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Effect of predicted protein-truncating genetic variants on the human transcriptome

Rivas, M. A., Pirinen, M., Conrad, D. F., Lek, M., Tsang, E. K., Karczewski, K. J., Maller, J. B., Kukurba, K. R., DeLuca, D. S., Fromer, M., Ferreira, P. G., Smith, K. S., Zhang, R., Zhao, F., Banks, E., Poplin, R., Ruderfer, D. M., Purcell, S. M., Tukiainen, T., Minikel, E. V., Stenson, Peter Daniel, Cooper, David Neil, Huang, K. H., Sullivan, T. J., Nedzel, J., Bustamante, C. D., Li, J. B., Daly, M. J., Guigo, R., Donnelly, P., Ardlie, K., Sammeth, M., Dermitzakis, E. T., McCarthy, M. I., Montgomery, S. B., Lappalainen, T., MacArthur, D. G., Segre, A. V., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Ward, L. D., Kheradpour, P., Iriarte, B., Meng, Y., Palmer, C. D., Esko, T., Winckler, W., Hirschhorn, J., Kellis, M., Getz, G., Shablin, A. A., Li, G., Zhou, Y.-H., Nobel, A. B., Rusyn, I., Wright, F. A., Battle, A., Mostafavi, S., Mele, M., Reverter, F., Goldmann, J., Koller, D., Gamazon, E. R., Im, H. K., Konkashbaev, A., Nicolae, D. L., Cox, N. J., Flutre, T., Wen, X., Stephens, M., Pritchard, J. K., Tu, Z., Zhang, B., Huang, T., Long, Q., Lin, L., Yang, J., Zhu, J., Liu, J., Brown, A., Mestichelli, B., Tidwell, D., Lo, E., Salvatore, M., Shad, S., Thomas, J. A., Lonsdale, J. T., Choi, R. C., Karasik, E., Ramsey, K., Moser, M. T., Foster, B. A., Gillard, B. M., Syron, J., Fleming, J., Magazine, H., Hasz, R., Walters, G. D., Bridge, J. P., Miklos, M., Sullivan, S., Barker, L. K., Traino, H., Mosavel, M., Siminoff, L. A., Valley, D. R., Rohrer, D. C., Jewel, S., Branton, P., Sobin, L. H., Barcus, M., Qi, L., Hariharan, P., Wu, S., Tabor, D., Shive, C., Smith, A. M., Buia, S. A., Undale, A. H., Robinson, K. L., Roche, N., Valentino, K. M., Britton, A., Burges, R., Bradbury, D., Hambright, K. W., Seleski, J., Korzeniewski, G. E., Erickson, K., Marcus, Y., Tejada, J., Taherian, M., Lu, C., Robles, B. E., Basile, M., Mash, D. C., Volpi, S., Struewing, J. P., Temple, G. F., Boyer, J., Colantuoni, D., Little, R., Koester, S., Carithers, L. J., Moore, H. M., Guan, P., Compton, C., Sawyer, S. J., Demchok, J. P., Vaught, J. B., Rabiner, C. A., Lockhart, N. C., Friedlander, M. R., 't Hoen, P. A. C., Monlong, J., Gonzalez-Porta, M., Kurbatova, N., Griebel, T., Barann, M., Wieland, T., Greger, L., van Iterson, M., Almlof, J., Ribeca, P., Pulyakhina, I., Esser, D., Giger, T., Tikhonov, A., Sultan, M., Bertier, G., Lizano, E., Buermans, H. P. J., Padioleau, I., Schwarzmayr, T., Karlberg, O., Ongen, H., Kilpinen, H., Beltran, S., Gut, M., Kahlem, K., Amstislavskiy, V., Stegle, O., Flicek, P., Strom, T. M., Lehrach, H., Schreiber, S., Sudbrak, R., Carracedo, A., Antonarakis, S. E., Hasler, R., Syvanen, A.-C., van Ommen, G.-J., Brazma, A., Meitinger, T., Rosenstiel, P., Gut, I. G. and Estivill, X. 2015. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348 (6235) , pp. 666-669. 10.1126/science.1261877

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Abstract

Accurate prediction of the functional effect of genetic variation is critical for clinical genome interpretation. We systematically characterized the transcriptome effects of protein-truncating variants, a class of variants expected to have profound effects on gene function, using data from the Genotype-Tissue Expression (GTEx) and Geuvadis projects. We quantitated tissue-specific and positional effects on nonsense-mediated transcript decay and present an improved predictive model for this decay. We directly measured the effect of variants both proximal and distal to splice junctions. Furthermore, we found that robustness to heterozygous gene inactivation is not due to dosage compensation. Our results illustrate the value of transcriptome data in the functional interpretation of genetic variants.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Subjects: Q Science > QH Natural history > QH426 Genetics
R Medicine > R Medicine (General)
Publisher: American Association for the Advancement of Science
ISSN: 0036-8075
Date of Acceptance: 2 April 2015
Last Modified: 10 Jun 2019 13:19
URI: http://orca.cf.ac.uk/id/eprint/84064

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