+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Accurate detection of copy number changes in DNA extracted from formalin-fixed, paraffin-embedded melanoma tissue using duplex ratio tests



Accurate detection of copy number changes in DNA extracted from formalin-fixed, paraffin-embedded melanoma tissue using duplex ratio tests



Journal of Molecular Diagnostics 15(5): 687-694



A minority of melanocytic lesions cannot confidently be classified as benign or malignant on histopathological examination, causing diagnostic uncertainty. DNA copy number changes can be used to distinguish nevi from melanoma, although the use of FFPE tissue can pose technical challenges. DNA copy number assays, called duplex ratio tests, have been developed with duplex real-time PCR, using a simple method with potential for high throughput. Five duplex ratio test assays targeting loci with common DNA copy number changes in melanoma were designed and tested using DNA extracted from FFPE samples microdissected from melanoma, common nevi, benign tonsil (10 each), and two melanoma cell lines. The assays proved accurate when DNA extracted from fresh and FFPE melanoma cell lines were compared (intraclass correlation coefficient, 0.99) and gave precise results when repeated on DNA from FFPE tissue (intraclass correlation coefficient range, 0.90 to 0.96). In combination, duplex ratio test values from three of the assays distinguished between the nevi and melanomas with 100% sensitivity (95% CI, 69.1% to 100%) and 100% specificity (95% CI, 69.1% to 100%). Duplex ratio test assays have been shown to be accurate and precise and can distinguish melanomas from common nevi using DNA from FFPE tissue. Appropriately designed assays could have value in assessment of other cancers.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 051329149

Download citation: RISBibTeXText

PMID: 23810241

DOI: 10.1016/j.jmoldx.2013.04.008


Related references

Detection of copy number changes in DNA from formalin fixed paraffin embedded tissues using paralogue ratio tests. Analytical Chemistry 83(9): 3484-3492, 2011

Detection of copy number changes at multiple loci in DNA prepared from formalin-fixed, paraffin-embedded tissue by multiplex ligation-dependent probe amplification. Methods in Molecular Biology 439: 101-108, 2008

Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Research 67(6): 2544-2551, 2007

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue. Genome Medicine 8(1): 121, 2016

Droplet digital PCR measurement of HER2 copy number alteration in formalin-fixed paraffin-embedded breast carcinoma tissue. Clinical Chemistry 59(6): 991-994, 2013

Next generation digital PCR measurement of hepatitis B virus copy number in formalin-fixed paraffin-embedded hepatocellular carcinoma tissue. Clinical Chemistry 61(1): 290-296, 2015

High-Throughput Amplicon-Based Copy Number Detection of 11 Genes in Formalin-Fixed Paraffin-Embedded Ovarian Tumour Samples by MLPA-Seq. Plos one 10(11): E0143006, 2015

Validation of quantitative PCR-based assays for detection of gene copy number aberrations in formalin-fixed, paraffin embedded solid tumor samples. Cancer Genetics 212-213: 24-31, 2017

Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study. Bmc Genomics 18(1): 526, 2017

Detection of mycobacterial DNA in formalin-fixed, paraffin-embedded tissue specimens by duplex polymerase chain reaction: application to histopathologic diagnosis. Modern Pathology 10(1): 78-83, 1997

Reliable detection of single copy integrated human papillomavirus in formalin-fixed paraffin-embedded tissue using a fully automated assay. Cancer 105(5): 354, 2005

Pyrosequencing of DNA extracted from formalin-fixed paraffin-embedded tissue. Methods in Molecular Biology 724: 181-190, 2011

Data analysis considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues. Cold Spring Harbor Protocols 2012(11): 1203-1209, 2012

Sample processing considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues. Cold Spring Harbor Protocols 2012(11): 1195-1202, 2012

High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer. Plos one 9(11): E111693, 2014