choi S, Lee J, et al. Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival. Cancer Inform. 2015;14:1-9doi: 10.4137/CIN.S13976.
Wang, Z., Choi, S., Lee, J., Huang, Y. T., Chen, F., Zhao, Y., Lin, X., Neuberg, D., Kim, J., & Christiani, D. C. (2015). Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival. Cancer informatics, 141-9. https://doi.org/10.4137/CIN.S13976
Wang, Zhaoxi, et al. "Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival." Cancer informatics vol. 14 (2015): 1-9. doi: https://doi.org/10.4137/CIN.S13976
Wang Z, Choi S, Lee J, Huang YT, Chen F, Zhao Y, Lin X, Neuberg D, Kim J, Christiani DC. Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival. Cancer Inform. 2015 Jan 27;14:1-9. doi: 10.4137/CIN.S13976. eCollection 2015. PMID: 25657573; PMCID: PMC4310616.
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PD-L1 testing using the clone 22C3 pharmDx kit for selection of patients with non-small cell lung cancer to receive immune checkpoint inhibitor therapy: are cytology cell blocks a viable option?.

Journal of the American Society of Cytopathology

Torous VF, Rangachari D, Gallant BP, Shea M, Costa DB, VanderLaan PA.
PMID: 29713584
J Am Soc Cytopathol. 2018 May-Jun;7(3):133-141. doi: 10.1016/j.jasc.2018.02.003. Epub 2018 Feb 16.

INTRODUCTION: Programmed death ligand 1 (PD-L1) testing of non-small cell lung cancer (NSCLC) specimens helps select patients most likely to respond to immune checkpoint inhibitors. PD-L1 immunohistochemical testing is approved for formalin-fixed, paraffin-embedded (FFPE) surgical pathology specimens; however, the...

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Torous VF, Rangachari D, Gallant BP, et al. PD-L1 testing using the clone 22C3 pharmDx kit for selection of patients with non-small cell lung cancer to receive immune checkpoint inhibitor therapy: are cytology cell blocks a viable option?. J Am Soc Cytopathol. 2018;7(3):133-141doi: 10.1016/j.jasc.2018.02.003.
Torous, V. F., Rangachari, D., Gallant, B. P., Shea, M., Costa, D. B., & VanderLaan, P. A. (2018). PD-L1 testing using the clone 22C3 pharmDx kit for selection of patients with non-small cell lung cancer to receive immune checkpoint inhibitor therapy: are cytology cell blocks a viable option?. Journal of the American Society of Cytopathology, 7(3), 133-141. https://doi.org/10.1016/j.jasc.2018.02.003
Torous, Vanda F, et al. "PD-L1 testing using the clone 22C3 pharmDx kit for selection of patients with non-small cell lung cancer to receive immune checkpoint inhibitor therapy: are cytology cell blocks a viable option?." Journal of the American Society of Cytopathology vol. 7,3 (2018): 133-141. doi: https://doi.org/10.1016/j.jasc.2018.02.003
Torous VF, Rangachari D, Gallant BP, Shea M, Costa DB, VanderLaan PA. PD-L1 testing using the clone 22C3 pharmDx kit for selection of patients with non-small cell lung cancer to receive immune checkpoint inhibitor therapy: are cytology cell blocks a viable option?. J Am Soc Cytopathol. 2018 May-Jun;7(3):133-141. doi: 10.1016/j.jasc.2018.02.003. Epub 2018 Feb 16. PMID: 29713584; PMCID: PMC5919255.
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TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

Cancer informatics

Huang YT, Hsu T, Christiani DC.
PMID: 25452685
Cancer Inform. 2014 Oct 15;13:15-23. doi: 10.4137/CIN.S13978. eCollection 2014.

The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes...

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Huang YT, Hsu T, Christiani DC. TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile. Cancer Inform. 2014;13:15-23doi: 10.4137/CIN.S13978.
Huang, Y. T., Hsu, T., & Christiani, D. C. (2014). TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile. Cancer informatics, 1315-23. https://doi.org/10.4137/CIN.S13978
Huang, Yen-Tsung, et al. "TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile." Cancer informatics vol. 13 (2014): 15-23. doi: https://doi.org/10.4137/CIN.S13978
Huang YT, Hsu T, Christiani DC. TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile. Cancer Inform. 2014 Oct 15;13:15-23. doi: 10.4137/CIN.S13978. eCollection 2014. PMID: 25452685; PMCID: PMC4218657.
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Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center.

Journal of oncology practice

Nguyen KS, Sanford RA, Huberman MS, Goldstein MA, McDonald DM, Farquhar M, Gangadharan SP, Kent MS, Michaud G, Majid A, Berman SM, Aronovitz JA, Nedea EA, Boiselle PM, Cohen DW, Kobayashi S, Costa DB.
PMID: 22548013
J Oncol Pract. 2012 Jan;8(1):57-62. doi: 10.1200/JOP.2011.000274. Epub 2011 Nov 22.

PURPOSE: Evidence-based treatment guidelines for non-small-cell lung cancer (NSCLC) exist to improve the quality of care for patients with this disease. However, how often evidence-based decisions are used for care of NSCLC is poorly understood.PATIENTS AND METHODS: We examined...

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Nguyen KS, Sanford RA, Huberman MS, et al. Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center. J Oncol Pract. 2011;8(1):57-62doi: 10.1200/JOP.2011.000274.
Nguyen, K. S., Sanford, R. A., Huberman, M. S., Goldstein, M. A., McDonald, D. M., Farquhar, M., Gangadharan, S. P., Kent, M. S., Michaud, G., Majid, A., Berman, S. M., Aronovitz, J. A., Nedea, E. A., Boiselle, P. M., Cohen, D. W., Kobayashi, S., & Costa, D. B. (2012). Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center. Journal of oncology practice, 8(1), 57-62. https://doi.org/10.1200/JOP.2011.000274
Nguyen, Kim-Son H, et al. "Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center." Journal of oncology practice vol. 8,1 (2012): 57-62. doi: https://doi.org/10.1200/JOP.2011.000274
Nguyen KS, Sanford RA, Huberman MS, Goldstein MA, McDonald DM, Farquhar M, Gangadharan SP, Kent MS, Michaud G, Majid A, Berman SM, Aronovitz JA, Nedea EA, Boiselle PM, Cohen DW, Kobayashi S, Costa DB. Patterns of care for non-small-cell lung cancer at an academic institution affiliated with a national cancer institute-designated cancer center. J Oncol Pract. 2012 Jan;8(1):57-62. doi: 10.1200/JOP.2011.000274. Epub 2011 Nov 22. PMID: 22548013; PMCID: PMC3266318.
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