Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium.
Nilsson CL., Berven F., Selheim F., Liu H., Moskal JR., Kroes RA., Sulman EP., Conrad CA., Lang FF., Andrén PE., Nilsson A., Carlsohn E., Lilja H., Malm J., Fenyö D., Subramaniyam D., Wang X., Gonzales-Gonzales M., Dasilva N., Diez P., Fuentes M., Végvári Á., Sjödin K., Welinder C., Laurell T., Fehniger TE., Lindberg H., Rezeli M., Edula G., Hober S., Marko-Varga G.
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.