Archival Fine-Needle Aspiration Cytopathology (FNAC) Samples

Abstract

Microarray technologies provide high-resolution maps of chromosome imbalances and epigenomic aberrations in the cancer cell genome. Such assays are often sensitive to sample DNA integrity , voiding the utility of many archival pathology specimens and necessitating the special handling of prospective clinical specimens. We have identified the remarkable preservation of higher-molecular weight DNA in archival fine-needle aspiration cytopathology specimens from patients greater than 10 years of age. We further demonstrate the outstanding technical performance of 57 fine-needle aspiration cytopathology samples for aberration detection on high-resolution comparative genomic hybridization array , DNA methylation , and single nucleotide polymor-phism genotyping platforms. Forty-four of 46 malignant aspirates in this study manifested unequivocal genomic aberrations. Importantly , matched Papanicolaou and Diff-Quik fine-needle aspiration cytopathology samples showed critical differences in DNA preservation and DNA integrity. Overall , this study identifies a largely untapped reserve of human pathology specimens for molecular profiling studies , with ramifications for the prospective collection of clinical biospecimens. The two most common modalities for collecting patient tissue samples for pathological analysis can be roughly divided into surgical and cytologic. The former includes core needle and surgical biopsy, and these are typically processed as formalin-fixed, paraffin-embedded (FFPE) samples. FFPE surgical pathology specimens currently comprise the foundation for retrospective clinical genetic profiling studies, and also are typically required for prospective patient enrollment in clinical trials. Alternatively, fine-needle aspiration cytology (FNAC) procedures may be used for rapid, cost-effective and accurate diagnosis with reduced patient morbidity. 1 Common anatomical sources for diagnostic FNAC specimens include breast, thyroid, lymph nodes, thoracic and visceral organs, and deep soft tissues. FNAC samples may be the only archival materials for certain diagnoses such as small cell lung cancer (SCLC). Body fluids and epithelial scrapes are another source of cytology preparation, including pleural effu-sion, ascitic fluid, cerebral-spinal fluid, cervical Pap-smears, and bronchial and esophageal brushings. Overall, cytologic preparations represent an estimated 10 to 20% of archival hospital pathology specimens, and may be significantly enriched for particular pathological diagnoses. We recently reported the excellent performance of archi-val FFPE samples for large-scale molecular profiling using the GoldenGate methylation assay, a modest-density bisul-fite genotyping platform. 2 However, the more-informative, higher-resolution genotyping arrays for tissue molecular profiling require DNA of higher molecular weight than is often retrieved from archival FFPE samples, because of requirements for unbiased whole genome amplification, which is compromised in FFPE samples over time. Thus, array