Big data from small samples: Informatics of next‐generation sequencing in cytopathology

Roy‐Chowdhuri, Sinchita; Routbort, Mark J.; Pantanowitz, Liron

doi:10.1002/cncy.21805

Cited by 11 publications

(11 citation statements)

References 50 publications

(88 reference statements)

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“…In keeping with the recent recommendations by the updated molecular testing guidelines for the selection of lung cancer patients for targeted therapy, our results provide additional support for the use of cytology specimens as a valuable sample source for molecular testing in patients with lung adenocarcinoma. NGS further enables testing of FNA material and helps avoid the potential risks associated with surgical biopsies [35][36][37][38][39][40][41][42].…”

Section: Discussionmentioning

confidence: 99%

Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations

Ruíz-Cordero

Khanna

et al. 2020

BMC Cancer

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Background: Gene expression profiling has consistently identified three molecular subtypes of lung adenocarcinoma that have prognostic implications. To facilitate stratification of patients with this disease into similar molecular subtypes, we developed and validated a simple, mutually exclusive classification. Methods: Mutational status of EGFR, KRAS, and TP53 was used to define seven mutually exclusive molecular subtypes. A development cohort of 283 cytology specimens of lung adenocarcinoma was used to evaluate the associations between the proposed classification and clinicopathologic variables including demographic characteristics, smoking history, fluorescence in situ hybridization and molecular results. For validation and prognostic assessment, 63 of the 283 cytology specimens with available survival data were combined with a separate cohort of 428 surgical pathology specimens of lung adenocarcinoma. Results: The proposed classification yielded significant associations between these molecular subtypes and clinical and prognostic features. We found better overall survival in patients who underwent surgery and had tumors enriched for EGFR mutations. Worse overall survival was associated with older age, stage IV disease, and tumors with co-mutations in KRAS and TP53. Interestingly, neither chemotherapy nor radiation therapy showed benefit to overall survival. Conclusions: The mutational status of EGFR, KRAS, and TP53 can be used to easily classify lung adenocarcinoma patients into seven subtypes that show a relationship with prognosis, especially in patients who underwent surgery, and these subtypes are similar to classifications based on more complex genomic methods reported previously.

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Section: Discussionmentioning

confidence: 99%

Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations

Ruíz-Cordero

Khanna

et al. 2020

BMC Cancer

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Section: Discussionmentioning

confidence: 99%

Simplified Molecular Classification of Lung Adenocarcinomas Based on EGFR, KRAS, and TP53 Mutations

Ruíz-Cordero

Khanna

et al. 2019

Preprint

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Introduction: Gene expression profiling has consistently identified three molecular subtypes of lung adenocarcinoma that have prognostic implications. To facilitate stratification of patients with this disease into similar molecular subtypes, we developed and validated a simple, mutually exclusive classification. Methods: Mutational status of EGFR, KRAS, and TP53 was used to define six mutually exclusive molecular subtypes. A development cohort of 283 cytology specimens of lung adenocarcinoma was used to evaluate the associations between the proposed classification and clinicopathologic variables including demographic characteristics, smoking history, fluorescence in situ hybridization and molecular results. For validation and prognostic assessment, 63 of the 283 cytology specimens with available survival data were combined with a separate cohort of 428 surgical pathology specimens of lung adenocarcinoma. Results: The proposed classification yielded significant associations between these molecular subtypes and clinical and prognostic features. We found better overall survival in patients who underwent surgery and had tumors enriched for EGFR mutations.Worse overall survival was associated with older age, stage IV disease, and tumors with co-mutations in KRAS and TP53. Interestingly, neither chemotherapy nor radiation therapy showed benefit to overall survival. Conclusions: The mutational status of EGFR, KRAS, and TP53 can be used to easily classify lung adenocarcinoma patients into six subtypes that show a relationship with prognosis, especially in patients who underwent surgery, and these subtypes are similar to classifications based on more complex genomic methods reported previously. BackgroundLung cancer is the main cause of cancer-related mortality in both men and women 1-3 . Lung adenocarcinoma accounts for approximately 40% of lung cancer cases 4-6 . Gene expression profiling of lung adenocarcinomas has consistently identified three molecular subtypes with prognostic implications 7-14 . The initial molecular classification of lung adenocarcinomas included the bronchoid, magnoid, and squamoid subtypes 11,15 . However, after comprehensive molecular profiling of a cohort of lung adenocarcinomas, The Cancer Genome Atlas Research Network proposed an updated nomenclature for this molecular classification that encompasses previous histopathologic, anatomic, Patient selection for development cohortWe retrospectively reviewed our institutional database for patients treated between May 1, 2010, and October 31, 2015, to identify cytologic specimens of patients with lung adenocarcinoma. Patients with TTF1-negative non-small cell lung cancer, small cell lung cancer, large cell carcinoma, squamous carcinoma, and poorly differentiated carcinoma not otherwise specified were excluded. We reviewed the patients' medical records for demographic characteristics, clinical information, fluorescence in situ hybridization (FISH) results for ALK, ROS1, MET, and/or RET, and mutation profiling data derived by next-generation sequenci...

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“…Genomic variants of different types often are found in the same tumor type and more extensive genetic profiling is requested on limited FNA material . We explored the use of a laboratory‐validated, RNA‐based NGS assay for the detection of gene fusions from direct cytology smears.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous detection of single‐nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA‐based next‐generation sequencing assay

Guseva

Jaber

Stence

et al. 2018

Cancer Cytopathology

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Big data from small samples: Informatics of next‐generation sequencing in cytopathology

Cited by 11 publications

References 50 publications

Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations

Simplified molecular classification of lung adenocarcinomas based on EGFR, KRAS, and TP53 mutations

Simplified Molecular Classification of Lung Adenocarcinomas Based on EGFR, KRAS, and TP53 Mutations

Simultaneous detection of single‐nucleotide variant, deletion/insertion, and fusion in lung and thyroid carcinoma using cytology specimen and an RNA‐based next‐generation sequencing assay

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