+ 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

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

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

Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.

Please choose payment method:

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

Accession: 057509355

Download citation: RISBibTeXText

PMID: 27846907

DOI: 10.1186/s13073-016-0375-z

Related references

Reference Size Matching, Whole-Genome Amplification, and Fluorescent Labeling as a Method for Chromosomal Microarray Analysis of Clinically Actionable Copy Number Alterations in Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Journal of Molecular Diagnostics 20(3): 279-288, 2018

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

Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Experimental and Molecular Pathology 104(3): 161-169, 2018

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. Plos one 4(5): E5548, 2009

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Research 38(14): E151, 2010

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

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

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, 2013

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

Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discovery 2(1): 23-24, 2012

High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip. Plos one 9(4): E92820, 2014

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

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

Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Human Mutation 26(4): 384-389, 2005