The use of haplotype-specific transcripts improves sample annotation consistency

Nicole Hartmann, Evert Luesink, Edward Khokhlovich, Joseph D Szustakowski, Lukas Baeriswyl, Joshua Peterson, Andreas Scherer, Nirmala R Nanguneri, Frank Staedtler
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mwbemhev3vagjfqqczhnr5d3vi" style="color: black;">Biomarker Research</a> </i> &nbsp;
Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research. Results: Candidate markers were explored through the application of Hartigans' dip test statistics to a publically available human whole genome microarray dataset. The marker performance was tested on 188 serial samples from 53 donors and of variable tissue origin from five public microarray datasets. A qualified transcript marker panel consisting of three probe sets for human
more &raquo; ... yte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in six of the 188 test samples. About 3% of the test samples require root-cause analysis due to unresolvable inaccuracies. Conclusions: The transcript marker panel consisting of HLA-DQA1 and HLA-DRB4 represents a robust, tissue-independent composite marker to assist control donor annotation concordance at the transcript level. Allele-selectivity of HLA genes renders them good candidates for "fingerprinting" with donor specific expression pattern.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2050-7771-2-17">doi:10.1186/2050-7771-2-17</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25285214">pmid:25285214</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4184161/">pmcid:PMC4184161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ax7y5bcpmrd25hwfws5wgfqb2i">fatcat:ax7y5bcpmrd25hwfws5wgfqb2i</a> </span>
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