Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology
| العنوان: | Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology |
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| المؤلفون: | Skaftason, Aron, Qu, Ying, Abdulla, Maysaa, Nordlund, Jessica, Berglund, Mattias, Bram Ednersson, Susanne, Andersson, Per‐Ola, Enblad, Gunilla, Amini, Rose-Marie, Rosenquist, Richard, Mansouri, Larry |
| المصدر: | Science for Life Laboratory – a national resource center for high–throughput molecular bioscience Genes, Chromosomes and Cancer. 61(1):27-36 |
| مصطلحات موضوعية: | Cancer Research, Genetics, capture-based RNA-sequencing, degraded RNA, DLBCL, gene expression profiling |
| الوصف: | Formalin-fixed, paraffin-embedded (FFPE) specimens are an underutilized resource in medical research, particularly in the setting of transcriptome sequencing, as RNA from these samples is often degraded. We took advantage of an exome capture-based RNA-sequencing protocol to explore global gene expression in paired fresh–frozen (FF) and FFPE samples from 16 diffuse large B-cell lymphoma (DLBCL) patients. While FFPE samples generated fewer mapped reads compared to their FF counterparts, these reads captured the same library complexity and had a similar number of genes expressed on average. Furthermore, gene expression demonstrated a high correlation when comparing housekeeping genes only or across the entire transcriptome (r = 0.99 for both comparisons). Differences in gene expression were primarily seen in lowly expressed genes and genes with small or large coding sequences. Using cell-of-origin classifiers and clinically relevant gene expression signatures for DLBCL, FF, and FFPE samples from the same biopsy paired nearly perfectly in clustering analysis. This was further confirmed in a validation cohort of 50 FFPE DLBCL samples. In summary, we found the biological differences between tumors to be far greater than artifacts created as a result of degraded RNA. We conclude that exome capture transcriptome sequencing data from archival samples can confidently be used for cell-of-origin classification of DLBCL samples. |
| وصف الملف: | electronic |
| URL الوصول: | https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-460484 https://doi.org/10.1002/gcc.23002 https://uu.diva-portal.org/smash/get/diva2:1617467/FULLTEXT01.pdf |
| قاعدة البيانات: | SwePub |
| تدمد: | 10452257 10982264 |
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| DOI: | 10.1002/gcc.23002 |