<?xml version="1.0" encoding="utf-8"?>
<export-example>
  <doc>
    <id>630</id>
    <completedYear>2015</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>25943</pageFirst>
    <pageLast>25961</pageLast>
    <pageNumber/>
    <edition/>
    <issue>28</issue>
    <volume>6</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>1</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics</title>
    <abstract language="eng">Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C·G &gt; T·A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (&lt;0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.</abstract>
    <parentTitle language="eng">Oncotarget</parentTitle>
    <identifier type="issn">1949-2553</identifier>
    <identifier type="urn">urn:nbn:de:kobv:526-opus4-6307</identifier>
    <enrichment key="SourceTitle">Munchel S., Hoang Y., Zhao Y., Cottrell J., Klotzle B., Godwin A. K., Koestler D., Beyerlein P., Fan J., Bibikova M., Chien J. Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics. Oncotarget. 2015; 6: 25943-25961. Retrieved from https://www.oncotarget.com/article/4671/text/</enrichment>
    <enrichment key="DOI_VoR">https://doi.org/10.18632/oncotarget.4671</enrichment>
    <licence>Creative Commons - CC BY 3.0 - Namensnennung 3.0 Unported</licence>
    <author>Sarah Munchel</author>
    <author>Yen Hoang</author>
    <author>Zhao Yue</author>
    <author>Joseph Cottrell</author>
    <author>Brandy Klotzle</author>
    <author>Andrew K. Godwin</author>
    <author>Devin Koestler</author>
    <author>Peter Beyerlein</author>
    <author>Jian-Bing Fan</author>
    <author>Marina Bibikova</author>
    <author>Jeremy Chien</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cancer genomics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>FFPE DNA</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>whole exome sequencing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>whole genome sequencing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>copy number alteration</value>
    </subject>
    <collection role="ddc" number="616">Krankheiten</collection>
    <collection role="institutes" number="">Fachbereich Ingenieur- und Naturwissenschaften</collection>
    <collection role="open_access" number="">open_access</collection>
    <collection role="green_open_access" number="1">Gold Open Access</collection>
    <thesisPublisher>Technische Hochschule Wildau</thesisPublisher>
    <file>https://opus4.kobv.de/opus4-th-wildau/files/630/4671-73549-2-PB.pdf</file>
  </doc>
</export-example>
