New approaches for genotyping paraffin wax embedded breast tissue from patients with cancer: the Iowa women's health study

B Thyagarajan; K E Anderson; F Kong; F R Selk; C F Lynch; M D Gross

doi:10.1136/jcp.2004.023374

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New approaches for genotyping paraffin wax embedded breast tissue from patients with cancer: the Iowa women's health study

Journal article

Open access

Peer reviewed

New approaches for genotyping paraffin wax embedded breast tissue from patients with cancer: the Iowa women's health study

B Thyagarajan, K E Anderson, F Kong, F R Selk, C F Lynch and M D Gross

Journal of clinical pathology, Vol.58(9), pp.955-961

09/2005

DOI: 10.1136/jcp.2004.023374

PMCID: PMC1770813

PMID: 16126877

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Abstract

The use of paraffin wax embedded tissue samples as a source of DNA for genotype analysis has been limited because of difficulties in DNA extraction and single nucleotide polymorphism (SNP) analysis. To test the feasibility of applying the combination of a commonly used DNA isolation procedure, PureGene, and a high throughput SNP analysis method, the polymerase chain reaction (PCR)-INVADER assay, to genotype several types of paraffin wax embedded breast tissues. Twenty formalin fixed, paraffin wax blocks were obtained from five participants in the Iowa women's health study. Each participant provided several types of tissue including normal lymph node, normal nipple/areola tissue, inflammatory/fibrotic breast tissue, or normal breast tissue, and tumour tissue. Good quality DNA (260/280 ratio >1.6) was obtained from all tissues. Normal lymph nodes yielded the largest amount of DNA (97.1 mug). DNA obtained from the samples was tested for a germline C1183T polymorphism in the MnSOD gene by three methods-PCR-RFLP (restriction fragment length polymorphism), INVADER assay, and PCR-INVADER assay. Of the 20 samples, PCR-RFLP genotyped 16, the PCR-INVADER assay 18, and the INVADER assay two. This methodology was then used to analyse five additional genotypes and confirmed the general applicability of the method. This study demonstrated the feasibility of (1) using several paraffin wax embedded breast tissues as a source of DNA for germline genetic analysis, with lymph nodes providing the highest yield, and (2) using the combination of a common extraction method with a high throughput SNP analysis method, the PCR-INVADER assay.

Feasibility Studies

Superoxide Dismutase - genetics

Humans

DNA, Neoplasm - isolation & purification

Genotype

DNA Repair - genetics

Polymerase Chain Reaction - methods

Paraffin Embedding

Breast Neoplasms - genetics

Polymorphism, Restriction Fragment Length

Female

Polymorphism, Single Nucleotide

DNA, Neoplasm - genetics

Details

Title: Subtitle: New approaches for genotyping paraffin wax embedded breast tissue from patients with cancer: the Iowa women's health study
Creators: B Thyagarajan - University of Minnesota, Division of Epidemiology, Suite 300, West Bank Office Building, Minneapolis, MN 55454, USA
K E Anderson - University of Minnesota
F Kong
F R Selk
C F Lynch
M D Gross
Resource Type: Journal article
Publication Details: Journal of clinical pathology, Vol.58(9), pp.955-961
Publisher: England
DOI: 10.1136/jcp.2004.023374
PMID: 16126877
PMCID: PMC1770813
ISSN: 0021-9746
eISSN: 1472-4146
Language: English
Date published: 09/2005
Academic Unit: Epidemiology
Record Identifier: 9983995032402771

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