Use of archival fine-needle aspirates for the allelotyping of tumors.
BACKGROUND
Loss of heterozygosity (LOH) analysis (allelotyping) based on polymorphic microsatellite DNA is one of the most powerful molecular tools currently available for studying carcinogenesis. However, allelotyping studies that require archival paraffin embedded tissues are often hampered by technical difficulties related to microdissection and poor DNA quality.


METHODS
The authors compared allelotyping results from 12 paraffin embedded breast carcinoma cases with those from matching alcohol fixed fine-needle aspiration (FNA) cytology slides obtained for routine diagnostic purposes, using 30 polymorphic microsatellite markers at chromosomes 3p, 4p, 4q, 5q, 6p, 8p, 9p, 11q, 17p, and 17q. Cells from the alcohol fixed FNA slides were dissected and processed in three different ways, and DNA dilution experiments were performed to determine the minimum number of cells required for accurate allelotyping.


RESULTS
LOH results were identical for paraffin embedded and alcohol fixed tumors for 97% of 114 polymerase chain reactions (PCR) when 1000-2000 cells were dissected from each FNA slide and DNA from 100 cells was used for each multiplex PCR. However, with lower cell numbers, the discordance rate increased and artifactual LOH was observed. Intratumor allelotype heterogeneity could not be documented.


CONCLUSIONS
The use of alcohol fixed cytology preparations improves the ease of PCR-based allelotyping and greatly expands the range of archival materials available for study. The allelotyping is accurate and reproducible when DNA from >/=25 cells is used in the initial multiplex PCR. Cancer (Cancer Cytopathol)
Euhus
D M
DM
Division of Surgical Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75235-9155, USA.
Maitra
A
A
Wistuba
I I
II
Ashfaq
R
R
Alberts
A
A
Gibbons
D
D
Gazdar
A F
AF
D000483:Alleles; D001707:Biopsy, Needle; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002452:Cell Count; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics; D002886:Chromosomes, Human, Pair 17 / Q000235:genetics; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics; D002895:Chromosomes, Human, Pair 5 / Q000235:genetics; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics; D004210:Dissection; D000431:Ethanol; D005260:Female; D005404:Fixatives; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity; D018895:Microsatellite Repeats / Q000235:genetics; D008866:Microsurgery; D016612:Paraffin Embedding; D011110:Polymorphism, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D016707:Tissue Fixation
D004273:DNA, Neoplasm; D005404:Fixatives; D000431:Ethanol