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1. Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Author

Northcott, PA, Shih, DJH, Peacock, J, Garzia, L, Sorana Morrissy, A, Zichner, T, Stútz, AM, Korshunov, A, Reimand, J, Schumacher, SE, Beroukhim, R, Ellison, DW, Marshall, CR, Lionel, AC, MacK, S, Dubuc, A, Yao, Y, Ramaswamy, V, Luu, B, Rolider, A, Cavalli, FMG, Wang, X, Remke, M, Wu, X, Chiu, RYB, Chu, A, Chuah, E, Corbett, RD, Hoad, GR, Jackman, SD, Li, Y, Lo, A, Mungall, KL, Ming Nip, K, Qian, JQ, Raymond, AGJ, Thiessen, N, Varhol, RJ, Birol, I, Moore, RA, Mungall, AJ, Holt, R, Kawauchi, D, Roussel, MF, Kool, M, Jones, DTW, Witt, H, Fernandez-L, A, Kenney, AM, Wechsler-Reya, RJ, Dirks, P, Aviv, T, Grajkowska, WA, Perek-Polnik, M, Haberler, CC, Delattre, O, Reynaud, SS, Doz, FF, Pernet-Fattet, SS, Cho, BK, Kim, SK, Wang, KC, Scheurlen, W, Eberhart, CG, Fèvre-Montange, M, Jouvet, A, Pollack, IF, Fan, X, Muraszko, KM, Yancey Gillespie, G, Di Rocco, C, Massimi, L, Michiels, EMC, Kloosterhof, NK, French, PJ, Kros, JM, Olson, JM, Ellenbogen, RG, Zitterbart, K, Kren, L, Thompson, RC, and Cooper, MK

Subjects
Oncogene Proteins, Fusion, DNA Copy Number Variations, Genome, Human, General Science & Technology, NF-kappa B, Genes, myc, Proteins, Nerve Tissue Proteins, Genomics, Translocation, Genetic, Transforming Growth Factor beta, Gene Duplication, Genomic Structural Variation, MD Multidisciplinary, Humans, Hedgehog Proteins, RNA, Long Noncoding, Cerebellar Neoplasms, Carrier Proteins, Child, Medulloblastoma, Signal Transduction
Abstract

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy. © 2012 Macmillan Publishers Limited. All rights reserved.

Published
2012
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2. Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Author

Northcott, P., Shih, D., Peacock, J., Garzia, L., Sorana Morrissy, A., Zichner, T., Stútz, A., Korshunov, A., Reimand, J., Schumacher, S., Beroukhim, R., Ellison, D., Marshall, C., Lionel, A., MacK, S., Dubuc, A., Yao, Y., Ramaswamy, V., Luu, B., Rolider, A., Cavalli, F., Wang, X., Remke, M., Wu, X., Chiu, R., Chu, A., Chuah, E., Corbett, R., Hoad, G., Jackman, S., Li, Y., Lo, A., Mungall, K., Ming Nip, K., Qian, J., Raymond, A., Thiessen, N., Varhol, Richard, Birol, I., Moore, R., Mungall, A., Holt, R., Kawauchi, D., Roussel, M., Kool, M., Jones, D., Witt, H., Fernandez-L, A., Kenney, A., Wechsler-Reya, R., Dirks, P., Aviv, T., Grajkowska, W., Perek-Polnik, M., Haberler, C., Delattre, O., Reynaud, S., Doz, F., Pernet-Fattet, S., Cho, B., Kim, S., Wang, K., Scheurlen, W., Eberhart, C., Fèvre-Montange, M., Jouvet, A., Pollack, I., Fan, X., Muraszko, K., Yancey Gillespie, G., Di Rocco, C., Massimi, L., Michiels, E., Kloosterhof, N., French, P., Kros, J., Olson, J., Ellenbogen, R., Zitterbart, K., Kren, L., Thompson, R., Cooper, M., Northcott, P., Shih, D., Peacock, J., Garzia, L., Sorana Morrissy, A., Zichner, T., Stútz, A., Korshunov, A., Reimand, J., Schumacher, S., Beroukhim, R., Ellison, D., Marshall, C., Lionel, A., MacK, S., Dubuc, A., Yao, Y., Ramaswamy, V., Luu, B., Rolider, A., Cavalli, F., Wang, X., Remke, M., Wu, X., Chiu, R., Chu, A., Chuah, E., Corbett, R., Hoad, G., Jackman, S., Li, Y., Lo, A., Mungall, K., Ming Nip, K., Qian, J., Raymond, A., Thiessen, N., Varhol, Richard, Birol, I., Moore, R., Mungall, A., Holt, R., Kawauchi, D., Roussel, M., Kool, M., Jones, D., Witt, H., Fernandez-L, A., Kenney, A., Wechsler-Reya, R., Dirks, P., Aviv, T., Grajkowska, W., Perek-Polnik, M., Haberler, C., Delattre, O., Reynaud, S., Doz, F., Pernet-Fattet, S., Cho, B., Kim, S., Wang, K., Scheurlen, W., Eberhart, C., Fèvre-Montange, M., Jouvet, A., Pollack, I., Fan, X., Muraszko, K., Yancey Gillespie, G., Di Rocco, C., Massimi, L., Michiels, E., Kloosterhof, N., French, P., Kros, J., Olson, J., Ellenbogen, R., Zitterbart, K., Kren, L., Thompson, R., and Cooper, M.

Abstract

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4a. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-?B signalling in Group 4, suggest future avenues for rational, targeted therapy. © 2012 Macmillan Publishers Limited. All rights reserved.

Published
2012

3. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Author

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, and Brooks AN

Abstract

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis., Competing Interests: Competing Interests Design of the project was discussed with Oxford Nanopore Technologies (ONT), Pacific Biosciences, and Lexogen. ONT provided partial support for flow cells and reagents. S.C-S and A.N.B. have received reimbursement for travel, accommodation, and conference fees to speak at events organized by ONT. A.N.B. is a consultant for Remix Therapeutics, Inc.

Published
2023
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