A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit <a rel="external noopener" href="https://cloudfront.escholarship.org/dist/prd/content/qt634301zm/qt634301zm.pdf?t=oh2094">the original URL</a>. The file type is <code>application/pdf</code>.
Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens
<span title="2012-04-06">2012</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a>
</i>
Preserved Fulltext
The utilization of archived, formalin-fixed paraffinembedded (FFPE) tumor samples for massive parallel sequencing has been challenging due to DNA damage and contamination with normal stroma. Here, we perform whole genome sequencing of DNA isolated from two triple-negative breast cancer tumors archived for >11 years as 5 mm FFPE sections and matched germline DNA. The tumor samples show differing amounts of FFPE damaged DNA sequencing reads revealed as relatively high alignment mismatch rates
<span class="external-identifiers">
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks299">doi:10.1093/nar/gks299</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22492626">pmid:22492626</a>
<a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3413110/">pmcid:PMC3413110</a>
<a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/boflcbwuafhephq64vwyij7z3y">fatcat:boflcbwuafhephq64vwyij7z3y</a>
</span>
more »
... ched for C · G > T · A substitutions compared to germline samples. This increase in mismatch rate is observable with as few as one million reads, allowing for an upfront evaluation of the sample integrity before whole genome sequencing. By applying innovative quality filters incorporating global nucleotide mismatch rates and local mismatch rates, we present a method to identify high-confidence somatic mutations even in the presence of FFPE induced DNA damage. This results in a breast cancer mutational profile consistent with previous studies and revealing potentially important functional mutations. Our study demonstrates the feasibility of performing genome-wide deep sequencing analysis of FFPE archived tumors of limited sample size such as residual cancer after treatment or metastatic biopsies.
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725040835/https://cloudfront.escholarship.org/dist/prd/content/qt634301zm/qt634301zm.pdf?t=oh2094" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext">
<button class="ui simple right pointing dropdown compact black labeled icon button serp-button">
<i class="icon ia-icon"></i>
Web Archive
[PDF]
<div class="menu fulltext-thumbnail">
<img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/3b/2e3bda92310bc45ceffb05f877534b084e78be41.180px.jpg" alt="fulltext thumbnail" loading="lazy">
</div>
</button>
</a>
<a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gks299">
<button class="ui left aligned compact blue labeled icon button serp-button">
<i class="unlock alternate icon" style="background-color: #fb971f;"></i>
oup.com
</button>
</a>
<a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413110" title="pubmed link">
<button class="ui compact blue labeled icon button serp-button">
<i class="file alternate outline icon"></i>
pubmed.gov
</button>
</a>