Abstract
Supercomputing and new sequencing techniques have dramatically increased the number of genomic sequences now publicly available. The rate in which new data is becoming available, however, far exceeds the rate in which one can perform analysis. Examining the wealth of information contained within genomic sequences presents numerous additional computational challenges necessitating high-performance machines. While there are many challenges in genomics that can greatly benefit from the development of more expedient machines, herein we will focus on just two projects which have direct clinical applications.
Chapter PDF
References
Walgate, R.: Weapons lab to develop Celeras new supercomputer. Genome Biol. (2001)
The International HapMap Consortium: A haplotype map of the human genome. Nature 437, 1299–1320 (2005)
Jares, P.: DNA microarray applications in functional genomics. Ultrastruct. Pathol. 30, 209–219 (2006)
Lockhart, D.J., Winzeler, E.A.: Genomics, gene expression and DNA arrays. Nature 405, 827–836 (2000)
Peeters, J.K., Van der Spek, P.J.: Growing applications and advancements in microarray technology and analysis tools. Cell Biochem. Biophys. 43, 149–166 (2005)
Geschwind, D.H.: DNA microarrays: translation of the genome from laboratory to clinic. Lancet Neurol. 2, 275–282 (2003)
Kimball, J.W.: Biology, 6th edn. Wm. C. Brown, Iowa (1994)
Robinson, J., Waller, M.J., Parham, P., de Groot, N., Bontrop, R., Kennedy, L.J., Stoehr, P., Marsh, S.G.E.: IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res. 31, 311–314 (2003)
Diepstra, A., Niens, M., Te Meerman, G.J., Poppema, S., van den Berg, A.: Genetic susceptibility to Hodgkins lymphoma associated with the human leukocyte antigen region. Eur. J. Haematol. Suppl. 75, 34–41 (2005)
Saftlas, A.F., Beydoun, H., Triche, E.: Immunogenetic determinants of preeclampsia and related pregnancy disorders: A systematic review. Obstet. Gynecol. 106, 162–167 (2005)
Ahmedov, G., Ahmedova, L., Sedlakova, P., Cinek, O.: Genetic association of type 1 diabetes in an Azerbaijanian population: the HLA-DQ, -DRB1*04, the insulin gene, and CTLA4. Pediatr. Diabetes 7, 88–93 (2006)
Listi, F., Candore, G., Balistreri, C.R., Grimaldi, M.P., Orlando, V., Vasto, S., Colonna-Romano, G., Lio, D., Licastro, F., Franceschi, C., Caruso, C.: Association between the HLA-A2 allele and Alzheimer disease. Rejuvenation Res. 9, 99–101 (2006)
Keet, I.P., Tang, J., Klein, M.R., LeBlanc, S., Enger, C., Rivers, C., Apple, R.J., Mann, D., Goedert, J.J., Miedema, F., Kaslow, R.A.: Consistent associations of HLA class I and II and transporter gene products with progression of human immunodeficiency virus type 1 infection in homosexual men. J. Infect. Dis. 180, 299–309 (1999)
Ovsyannikova, I.G., Vierkant, R.A., Poland, G.A.: Importance of HLA-DQ and HLA-DP polymorphisms in cytokine responses to naturally processed HLA-DR-derived measles virus peptides. Vaccine 24, 5381–5389 (2006)
Ovsyannikova, I.G., Pankratz, V.S., Vierkant, R.A., Jacobson, R.M., Poland, G.A.: Human leukocyte antigen haplotypes in the genetic control of immune response to measles–mumps–rubella vaccine. J. Infect. Dis. 193, 655–663 (2006)
Morishima, Y., Sasazuki, T., Inoko, H., Juji, T., Akaza, T., Yamanoto, K., Ishikawa, Y., Kato, S., Sao, H., Sakamaki, H., Kawa, K., Hamajima, N., Asano, S., Kodera, Y.: The clinical significance of human leukocyte antigen allele compatibility in patients receiving a marrow transplant from serologically HLA-A, HLA-B, and HLA-DR matched unrelated donors. Blood 99, 4200–4206 (2002)
Haddock, S.H., Quartararo, C., Cooley, P., Dao, D.D.: Low-resolution typing of HLA-DQA1 using DNA microarray. Methods Mol. Biol. 170, 201–210 (2001)
Consolandi, C., Frosini, A., Pera, C., Ferrara, G.B., Bordoni, R., Castiglioni, B., Rizzi, E., Mezzelani, A., Bernardi, L.R., De Bellis, G., Battaglia, C.: Polymorphism analysis within the HLA-A locus by universal oligonucleotide array. Hum. Mutat. 24, 428–434 (2004)
Palmisano, G.L., Delfino, L., Fiore, M., Longo, A., Ferrara, G.B.: Single nucleotide polymorphisms detection based on DNA microarray technology: HLA as a model. Autoimmun. Rev. 4, 510–514 (2005)
Bang-Ce, Y., Xiaohe, C., Ye, F., Songyang, L., Bincheng, Y., Peng, Z.: Simultaneous genotyping of DRB1/3/4/5 loci by oligonucleotide microarray. J. Mol. Diagn. 7, 592–599 (2005)
Wells, D.: Advances in preimplantation genetic diagnosis. Eur. J. Obstet. Gynecol. Reprod. Biol. 115, S97–S101 (2004)
Herwig, R., Schmidt, A., Steinfath, M., OBrian, J., Seidel, H., Meier-Ewert, S., Lehrach, H., Radelof, U.: Information theoretical probe selection for hybridization experiments. Bioinformatics 16, 890–898 (2000)
Borneman, J., Chrobak, M., Vedova, C.D., Figueroa, A., Jiang, T.: Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17, S39–S48 (2001)
Rash, S., Gusfield, D.: String barcoding: uncovering optimal virus signatures. In: Myers, G., Hannenballi, S., Istrail, S., Perzner, P., Waterman, M. (eds.) RECOMB ’02: Proceedings of the Sixth Annual International Conference on Computational Biology, pp. 254–261. ACM Press, New York (2002)
Klau, G.W., Rahmann, S., Schliep, A., Vingron, M., Reinert, K.: Optimal robust nonunique probe selection using integer linear programming. Bioinformatics 20, I186–I193 (2004)
Schliep, A., Torney, D.C., Rahmann, S.: Group testing with DNA chips: generating designs and decoding experiments. In: Proc. IEEE Comput. Soc. Bioinform. Conf. 2, pp. 84–91. IEEE, Los Alamitos (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Putonti, C., Zhang, M., Johnsson, L., Fofanov, Y. (2007). Two Challenges in Genomics That Can Benefit from Petascale Platforms. In: Lehner, W., Meyer, N., Streit, A., Stewart, C. (eds) Euro-Par 2006 Workshops: Parallel Processing. Euro-Par 2006. Lecture Notes in Computer Science, vol 4375. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72337-0_31
Download citation
DOI: https://doi.org/10.1007/978-3-540-72337-0_31
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-72226-7
Online ISBN: 978-3-540-72337-0
eBook Packages: Computer ScienceComputer Science (R0)