Fluorescent In Situ Hybridization (FISH) to Identify Genetic Changes in Fine Needle Biopsy of Lung Lesions Prepared by Jin Jen NCI

Why the Need? Spiral CT screening is highly sensitive for detecting lung cancers in patients at high risk. Spiral CT plus fine needle biopsy increases the diagnostic rate of accurate diagnoses but a portion of the cases are undetermined. Molecular markers might be used to assist clinical diagnosis by detecting the presence of specific chromosomal amplifications.

How it is Possible? Tumors are highly genetically unstable. Tumor related changes often are reflected at the chromosome level and are, by definition, specific to tumors. Genetic analyses can be done in very small tissues and are not subject to the method of detection.

Minimal Chromosome Probes That Can Detect Most Lung Cancers (n = 84) Amplifications # Detectable by Based on Any Alteration (n =84) Percentage 1q, 3q, 5p, 8q 83 98.8% 1q, 5q, 8q 80 95.2% 1q, 3q, 8q 78 92.3% 1q, 3q, 5p 77 91.7% 3q, 5p, 8q 75 89.3%

Method to Identify Genetic Changes in FNAs by FISH Identify and prepare BAC probes unique to specific chromosomal regions Protease digestion of biopsy samples and isolate nuclei Hybridization with fluorescently labeled BAC probes Visualize under fluorescent microscope for Ch. copy number changes Because of the limited time, I will only introduced to one such analysis called … It is basically a method that detects and allows for direct visualization of chromosome number changes in single cells. The general protocol for FISH is list here which involves the ……… Correlate copy number changes with cytological/pathological findings and clinical outcome

Detecting Lung Cancer in FNA-obtained Spiral CT Identified Lung Lesions Probes Labeling: 1q and 5q (green) 8q and 3q (red) nuclei (blue) Samples: 20 paraffin embedded FNA samples 20 formalin fixed biopsies. All samples have pathology and clinical information. 20 malignant 10 benign specific 10 benign non-specific

Sample 503 (Normal Lung) Green: 5p Red: 8q Normal samples often show 2 signals/cells representing their diploid status.

Sample 577 (Normal Lung) Green: 5p, 2 signals/cell Red: 8q, 2 signals/cell

Cornell Sample: JJ001 Green: 1q, 5 signals Red: 3q, 4 signals Green: 5p, 9 signals

Sample: JJ003 Green: 1q, 6 signals Red: 3q, 4 signals A case is considered neoplastic or tumor when 5 or more signals were observed in a cell by one or more probes.

Sample: JJ005 Green: 1q, 8 signals Red: 3q, 12 signals

Sample JJ006 Green: 1q, 4 signals Red: 3q, 5 signals Green: 5p, 4 signals Red: 8q, 5 signals

Sample: JJ010 Red: 8q, 6 signals Green: 5p, 5 signals

Sample: JJ011 Green: 1q, 2 signals Red: 3p, 6 signals

Sample: JJ012 Green: 1q, 2 signals Red: 3p, 2 signals Green: 5p, 2 signals Red: 8q, 2 signals

Sample: JJ014 Green: 1q, >7 signals Red: 3p, 2 signals

Sample: JJ017 Green: 5p, 10 signals Red: 8q, 7 signals

Sample: JJ018 Green: 5p, 3 signals Red: 8q, 6 signals