20 Nisan 2021 Veri seti Açık Erişim

Batuhan KISAKOL; Şahin SARIHAN; Mehmet Arif ERGÜN; Mehmet BAYSAN

MARC21 XML

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Clinical bioinformatics</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">next generation sequencing</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">cancer</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">mapping algorithms</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">variant discovery algorithms</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:zenodo.org:114556</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;The importance of next generation sequencing (NGS) rises in cancer research as accessing this key technology becomes easier for researchers. The sequence data created by NGS technologies must be processed by various bioinformatics algorithms within a pipeline in order to convert raw data to meaningful information. Mapping and variant calling are the two main steps of these analysis pipelines, and many algorithms are available for these steps. Therefore, detailed benchmarking of these algorithms in different scenarios is crucial for the efficient utilization of sequencing technologies. In this study, we compared the performance of twelve pipelines (three mapping and four variant discovery algorithms) with recommended settings to capture single nucleotide variants. We observed significant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples with overall high specificity and low sensitivity. Additional to the individual evaluation of pipelines, we also constructed and tested the performance of pipeline combinations. In these analyses, we observed that certain pipelines complement each other much better than others and display superior performance than individual pipelines. This suggests that adhering to a single pipeline is not optimal for cancer sequencing analysis and sample heterogeneity should be considered in algorithm optimization.&lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">dataset</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="a">Creative Commons Attribution-NonCommercial</subfield>
    <subfield code="u">https://creativecommons.org/licenses/by-nc/4.0/</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="0">(orcid)0000-0002-8732-5216</subfield>
    <subfield code="a">Batuhan KISAKOL</subfield>
    <subfield code="u">Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="z">md5:e1d3d932833993b24393c920907d0d5e</subfield>
    <subfield code="s">13459927</subfield>
    <subfield code="u">https://aperta.ulakbim.gov.trrecord/114556/files/BIY-2008-8-Supp-Table2.xlsx</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="z">md5:048d7e5876da7805d0eeeb71872c0ac1</subfield>
    <subfield code="s">101640</subfield>
    <subfield code="u">https://aperta.ulakbim.gov.trrecord/114556/files/BIY-2008-8-Supp-Table3.xlsx</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="z">md5:92061d7b270909b4767f89faf01eac4d</subfield>
    <subfield code="s">3008864</subfield>
    <subfield code="u">https://aperta.ulakbim.gov.trrecord/114556/files/Supplementary Figures.docx</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="z">md5:52b449f25f41d347d2810b605852794f</subfield>
    <subfield code="s">17536</subfield>
    <subfield code="u">https://aperta.ulakbim.gov.trrecord/114556/files/Supplementary Table 1.docx</subfield>
  </datafield>
  <controlfield tag="005">20210423092420.0</controlfield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2021-04-20</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.3906/biy-2008-8-sup</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="4">
    <subfield code="v">45</subfield>
    <subfield code="p">Turkish Journal of Biology</subfield>
    <subfield code="c">114-126</subfield>
    <subfield code="n">2</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="0">(orcid)0000-0002-2597-1001</subfield>
    <subfield code="a">Şahin SARIHAN</subfield>
    <subfield code="u">Computer Engineering Department, Faculty of Engineering, Marmara University, İstanbul, Turkey</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="0">(orcid)0000-0002-9399-1530</subfield>
    <subfield code="a">Mehmet Arif ERGÜN</subfield>
    <subfield code="u">Computer Engineering Department, Faculty of Computer and Informatics Engineering, İstanbul Technical University, İstanbul, Turkey</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="0">(orcid)0000-0001-7359-2965</subfield>
    <subfield code="a">Mehmet BAYSAN</subfield>
    <subfield code="u">Computer Engineering Department, Faculty of Computer and Informatics Engineering, İstanbul Technical University, İstanbul, Turkey</subfield>
  </datafield>
  <controlfield tag="001">114556</controlfield>
</record>