Integrated transcriptomic–genomic tool Texomer profiles cancer tissues

Fang Wang, Shaojun Zhang, Tae Beom Kim, Yu yu Lin, Ramiz Iqbal, Zixing Wang, Vakul Mohanty, Kanishka Sircar, Jose A. Karam, Michael C. Wendl, Funda Meric-Bernstam, John N. Weinstein, Li Ding, Gordon Mills, Ken Chen

Research output: Contribution to journalArticle

Abstract

Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer (https://github.com/KChen-lab/Texomer) that performs allele-specific, tumor-deconvoluted transcriptome–exome integration of autologous bulk whole-exome and transcriptome sequencing data. Texomer results in substantially improved accuracy in sample categorization and functional variant prioritization.

Original languageEnglish (US)
Pages (from-to)401-404
Number of pages4
JournalNature Methods
Volume16
Issue number5
DOIs
StatePublished - May 1 2019
Externally publishedYes

Fingerprint

Transcriptome
Tumors
Genes
Tissue
Exome
Neoplasms
Alleles
Genome

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Wang, F., Zhang, S., Kim, T. B., Lin, Y. Y., Iqbal, R., Wang, Z., ... Chen, K. (2019). Integrated transcriptomic–genomic tool Texomer profiles cancer tissues. Nature Methods, 16(5), 401-404. https://doi.org/10.1038/s41592-019-0388-9

Integrated transcriptomic–genomic tool Texomer profiles cancer tissues. / Wang, Fang; Zhang, Shaojun; Kim, Tae Beom; Lin, Yu yu; Iqbal, Ramiz; Wang, Zixing; Mohanty, Vakul; Sircar, Kanishka; Karam, Jose A.; Wendl, Michael C.; Meric-Bernstam, Funda; Weinstein, John N.; Ding, Li; Mills, Gordon; Chen, Ken.

In: Nature Methods, Vol. 16, No. 5, 01.05.2019, p. 401-404.

Research output: Contribution to journalArticle

Wang, F, Zhang, S, Kim, TB, Lin, YY, Iqbal, R, Wang, Z, Mohanty, V, Sircar, K, Karam, JA, Wendl, MC, Meric-Bernstam, F, Weinstein, JN, Ding, L, Mills, G & Chen, K 2019, 'Integrated transcriptomic–genomic tool Texomer profiles cancer tissues', Nature Methods, vol. 16, no. 5, pp. 401-404. https://doi.org/10.1038/s41592-019-0388-9
Wang F, Zhang S, Kim TB, Lin YY, Iqbal R, Wang Z et al. Integrated transcriptomic–genomic tool Texomer profiles cancer tissues. Nature Methods. 2019 May 1;16(5):401-404. https://doi.org/10.1038/s41592-019-0388-9
Wang, Fang ; Zhang, Shaojun ; Kim, Tae Beom ; Lin, Yu yu ; Iqbal, Ramiz ; Wang, Zixing ; Mohanty, Vakul ; Sircar, Kanishka ; Karam, Jose A. ; Wendl, Michael C. ; Meric-Bernstam, Funda ; Weinstein, John N. ; Ding, Li ; Mills, Gordon ; Chen, Ken. / Integrated transcriptomic–genomic tool Texomer profiles cancer tissues. In: Nature Methods. 2019 ; Vol. 16, No. 5. pp. 401-404.
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