Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine.
Proteogenomics is a multi-omics research field that has the aim to efficiently integrate genomics, transcriptomics and proteomics. With this approach it is possible to identify new patient-specific proteoforms that may have implications in disease development, specifically in cancer. Understanding the impact of a large number of mutations detected at the genomics level is needed to assess the effects at the proteome level. Proteogenomics data integration would help in identifying molecular changes that are persistent across multiple molecular layers and enable better interpretation of molecular mechanisms of disease, such as the causal relationship between single nucleotide polymorphisms (SNPs) and the expression of transcripts and translation of proteins compared to mainstream proteomics approaches. Identifying patient-specific protein forms and getting a better picture of molecular mechanisms of disease opens the avenue for precision and personalized medicine. Proteogenomics is, however, a challenging interdisciplinary science that requires the understanding of sample preparation, data acquisition and processing for genomics, transcriptomics and proteomics. This chapter aims to guide the reader through the technology and bioinformatics aspects of these multi-omics approaches, illustrated with proteogenomics applications having clinical or biological relevance.
Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Ruggero
R
Barbieri
European Research Institute for the Biology of Ageing, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
Victor
V
Guryev
Department of Pathology & Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Corry-Anke
CA
Brandsma
IBM T.J. Watson Research Centre, 1101 Kitchawan Road, Yorktown Heights, New York, 10598, NY, USA.
Frank
F
Suits
Department of Analytical Biochemistry, Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
Rainer
R
Bischoff
Department of Analytical Biochemistry, Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. p.l.horvatovich@rug.nl.
Peter
P
Horvatovich
D000595:Amino Acid Sequence; D001483:Base Sequence; D002460:Cell Line; D002874:Chromosome Mapping / Q000379:methods* / Q000706:statistics & numerical data; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D013058:Mass Spectrometry; D020641:Polymorphism, Single Nucleotide; D057285:Precision Medicine / Q000379:methods; D000071696:Proteogenomics / Q000295:instrumentation / Q000379:methods*; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012984:Software
D020543:Proteome; D012333:RNA, Messenger
DNA/RNA next generation sequencing; Genomics; Mass spectrometry; Proteogenomics; Proteomics