An efficient method for the assessment of DNA quality of archival microdissected specimens

Arek Siwoski, Adrian Ishkanian, Cathie Garnis, Lewei Zhang, Miriam Rosin, Wan L. Lam

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

There will be an increasing need of methods for assessing the suitability of specimens for genetic-based assays as DNA markers become an integral part of molecular diagnosis. The targeting of specimens for specific analyses will require the ability to rapidly screen for DNA quality. Conventional methods such as Southern analysis and gene specific-polymerase chain reaction (PCR) often require quantities of material that represent a significant portion of the specimen, especially in microdissected samples. Here we describe a novel application of a commonly used PCR-based DNA-fingerprinting technology that requires minimal quantities of DNA to simultaneously assess multiple regions throughout the genome for DNA quality. Randomly amplified polymorphic DNA (RAPD) PCR generates DNA fragments of a broad size range with the product size reflecting the degree of sample fragmentation. Fourteen DNA samples extracted from cells microdissected from seven formalin-fixed, paraffin-embedded oral cancer biopsies were assessed for DNA quality using gene-specific PCR and RAPD-PCR. Although the more conventional assay required 2-ng DNA (or 300-cell equivalents) to examine DNA quality at a single locus, RAPD-PCR provided a more informative profile of DNA quality from the same microdissected archival specimens.

Original languageEnglish (US)
Pages (from-to)889-892
Number of pages4
JournalModern Pathology
Volume15
Issue number8
DOIs
StatePublished - Aug 2002
Externally publishedYes

Fingerprint

DNA
Polymerase Chain Reaction
DNA-Directed DNA Polymerase
DNA Fingerprinting
Mouth Neoplasms
Genetic Markers
Paraffin
Formaldehyde
Genes
Genome
Technology
Biopsy

Keywords

  • DNA quality
  • Formalin-fixed archival biopsy
  • Microdissection
  • Randomly amplified polymorphic DNA-polymerase chain reaction

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

An efficient method for the assessment of DNA quality of archival microdissected specimens. / Siwoski, Arek; Ishkanian, Adrian; Garnis, Cathie; Zhang, Lewei; Rosin, Miriam; Lam, Wan L.

In: Modern Pathology, Vol. 15, No. 8, 08.2002, p. 889-892.

Research output: Contribution to journalArticle

Siwoski, A, Ishkanian, A, Garnis, C, Zhang, L, Rosin, M & Lam, WL 2002, 'An efficient method for the assessment of DNA quality of archival microdissected specimens', Modern Pathology, vol. 15, no. 8, pp. 889-892. https://doi.org/10.1097/01.MP.0000024288.63070.4F
Siwoski, Arek ; Ishkanian, Adrian ; Garnis, Cathie ; Zhang, Lewei ; Rosin, Miriam ; Lam, Wan L. / An efficient method for the assessment of DNA quality of archival microdissected specimens. In: Modern Pathology. 2002 ; Vol. 15, No. 8. pp. 889-892.
@article{62d7026c86e74380b31cb98b42622a8d,
title = "An efficient method for the assessment of DNA quality of archival microdissected specimens",
abstract = "There will be an increasing need of methods for assessing the suitability of specimens for genetic-based assays as DNA markers become an integral part of molecular diagnosis. The targeting of specimens for specific analyses will require the ability to rapidly screen for DNA quality. Conventional methods such as Southern analysis and gene specific-polymerase chain reaction (PCR) often require quantities of material that represent a significant portion of the specimen, especially in microdissected samples. Here we describe a novel application of a commonly used PCR-based DNA-fingerprinting technology that requires minimal quantities of DNA to simultaneously assess multiple regions throughout the genome for DNA quality. Randomly amplified polymorphic DNA (RAPD) PCR generates DNA fragments of a broad size range with the product size reflecting the degree of sample fragmentation. Fourteen DNA samples extracted from cells microdissected from seven formalin-fixed, paraffin-embedded oral cancer biopsies were assessed for DNA quality using gene-specific PCR and RAPD-PCR. Although the more conventional assay required 2-ng DNA (or 300-cell equivalents) to examine DNA quality at a single locus, RAPD-PCR provided a more informative profile of DNA quality from the same microdissected archival specimens.",
keywords = "DNA quality, Formalin-fixed archival biopsy, Microdissection, Randomly amplified polymorphic DNA-polymerase chain reaction",
author = "Arek Siwoski and Adrian Ishkanian and Cathie Garnis and Lewei Zhang and Miriam Rosin and Lam, {Wan L.}",
year = "2002",
month = "8",
doi = "10.1097/01.MP.0000024288.63070.4F",
language = "English (US)",
volume = "15",
pages = "889--892",
journal = "Modern Pathology",
issn = "0893-3952",
publisher = "Nature Publishing Group",
number = "8",

