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Translational Database Selection and Multiplexed Sequence Capture for Up Front Filtering of Reliable Breast Cancer Biomarker Candidates
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0002-2207-7370
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Proteomics (closed 20130101).ORCID iD: 0000-0003-0605-8417
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2011 (English)In: PLOS ONE, ISSN 1932-6203, Vol. 6, no 6, e20794- p.Article in journal (Refereed) Published
Abstract [en]

Biomarker identification is of utmost importance for the development of novel diagnostics and therapeutics. Here we make use of a translational database selection strategy, utilizing data from the Human Protein Atlas (HPA) on differentially expressed protein patterns in healthy and breast cancer tissues as a means to filter out potential biomarkers for underlying genetic causatives of the disease. DNA was isolated from ten breast cancer biopsies, and the protein coding and flanking non-coding genomic regions corresponding to the selected proteins were extracted in a multiplexed format from the samples using a single DNA sequence capture array. Deep sequencing revealed an even enrichment of the multiplexed samples and a great variation of genetic alterations in the tumors of the sampled individuals. Benefiting from the upstream filtering method, the final set of biomarker candidates could be completely verified through bidirectional Sanger sequencing, revealing a 40 percent false positive rate despite high read coverage. Of the variants encountered in translated regions, nine novel non-synonymous variations were identified and verified, two of which were present in more than one of the ten tumor samples.

Place, publisher, year, edition, pages
2011. Vol. 6, no 6, e20794- p.
Keyword [en]
GENE-EXPRESSION PROFILES, DIAGNOSTIC MARKERS, IDENTIFICATION, AMPLIFICATION, TECHNOLOGIES, MICROARRAYS, GENOME
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-35602DOI: 10.1371/journal.pone.0020794ISI: 000291730000024Scopus ID: 2-s2.0-79958814978OAI: oai:DiVA.org:kth-35602DiVA: diva2:429766
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note
QC 20110705Available from: 2011-07-05 Created: 2011-07-04 Last updated: 2011-12-06Bibliographically approved

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Hober, Sophia

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