Chromosome 19 Annotations
with Disease Speciation: A First Report from the Global Research Consortium
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Abstract
A first research development progress report of the Chromosome
19 Consortium with members from Sweden, Norway, Spain, United States,
China and India, a part of the Chromosome-centric Human Proteome Project
(C-HPP) global initiative, is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159
peptides, a pilot study was conducted using a subset with 125 isotope-labeled
peptides. We applied an annotation strategy with triple quadrupole,
ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality
of data within and in between these instrumental set-ups. LC–MS
conditions were outlined by multiplex assay developments, followed
by MRM assay developments. SRM was applied to biobank samples, quantifying
kallikrein 3 (prostate specific antigen) in plasma from prostate cancer
patients. The antibody production has been initiated for more than
1200 genes from the entire chromosome 19, and the progress developments
are presented. We developed a dedicated transcript microarray to serve
as the mRNA identifier by screening cancer cell lines. NAPPA protein
arrays were built to align with the transcript data with the Chromosome
19 NAPPA chip, dedicated to 90 proteins, as the first development
delivery. We have introduced an IT-infrastructure utilizing a LIMS
system that serves as the key interface for the research teams to
share and explore data generated within the project. The cross-site
data repository will form the basis for sample processing, including
biological samples as well as patient samples from national Biobanks