A computational analysis of the genetic and transcript diversity at the kallikrein locus

References

Alley, M.C., Scudiero, D.A., Monks, A., Hursey, M.L., Czerwinski, M.J., Fine, D.L., Abbott, B.J., Mayo, J.G., Shoemaker, R.H., and Boyd, M.R. (1988). Feasibility of drug screening with panels of human tumor cell lines using a microculture tetrazolium assay. Cancer Res. 48, 589–601.Suche in Google Scholar

Batra, J., O’Mara, T., Patnala, R., Lose, F., and Clements, J.A. (2012). Genetic polymorphisms in the human tissue kallikrein (KLK) locus and their implication in various malignant and non-malignant diseases. Biol. Chem. 393, 1365–1390.10.1515/hsz-2012-0211Suche in Google Scholar

Bayani, J., Marrano, P., Graham, C., Zheng, Y., Li, L., Katsaros, D., Lassus, H., Butzow, R., Squire, J.A., and Diamandis, E.P. (2011). Genomic instability and copy-number heterogeneity of chromosome 19q, including the kallikrein locus, in ovarian carcinomas. Mol. Oncol. 5, 48–60.10.1016/j.molonc.2010.08.002Suche in Google Scholar

Chelala, C., Khan, A., and Lemoine, N.R. (2009). SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 25, 655–661.10.1093/bioinformatics/btn653Suche in Google Scholar

Gan, L., Lee, I., Smith, R., Argonza-Barrett, R., Lei, H., McCuaig, J., Moss, P., Paeper, B., and Wang, K. (2000). Sequencing and expression analysis of the serine protease gene cluster located in chromosome 19q13 region. Gene 257, 119–130.10.1016/S0378-1119(00)00382-6Suche in Google Scholar

Genomes Project, C., Abecasis, G.R., Altshuler, D., Auton, A., Brooks, L.D., Durbin, R.M., Gibbs, R.A., Hurles, M.E., and McVean, G.A. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073.10.1038/nature09534Suche in Google Scholar PubMed PubMed Central

Girgis, A.H., Bui, A., White, N.M., and Yousef, G.M. (2012). Integrated genomic characterization of the kallikrein gene locus in cancer. Anticancer Res. 32, 957–963.Suche in Google Scholar

Gymrek, M., Golan, D., Rosset, S., and Erlich, Y. (2012). lobSTR: A short tandem repeat profiler for personal genomes. Genome Res. 22, 1154–1162.10.1007/978-3-642-29627-7_7Suche in Google Scholar

Harvey, T.J., Hooper, J.D., Myers, S.A., Stephenson, S.A., Ashworth, L.K., and Clements, J.A. (2000). Tissue-specific expression patterns and fine mapping of the human kallikrein (KLK) locus on proximal 19q13.4. J. Biol. Chem. 275, 37397–37406.10.1074/jbc.M004525200Suche in Google Scholar PubMed

Iyer, M.K., Niknafs, Y.S., Malik, R., Singhal, U., Sahu, A., Hosono, Y., Barrette, T.R., Prensner, J.R., Evans, J.R., Zhao, S., et al. (2015). The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet. 47, 199–208.10.1038/ng.3192Suche in Google Scholar PubMed PubMed Central

Koumandou, V.L. and Scorilas, A. (2013). Evolution of the plasma and tissue kallikreins, and their alternative splicing isoforms. PLoS One 8, e68074.10.1371/journal.pone.0068074Suche in Google Scholar PubMed PubMed Central

Kurlender, L., Borgono, C., Michael, I.P., Obiezu, C., Elliott, M.B., Yousef, G.M., and Diamandis, E.P. (2005). A survey of alternative transcripts of human tissue kallikrein genes. Biochim. Biophys. Acta 1755, 1–14.10.1016/j.bbcan.2005.02.001Suche in Google Scholar PubMed

Lai, J., Lehman, M.L., Dinger, M.E., Hendy, S.C., Mercer, T.R., Seim, I., Lawrence, M.G., Mattick, J.S., Clements, J.A., and Nelson, C.C. (2010). A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells. RNA 16, 1156–1166.10.1261/rna.2019810Suche in Google Scholar PubMed PubMed Central

Lawrence, M.G., Lai, J., and Clements, J.A. (2010). Kallikreins on steroids: structure, function, and hormonal regulation of prostate-specific antigen and the extended kallikrein locus. Endocr. Rev. 31, 407–446.10.1210/er.2009-0034Suche in Google Scholar PubMed

Lindahl, P., Sall, T., Bjartell, A., Johansson, A.M., Lilja, H., and Hallden, C. (2013). Copy number variants in the kallikrein gene cluster. PLoS One 8, e69097.10.1371/journal.pone.0069097Suche in Google Scholar PubMed PubMed Central

Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380.10.1038/nature03959Suche in Google Scholar PubMed PubMed Central

Parikh, H., Deng, Z., Yeager, M., Boland, J., Matthews, C., Jia, J., Collins, I., White, A., Burdett, L., Hutchinson, A., et al. (2010). A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33. Hum. Genet. 127, 91–99.10.1007/s00439-009-0751-5Suche in Google Scholar PubMed PubMed Central

Parra, G., Reymond, A., Dabbouseh, N., Dermitzakis, E.T., Castelo, R., Thomson, T.M., Antonarakis, S.E., and Guigo, R. (2006). Tandem chimerism as a means to increase protein complexity in the human genome. Genome. Res. 16, 37–44.10.1101/gr.4145906Suche in Google Scholar PubMed PubMed Central

Prassas, I., Eissa, A., Poda, G., and Diamandis, E.P. (2015). Unleashing the therapeutic potential of human kallikrein-related serine proteases. Nat. Rev. Drug Discov. 14, 183–202.10.1038/nrd4534Suche in Google Scholar PubMed

Scorilas, A. and Mavridis, K. (2014). Predictions for the future of kallikrein-related peptidases in molecular diagnostics. Expert Rev. Mol. Diagn. 14, 713–722.10.1586/14737159.2014.928207Suche in Google Scholar PubMed

Shankavaram, U.T., Varma, S., Kane, D., Sunshine, M., Chary, K.K., Reinhold, W.C., Pommier, Y., and Weinstein, J.N. (2009). CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics 10, 277.10.1186/1471-2164-10-277Suche in Google Scholar PubMed PubMed Central

Sukumar, N., Scott, E., Dimitromanolakis, A., Misiak, A., Prassas, I., Diamandis, E.P., and Konvalinka, A. (2014). Mining for single nucleotide variants (SNVs) at the kallikrein locus with predicted functional consequences. Biol. Chem. 395, 1037–1050.10.1515/hsz-2014-0136Suche in Google Scholar PubMed

van Dijk, E.L., Auger, H., Jaszczyszyn, Y., and Thermes, C. (2014). Ten years of next-generation sequencing technology. Trends Genet. 30, 418–426.10.1016/j.tig.2014.07.001Suche in Google Scholar PubMed

Yousef, G.M., Luo, L.Y., and Diamandis, E.P. (1999). Identification of novel human kallikrein-like genes on chromosome 19q13.3-q13.4. Anticancer Res 19, 2843–2852.Suche in Google Scholar