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The use of haplotype-specific transcripts improves sample annotation consistency

Hartmann, Nicole, Luesink, Evert, Khokhlovich, Edward, Szustakowski, Joseph, Baeriswyl, Lukas, Peterson, Joshua, Scherer, Andreas, Nirmala, Nanguneri and Staedtler, Frank (2014) The use of haplotype-specific transcripts improves sample annotation consistency. Biomarker Research, 2 (17).


Background: Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research.
Materials and methods: 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.
Results: A qualified transcript marker panel consisting of three probe sets for human leukocyte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in about 5% of the 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.

Item Type: Article
Keywords: HLA-DQA1, HLA-DRB4, microarray quality control (QC), biomarkers, dip test, mRNA
Date Deposited: 13 Oct 2015 13:12
Last Modified: 13 Oct 2015 13:12


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