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  • Moens, Lotte N. J.Uppsala universitet,Institutionen för immunologi, genetik och patologi (author)

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples

  • Article/chapterEnglish2015

Publisher, publication year, extent ...

  • Elsevier BV,2015
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:su-123776
  • https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-123776URI
  • https://doi.org/10.1016/j.jmoldx.2015.06.009DOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-269252URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomotecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment Length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and Lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Falk-Sörqvist, ElinUppsala universitet,Molekylära verktyg(Swepub:uu)elifa876 (author)
  • Ljungström, ViktorUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)viklj600 (author)
  • Mattsson, JohannaUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)johma961 (author)
  • Sundström, MagnusUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)magnsund (author)
  • La Fleur, LinneaUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)linla513 (author)
  • Mathot, LucyUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)lucma494 (author)
  • Micke, PatrickUppsala universitet,Experimentell och klinisk onkologi(Swepub:uu)patmi676 (author)
  • Nilsson, MatsUppsala universitet,Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab),Molekylära verktyg,Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, S-10691 Stockholm, Sweden.(Swepub:uu)matsnils (author)
  • Botling, JohanUppsala universitet,Institutionen för immunologi, genetik och patologi(Swepub:uu)johanbot (author)
  • Uppsala universitetInstitutionen för immunologi, genetik och patologi (creator_code:org_t)

Related titles

  • In:Journal of Molecular Diagnostics: Elsevier BV17:6, s. 729-7391525-15781943-7811

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