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The use of haplotype-specific transcripts improves sample annotation consistency
<span title="">2014</span>
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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
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<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>
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... 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.
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