Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.

Author(s): Killian JK, Walker RL, Suuriniemi M, Jones L, Scurci S, Singh P, Cornelison R, Harmon S, Boisvert N, Zhu J, Wang Y, Bilke S, Davis S, Giaccone G, Smith WI Jr, Meltzer PS

Publication: J Mol Diagn, 2010, Vol. 12, Page 739-45

PubMed ID: 20959611 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of prior staining of FNAC with DQ or Pap on DNA yield, size, and utility for microarray analysis. FNAC from suspected lymphoma and small cell lung carcinoma specimens were obtained from lower back, abdomen, thyroid, lung, thorax spleen, cervix, neck, submandibular glands, bronchus and retroperitoneum and stained 11-16 years prior to the study.

   Summary of Findings:

   The yield of DNA obtained from DQ and PAP-stained FNAC was roughly equivalent, but while the DNA from PAP-stained specimens was almost all below 400 bp in length, DQ-stained specimens contained fragments up to 50,000 bp long. The DQ-stained specimens were successful for all profiling assays, and genomic structural aberrations were identified in 44 of 46 malignant smears. Despite the DNA degradation, similar genotyping and methylation results were obtained using PAP-stained specimens but with more background noise.

   Biospecimens

   • Cell - Lymph Node

   Preservative Types

   • Other Preservative

   Diagnoses:

   • Neoplastic - Benign
   • Neoplastic - Carcinoma
   • Neoplastic - Mixed type
   • Neoplastic - Lymphoma

   Platform:

   Analyte	Technology Platform
   DNA	DNA microarray
   DNA	Electrophoresis
   Morphology	Light microscopy

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Time at room temperature	11-16 years
   Biospecimen Acquisition	Pathology ink	Papanicolaou Diff-Quick
   DNA microarray Specific	Technology platform	Agilent 105K or 180 K CGH Illumina Infinium 370K or 610K genotyping Illumina Infinium methylation 27K
   Biospecimen Preservation	Type of fixation/preservation	Air-dried Alcohol

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