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HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples
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Number of Authors: 10
2015 (English)In: Journal of Molecular Diagnostics, ISSN 1525-1578, E-ISSN 1943-7811, Vol. 17, no 6, 729-739 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2015. Vol. 17, no 6, 729-739 p.
National Category
Microbiology in the medical area Cell and Molecular Biology Medical Genetics
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URN: urn:nbn:se:su:diva-123776DOI: 10.1016/j.jmoldx.2015.06.009ISI: 000363830000013PubMedID: 26354930OAI: oai:DiVA.org:su-123776DiVA: diva2:889358
Available from: 2015-12-23 Created: 2015-12-07 Last updated: 2016-05-16Bibliographically approved

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Nilsson, Mats
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Department of Biochemistry and BiophysicsScience for Life Laboratory (SciLifeLab)
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Microbiology in the medical areaCell and Molecular BiologyMedical Genetics

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