Clinical validation of the 50 gene AmpliSeq Cancer Panel V2 for use on a next generation sequencing platform using formalin fixed, paraffin embedded and fine needle aspiration tumour specimens

11100 Background: FNA is a common diagnostic procedure for the evaluation of pulmonary and pancreatic masses. We sought to determine whether NGS could be performed on these small specimens and to characterize heterogeneity across classes of genomic alterations (GA) in a subset of paired FNA and matched resected primary tumors. Methods: DNA was isolated from formalin fixed paraffin embedded (FFPE) sections of FNA cell blocks using 40µm total sections for NSCLC and 20µm total sections for pancreatic cancers in a CLIA-certified lab (Foundation Medicine). DNA sequencing was performed for 3,320 exons of 182 cancer-related genes and 37 introns of 14 genes frequently rearranged in cancer on indexed, adaptor ligated, hybridization-captured libraries to a median depth of 931x for the NSCLC and 416x for the pancreatic FNAs. Results: Genomic profiles were successfully generated from 19/19 of the NSCLC and 22/23 of the pancreatic FNA cases. We found 97 GA in the 19 NSCLC FNAs (range 2-9, average 5.1 GA per patient). 68% of the patients had GA in TP53 and 21% in KRAS. Only 16% (3/19) patients did not exhibit an actionable alteration. We found 99 GA in the 23 pancreatic cancer FNAs (range 0-12, average 4.3 per patient). 74% of the patients had GA in KRAS. There was 94% concordance of GA found in 4 matched FNA and primary tumor pairs for the pancreatic cases. For the single discordance, manual inspection of the reads of the discordant allele indicated evidence of loss of heterozygosity. Conclusions: NGS can be reliably performed on small FNA samples processed into cell blocks, and the GA discovered significantly correlates with the GA found in matched primary tumors. This study demonstrates the feasibility of NGS in analyzing FNA samples and further broadens the spectrum of commonly encountered specimen types to which this approach can be successfully applied.

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Optimizing nucleic acid extraction from thyroid fine-needle aspiration cells in stained slides, formalin-fixed/paraffin-embedded tissues, and long-term stored blood samples

Arquivos Brasileiros de Endocrinologia & Metabologia ◽

10.1590/s0004-27302012000900004 ◽

2012 ◽

Vol 56 (9) ◽

pp. 618-626 ◽

Cited By ~ 20

Author(s):

Marina M. L. Kizys ◽

Mirian G. Cardoso ◽

Susan C. Lindsey ◽

Michelle Y. Harada ◽

Fernando A. Soares ◽

...

Keyword(s):

Nucleic Acids ◽

Fine Needle Aspiration ◽

Needle Aspiration ◽

Proteinase K ◽

Acid Extraction ◽

Salting Out ◽

Fine Needle ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Formalin Fixed

OBJECTIVE: Adequate isolation of nucleic acids from peripheral blood, fine-needle aspiration cells in stained slides, and fresh and formalin-fixed/paraffin-embedded tissues is crucial to ensure the success of molecular endocrinology techniques, especially when samples are stored for long periods, or when no other samples can be collected from patients who are lost to follow-up. Here, we evaluate several procedures to improve current methodologies for DNA (salting-out) and RNA isolation. MATERIALS AND METHODS: We used proteinase K treatment, heat shock, and other adaptations to increase the amount and quality of the material retrieved from the samples. RESULTS: We successfully isolated DNA and RNA from the samples described above, and this material was suitable for PCR, methylation profiling, real-time PCR and DNA sequencing. CONCLUSION: The techniques herein applied to isolate nucleic acids allowed further reliable molecular analyses. Arq Bras Endocrinol Metab. 2012;56(9):618-26

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Comparison of Fluorometric and UV Spectrophotometric Findings for DNA Isolated From Formalin-Fixed Paraffin-Embedded Blocks, Fine Needle Aspiration Cytology Smears, and Blood

Cureus ◽

10.7759/cureus.19583 ◽

2021 ◽

Author(s):

Pranoy Paul ◽

Swati Rajput ◽

Prashant Joshi ◽

Manisha Naithani ◽

Nilotpal Chowdhury ◽

...

Keyword(s):

Fine Needle Aspiration ◽

Fine Needle Aspiration Cytology ◽

Needle Aspiration ◽

Aspiration Cytology ◽

Fine Needle ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Embedded Blocks ◽

Needle Aspiration Cytology ◽

Formalin Fixed

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Fine-Needle Aspiration Biopsy in Parotid Masses

Tumori Journal ◽

10.1177/030089168306900509 ◽

1983 ◽

Vol 69 (5) ◽

pp. 417-421 ◽

Cited By ~ 8

Author(s):

Aldo Bono ◽

Fausto Chiesa ◽

Luigi Sala ◽

Alberto Azzarelli ◽

Silvana Pilotti ◽

...

Keyword(s):

Malignant Tumors ◽

High Sensitivity ◽

Needle Aspiration ◽

Combined Method ◽

Cytologic Examination ◽

Fine Needle ◽

Parotid Tumors ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Formalin Fixed

Seventy-nine cases of parotid masses were punctured by fine needle for cytologic examination and subsequently operated on. Of the material obtained, conventional smears, as well as formalin-fixed, paraffin-embedded histologic sections were prepared. The two procedures detected 16 malignant tumors and 63 nonmalignant lesions, with a high sensitivity (86%) and absolute specificity (100%). These data confirm the validity of this combined method and favor the complementary use of the two procedures, which improves the accuracy (80%) of preoperative diagnosis and histologic typing of parotid tumors.

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