title: The use of haplotype-specific transcripts improves sample annotation consistency.
abstract: BACKGROUND
  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 leukocyte 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.
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Nicole
authors.initials: N
authors.lastname: Hartmann
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Evert
authors.initials: E
authors.lastname: Luesink
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Edward
authors.initials: E
authors.lastname: Khokhlovich
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Szustakowski
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Lukas
authors.initials: L
authors.lastname: Baeriswyl
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Joshua
authors.initials: J
authors.lastname: Peterson
authors.affiliation: Spheromics, Kontiolahti, Finland.
authors.forename: Andreas
authors.initials: A
authors.lastname: Scherer
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Nirmala R
authors.initials: NR
authors.lastname: Nanguneri
authors.affiliation: Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland.
authors.forename: Frank
authors.initials: F
authors.lastname: Staedtler
keywords: Biomarkers; Dip test; HLA-DQA1; HLA-DRB4; Microarray quality control (QC); mRNA