From Genome Sequencing to Bedside

T. Lecroq; L. F. Soualmia

doi:10.1055/s-0038-1638852

Yearbook of Medical Informatics, Inhaltsverzeichnis

Yearb Med Inform 2013; 22(01): 175-177
DOI: 10.1055/s-0038-1638852

Original Article

Georg Thieme Verlag KG Stuttgart

From Genome Sequencing to Bedside

Findings from the Section on Bioinformatics and Translational InformaticsSection Editors for the IMIA Yearbook Section on Bioinformatics and Translational Informatics

T. Lecroq

¹Normandie University, University of Rouen, LITIS EA 4108, Information Processing in Biology & Health, Mont-Saint-Aignan, France

,

L. F. Soualmia

¹Normandie University, University of Rouen, LITIS EA 4108, Information Processing in Biology & Health, Mont-Saint-Aignan, France

› Institutsangaben

Abstract

Summary

Objectives: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine.

Method: We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review.

Results: The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding the Human Genome and Medicine. Exploiting genomic data depends on having the appropriate reference annotation available. In the first article, the goal of the GENCODE Consortium is to produce and publish The GENCODE human reference gene set. As a result it is composed by merged manual and automatic annotations, which are frequently updated from public experimental databases. The quality of genome sequencing is platform-dependant. In the second article, a generic database independent from the sequencing technologies, Huvariome, can help to identify errors and inconsistencies in sequencing. To understand complex diseases of patients it will be of great importance to detect rare gene variants. This is the aim of the third study. Finally, in the last article, the plasma's DNA of healthy individual and patients suffering from cancer is compared.

Conclusions: The current research activities attest to the continuous convergence of Bioinformatics and Medical Informatics for clinical practice. For instance, a direct use of high throughput sequencing technologies for patients could aid the diagnosis of complex diseases (such as cancer) without invasive surgery (such as biopsy) but only with blood analysis. However, ongoing genomic tests will generate massive amounts of data and will imply new trends in the near future: “Big Data” and smart health management.

Keywords

Translational Medical Research - Computational Biology - Gene expression - Genome - Medical Informatics

Volltext

Referenzen

References
1 Yip YL. Unlocking the potential of electronic health records for translational research. Findings from the section on the bioinformatics and translational informatics. Yearb Med Inform 2012; 7 (1) 135-8.
2 Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975; 94 (3) 441-8.
3 Kohane IS, Churchill SE, Murphy SN. A translational engine at the national scale: informatics for integrating biology and the bedside. J Am Med Inform Assoc 2012; Mar-Apr 19 (2) 181-5.
4 Roden DM, Xu H, Denny JC, Wilke RA. Electronic medical records as a tool in clinical pharmacology: opportunities and challenges. Clin Pharmacol Ther 2012; Jun 91 (6) 1083-6.
5 Liu ZP, Wang Y, Zhang XS, Chen L. Network-based analysis of complex diseases. IET Syst Biol 2012; Feb 6 (1) 22-33.
6 Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2012; Sep 22 (9) 1760-74.
7 Stubbs A, McClellan EA, Horsman S, Hiltemann SD, Palli I, Nouwens S. et al. Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection. J Clin Bioinforma 2012; Nov 19 2 (1) 19.
8 Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S. et al NHLBI Exome Sequencing Project. Evolution and functional impact ofrare coding variation from deep sequencing of human exomes. Science 2012; Jul 6 337 (6090) 64-9.
9 Tian Q, Price ND, Hood L. Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med 2012; Feb 271 (2) 111-21.
10 Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S. et al. Comprehensive analysis ofthe genome transcriptome and proteome landscapes of three tumor cell lines. Genome Med 2012; Nov 18 4 (11) 86.
11 Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D. et al. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012 Nov 28 4. (162) 162ra154.
12 The ENCODE Project Consortium. A user's guide to the ENCyclopedia Of DNA Elements (ENCODE). PLoS Biol. 2011 9. (4) e1001046.