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dc.contributor.authorunicampConte, Ana Luiza Ongaro Seidinger-
dc.contributor.authorunicampYunes, José Andrés-
dc.titleA simplified approach using taqman low-density array for medulloblastoma subgroupingpt_BR
dc.contributor.authorCruzeiro, Gustavo Alencastro Veiga-
dc.contributor.authorSalomão, Karina Bezerra-
dc.contributor.authorBiagi Jr, Carlos Alberto Oliveira de-
dc.contributor.authorBaumgartner, Martin-
dc.contributor.authorSturm, Dominik-
dc.contributor.authorLira, Régia Caroline Peixoto-
dc.contributor.authorMagalhães, Taciani de Almeida-
dc.contributor.authorMilan, Mirella Baroni-
dc.contributor.authorSilveira, Vanessa da Silva-
dc.contributor.authorSaggioro, Fabiano Pinto-
dc.contributor.authorOliveira, Ricardo Santos de-
dc.contributor.authorKlinger, Paulo Henrique dos Santos-
dc.contributor.authorSeidinger, Ana Luiza-
dc.contributor.authorYunes, José Andrés-
dc.contributor.authorQueiroz, Rosane Gomes de Paula-
dc.contributor.authorOba-Shinjo, Sueli Mieko-
dc.contributor.authorScrideli, Carlos Alberto-
dc.contributor.authorNagahashi, Suely Marie Kazue-
dc.contributor.authorTone, Luiz Gonzaga-
dc.contributor.authorValera, Elvis Terci-
dc.subjectAnálise de coortept_BR
dc.subjectReação em cadeia da polimerasept_BR
dc.subject.otherlanguageCohort analysispt_BR
dc.subject.otherlanguagePolymerase chain reactionpt_BR
dc.description.abstractNext-generation sequencing platforms are routinely used for molecular assignment due to their high impact for risk stratification and prognosis in medulloblastomas. Yet, low and middle-income countries still lack an accurate cost-effective platform to perform this allocation. TaqMan Low Density array (TLDA) assay was performed using a set of 20 genes in 92 medulloblastoma samples. The same methodology was assessed in silico using microarray data for 763 medulloblastoma samples from the GSE85217 study, which performed MB classification by a robust integrative method (Transcriptional, Methylation and cytogenetic profile). Furthermore, we validated in 11 MBs samples our proposed method by Methylation Array 450 K to assess methylation profile along with 390 MB samples (GSE109381) and copy number variations. TLDA with only 20 genes accurately assigned MB samples into WNT, SHH, Group 3 and Group 4 using Pearson distance with the average-linkage algorithm and showed concordance with molecular assignment provided by Methylation Array 450 k. Similarly, we tested this simplified set of gene signatures in 763 MB samples and we were able to recapitulate molecular assignment with an accuracy of 99.1% (SHH), 94.29% (WNT), 92.36% (Group 3) and 95.40% (Group 4), against 97.31, 97.14, 88.89 and 97.24% (respectively) with the Ward.D2 algorithm. t-SNE analysis revealed a high level of concordance (k = 4) with minor overlapping features between Group 3 and Group 4. Finally, we condensed the number of genes to 6 without significantly losing accuracy in classifying samples into SHH, WNT and non-SHH/non-WNT subgroups. Additionally, we found a relatively high frequency of WNT subgroup in our cohort, which requires further epidemiological studies. TLDA is a rapid, simple and cost-effective assay for classifying MB in low/middle income countries. A simplified method using six genes and restricting the final stratification into SHH, WNT and non-SHH/non-WNT appears to be a very interesting approach for rapid clinical decision-makingpt_BR
dc.relation.ispartofActa neuropathologica communicationspt_BR
dc.relation.ispartofabbreviationActa neuropathol communpt_BR
dc.publisher.countryReino Unidopt_BR
dc.publisherSpringer Naturept_BR
dc.description.sponsordocumentnumber2013/12006-3; 2014/19976-0; 2014/20341-0; 04/12133-6; 2013/02162-8pt_BR
dc.description.provenanceSubmitted by Susilene Barbosa da Silva ( on 2020-05-08T15:28:38Z No. of bitstreams: 0. Added 1 bitstream(s) on 2020-08-27T19:15:29Z : No. of bitstreams: 1 000460503900003.pdf: 4145167 bytes, checksum: df4557b03efa4dbd496b07cf325e60a2 (MD5)en
dc.description.provenanceMade available in DSpace on 2020-05-08T15:28:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-12en
dc.contributor.departmentSem informaçãopt_BR
dc.contributor.departmentSem informaçãopt_BR
dc.contributor.unidadeInstituto de Biologiapt_BR
dc.contributor.unidadeInstituto de Biologiapt_BR
dc.subject.keywordMolecular subgroupspt_BR
dc.creator.orcidSem informaçãopt_BR
dc.type.formArtigo de pesquisapt_BR
dc.description.sponsorNoteThis study was funded by FAPESP (grant numbers 2013/12006-3; 2014/19976-0; 2014/20341-0; 04/12133-6 and 2013/02162-8). We want to thank Dr. David T. W. Jones from DKFZ who kindly helped with methylation profile analysis and medulloblastoma molecular assignment. Finally, we want to thank and acknowledge patients and families affected by medulloblastoma for their generous contributions to these studies. We also had support of FAEPA (Fundação de Amparo ao Ensino, Pesquisa e Assistência do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto-USP) for publicationpt_BR
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