Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jan 4;12(1):135-50.
doi: 10.1021/pr3008607. Epub 2012 Dec 18.

Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium

Carol L Nilsson  1 , Frode Berven, Frode Selheim, Huiling Liu, Joseph R Moskal, Roger A Kroes, Erik P Sulman, Charles A Conrad, Frederick F Lang, Per E Andrén, Anna Nilsson, Elisabet Carlsohn, Hans Lilja, Johan Malm, David Fenyö, Devipriya Subramaniyam, Xiangdong Wang, Maria Gonzales-Gonzales, Noelia Dasilva, Paula Diez, Manuel Fuentes, Ákos Végvári, Karin Sjödin, Charlotte Welinder, Thomas Laurell, Thomas E Fehniger, Henrik Lindberg, Melinda Rezeli, Goutham Edula, Sophia Hober, György Marko-Varga
Affiliations

Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium

Carol L Nilsson et al. J Proteome Res. .

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.

PubMed Disclaimer

Conflict of interest statement

8. CONFLICT OF INTEREST

Dr. Hans Lilja holds patents for free PSA, intact PSA, and hK2 assays.

Figures

Figure 1
Figure 1
Illustration of the elements and workflow that will form the basis for the objectives and goals within the Chromosome 19 Consortium.
Figure 2
Figure 2
Identification of proteins by using (A) UniProt (version 2012_04 April 18, 2012) and (B) neXtProt database (version 2012_04_10). Localization (C) and functions (D) of proteins presented are based on database search in PRIDE.
Figure 2
Figure 2
Identification of proteins by using (A) UniProt (version 2012_04 April 18, 2012) and (B) neXtProt database (version 2012_04_10). Localization (C) and functions (D) of proteins presented are based on database search in PRIDE.
Figure 2
Figure 2
Identification of proteins by using (A) UniProt (version 2012_04 April 18, 2012) and (B) neXtProt database (version 2012_04_10). Localization (C) and functions (D) of proteins presented are based on database search in PRIDE.
Figure 2
Figure 2
Identification of proteins by using (A) UniProt (version 2012_04 April 18, 2012) and (B) neXtProt database (version 2012_04_10). Localization (C) and functions (D) of proteins presented are based on database search in PRIDE.
Figure 3
Figure 3
Schematic illustration of the workflow applied within the pilot study.
Figure 4
Figure 4
The results from the comprehensive MS analysis of synthetic peptides used in the Pilot Study.
Figure 5
Figure 5
Categories of the MRM results illustrated by selected examples.
Figure 6
Figure 6
Illustration of the biobanking workflow (A). Selected MRM transitions of the signature peptides of PSA (B). PSA 3D structure with indication of the tryptic peptides used for identification (C).
Figure 6
Figure 6
Illustration of the biobanking workflow (A). Selected MRM transitions of the signature peptides of PSA (B). PSA 3D structure with indication of the tryptic peptides used for identification (C).
Figure 6
Figure 6
Illustration of the biobanking workflow (A). Selected MRM transitions of the signature peptides of PSA (B). PSA 3D structure with indication of the tryptic peptides used for identification (C).
Figure 7
Figure 7
Schematic overview of the workflow status of Chromosome 19 genes.
Figure 8
Figure 8
Clustering of chromosome 19 genes differentially expressed in breast cancer, prostate cancer, lung cancer, brain cancer and leukemia.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Hancock W, Omenn G, Legrain P, Paik YK. Proteomics, Human Proteome Project, and Chromosomes. J Proteome Res. 2011;10(1):210–210. - PubMed
    1. Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers CH, Corthals GL, Costello CE, Deutsch EW, Domon B, Hancock W, He FC, Hochstrasser D, Marko-Varga G, Salekdeh GH, Sechi S, Snyder M, Srivastava S, Uhlen M, Wu CH, Yamamoto T, Paik YK, Omenn GS. The Human Proteome Project: Current State and Future Direction. Mol Cell Proteomics. 2011;10(7) - PMC - PubMed
    1. Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan FF, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, Marko-Varga G, Deutsch EW, Kim H, Kwon JY, Aebersold R, Bairoch A, Taylor AD, Kim KY, Lee EY, Hochstrasser D, Legrain P, Hancock WS. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol. 2012;30(3):221–223. - PubMed
    1. Uhlén M, Oksvold P, Älgenäs C, Hamsten C, Fagerberg L, Klevebring D, Lundberg E, Odeberg J, Pontén F, Kondo T, Sivertsson A. Antibody-based protein profiling of the human chromosome 21. Mol Cell Proteomics. 2011;11(3):M111.013458. - PMC - PubMed
    1. A Gene-centric Human Proteome Project. Mol Cell Proteomics. 2010;9(2):427–429. - PMC - PubMed

Publication types