}

TY - JOUR

T1 - An efficient method for the assessment of DNA quality of archival microdissected specimens

AU - Siwoski, Arek

AU - Ishkanian, Adrian

AU - Garnis, Cathie

AU - Zhang, Lewei

AU - Rosin, Miriam

AU - Lam, Wan L.

PY - 2002/8

Y1 - 2002/8

N2 - There will be an increasing need of methods for assessing the suitability of specimens for genetic-based assays as DNA markers become an integral part of molecular diagnosis. The targeting of specimens for specific analyses will require the ability to rapidly screen for DNA quality. Conventional methods such as Southern analysis and gene specific-polymerase chain reaction (PCR) often require quantities of material that represent a significant portion of the specimen, especially in microdissected samples. Here we describe a novel application of a commonly used PCR-based DNA-fingerprinting technology that requires minimal quantities of DNA to simultaneously assess multiple regions throughout the genome for DNA quality. Randomly amplified polymorphic DNA (RAPD) PCR generates DNA fragments of a broad size range with the product size reflecting the degree of sample fragmentation. Fourteen DNA samples extracted from cells microdissected from seven formalin-fixed, paraffin-embedded oral cancer biopsies were assessed for DNA quality using gene-specific PCR and RAPD-PCR. Although the more conventional assay required 2-ng DNA (or 300-cell equivalents) to examine DNA quality at a single locus, RAPD-PCR provided a more informative profile of DNA quality from the same microdissected archival specimens.

AB - There will be an increasing need of methods for assessing the suitability of specimens for genetic-based assays as DNA markers become an integral part of molecular diagnosis. The targeting of specimens for specific analyses will require the ability to rapidly screen for DNA quality. Conventional methods such as Southern analysis and gene specific-polymerase chain reaction (PCR) often require quantities of material that represent a significant portion of the specimen, especially in microdissected samples. Here we describe a novel application of a commonly used PCR-based DNA-fingerprinting technology that requires minimal quantities of DNA to simultaneously assess multiple regions throughout the genome for DNA quality. Randomly amplified polymorphic DNA (RAPD) PCR generates DNA fragments of a broad size range with the product size reflecting the degree of sample fragmentation. Fourteen DNA samples extracted from cells microdissected from seven formalin-fixed, paraffin-embedded oral cancer biopsies were assessed for DNA quality using gene-specific PCR and RAPD-PCR. Although the more conventional assay required 2-ng DNA (or 300-cell equivalents) to examine DNA quality at a single locus, RAPD-PCR provided a more informative profile of DNA quality from the same microdissected archival specimens.

KW - DNA quality

KW - Formalin-fixed archival biopsy

KW - Microdissection

KW - Randomly amplified polymorphic DNA-polymerase chain reaction

UR - http://www.scopus.com/inward/record.url?scp=0036668011&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036668011&partnerID=8YFLogxK

U2 - 10.1097/01.MP.0000024288.63070.4F

DO - 10.1097/01.MP.0000024288.63070.4F

M3 - Article

VL - 15

SP - 889

EP - 892

JO - Modern Pathology

JF - Modern Pathology

SN - 0893-3952

IS - 8

ER -