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Translational Datab...
Translational Database Selection and Multiplexed Sequence Capture for Up Front Filtering of Reliable Breast Cancer Biomarker Candidates
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- Ståhl, Patrik L. (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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Bjursell, Magnus K. (författare)
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- Mahdessian, Hovsep (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Hober, Sophia (författare)
- KTH,Proteomik
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- Jirström, Karin (författare)
- Lund University,Lunds universitet,Tumörmikromiljö,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Tumor microenvironment,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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- Lundeberg, Joakim (författare)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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(creator_code:org_t)
- 2011-06-15
- 2011
- Engelska.
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:6, s. e20794-
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
Nyckelord
- GENE-EXPRESSION PROFILES
- DIAGNOSTIC MARKERS
- IDENTIFICATION
- AMPLIFICATION
- TECHNOLOGIES
- MICROARRAYS
- GENOME
- Bioengineering
- Bioteknik
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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