Archival fine-needle aspiration cytopathology (FNAC) samples: untapped resource for clinical molecular profiling.
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 polymorphism 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.
Killian
J Keith
JK
Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Bethesda, MD 20892-4265, USA.
Walker
Robert L
RL
Suuriniemi
Miia
M
Jones
Laura
L
Scurci
Stephanie
S
Singh
Parvati
P
Cornelison
Robert
R
Harmon
Shannon
S
Boisvert
Nichole
N
Zhu
Jack
J
Wang
Yonghong
Y
Bilke
Sven
S
Davis
Sean
S
Giaccone
Giuseppe
G
Smith
William I
WI
Meltzer
Paul S
PS
D000368:Aged; D000369:Aged, 80 and over; D044963:Biopsy, Fine-Needle / Q000379:methods*; D002874:Chromosome Mapping; D016000:Cluster Analysis; D004247:DNA / Q000032:analysis*; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008875:Middle Aged; D009369:Neoplasms / Q000235:genetics / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011309:Preservation, Biological / Q000379:methods*; D013997:Time Factors; D055815:Young Adult
D004247:DNA