title: Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium.
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.
authors.affiliation: Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch, Galveston, Texas 77555, United States.
authors.forename: Carol L
authors.initials: CL
authors.lastname: Nilsson
authors.forename: Frode
authors.initials: F
authors.lastname: Berven
authors.forename: Frode
authors.initials: F
authors.lastname: Selheim
authors.forename: Huiling
authors.initials: H
authors.lastname: Liu
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Moskal
authors.forename: Roger A
authors.initials: RA
authors.lastname: Kroes
authors.forename: Erik P
authors.initials: EP
authors.lastname: Sulman
authors.forename: Charles A
authors.initials: CA
authors.lastname: Conrad
authors.forename: Frederick F
authors.initials: FF
authors.lastname: Lang
authors.forename: Per E
authors.initials: PE
authors.lastname: Andrén
authors.forename: Anna
authors.initials: A
authors.lastname: Nilsson
authors.forename: Elisabet
authors.initials: E
authors.lastname: Carlsohn
authors.forename: Hans
authors.initials: H
authors.lastname: Lilja
authors.forename: Johan
authors.initials: J
authors.lastname: Malm
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
authors.forename: Devipriya
authors.initials: D
authors.lastname: Subramaniyam
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Wang
authors.forename: Maria
authors.initials: M
authors.lastname: Gonzales-Gonzales
authors.forename: Noelia
authors.initials: N
authors.lastname: Dasilva
authors.forename: Paula
authors.initials: P
authors.lastname: Diez
authors.forename: Manuel
authors.initials: M
authors.lastname: Fuentes
authors.forename: Ákos
authors.initials: Á
authors.lastname: Végvári
authors.forename: Karin
authors.initials: K
authors.lastname: Sjödin
authors.forename: Charlotte
authors.initials: C
authors.lastname: Welinder
authors.forename: Thomas
authors.initials: T
authors.lastname: Laurell
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Fehniger
authors.forename: Henrik
authors.initials: H
authors.lastname: Lindberg
authors.forename: Melinda
authors.initials: M
authors.lastname: Rezeli
authors.forename: Goutham
authors.initials: G
authors.lastname: Edula
authors.forename: Sophia
authors.initials: S
authors.lastname: Hober
authors.forename: György
authors.initials: G
authors.lastname: Marko-Varga
mesh_terms: D002888:Chromosomes, Human, Pair 19 / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D015870:Gene Expression; D015894:Genome, Human; D006801:Humans; D013058:Mass Spectrometry; D040081:Protein Array Analysis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D020543:Proteome; D012333:RNA, Messenger