The importance of evaluation of DNA amplificability in KRAS mutation testing with dideoxy sequencing using formalin-fixed and paraffin-embedded colorectal cancer tissues.
Author(s): Okayama N, Nishioka M, Hazama S, Sakai K, Suehiro Y, Maekawa M, Sakamoto J, Iwamoto S, Kato T, Mishima H, Oka M, Hinoda Y
Publication: Jpn J Clin Oncol, 2011, Vol. 41, Page 165-71
PubMed ID: 20926413 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of duration of fixation, deparaffinization, and storage on DNA quantity and quality from FFPE colorectal cancer specimens.
Summary of Findings:
Amplification of products less than 278 bp long was possible in all specimens, regardless of time in fixative and storage duration, but amplification of products between 298 and 313 bp long failed in 2 of 19 specimens, including the specimen stored for 63 months. Amplification of products longer than 313 bp failed in most specimens, regardless of time in fixative or storage duration. Amplification of 201, 240 and 360 bp fragments of KRAS was possible in all specimens, regardless of deparaffinization time, but more DNA was isolated from specimens treated with xylene for at least 60 min.
Biospecimens
Preservative Types
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA Spectrophotometry DNA PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Analyte Extraction and Purification Deparaffinization Xylene 10 min
Xylene 60 min
Xylene 180 min
Xylene overnight
Storage Storage duration 9 months
11 months
13 months
15 months
16 months
18 months
20 months
23 months
24 months
26 months
28 months
29 months
39 months
63 months
Biospecimen Preservation Time in fixative 10 days
11 days
12 days
18 days
19 days
20 days
4 days
6 days
7 days
8 days
9 days
PCR Specific Targeted nucleic acid KRAS
UGT1A1
UGT1A7
UGT1A9
XPC
XPD
TNF-alpha
MIF
IL-1 beta
PCR Specific Length of gene fragment 96 bp
201 bp
221 bp
240 bp
241 bp
258 bp
278 bp
298 bp
313 bp
360 bp
555 bp
565 bp