Optimizing nucleic acid extraction and transcriptome evaluation from low-input, fixed clinical samples
Campbell, K. M.; Medina, E.; Baselga Carretero, I.; Teper, Y.; Elumalai, R.; Miller, R.; Pal, K.; Pitzer, J.; Daviso, E.; Carstens, C.; Laugharn, J.; Hugo, W.; Chen, J. M.; Vega-Crespo, A.; Jilani, S.; Garcilazo, I. P.; Dong, L.; Li, X.; Hu-Lieskovan, S.; Ribas, A.
Show abstract
Tumor biopsies are commonly formalin-fixed and paraffin-embedded (FFPE) for long-term and efficient storage. However, FFPE preservation can greatly compromise the quality of samples, the extraction of nucleic acids, and feasibility of downstream studies, including RNA sequencing. These challenges are especially evident in the studies of clinical trial samples, where the sizes of biopsies often limit the amount of material available for study. Here, we evaluate two nucleic acid extraction kits (Covaris truXTRAC FFPE tNA Plus, QIAGEN miRNeasy FFPE) and three hybridized-capture-based RNA sequencing library preparations (Agilent SureSelect XT RNA Direct, Agilent SureSelect XT HS, and Illumina TruSeq RNA Exome) to evaluate the impact of these sample processing steps on transcriptome evaluation in a melanoma biopsy procured in a clinical setting and preserved by FFPE. While there exist many options for extraction and library preparation that are appropriate for RNA sequencing from FFPE samples, we observed that combinations of experimental approaches may have subtle impacts on downstream analysis, including gene expression quantification and fusion detection.
Matching journals
The top 10 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Reproducible and sensitive micro-tissue RNA-sequencing from formalin-fixed paraffin-embedded tissue for spatial gene expression analysis 94%
- System Analysis Of The Sequencing Quality Of Human Whole Exome Samples On Bgi Ngs Platform 94%
- Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules 93%
Similar papers in this journal
- Single cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy 94%
- Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry 94%
- Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols 93%
Similar papers in this journal
- Covering all your bases: incorporating intron signal from RNA-seq data 94%
- Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries 94%
- miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline 93%
Similar papers in this journal
- Small RNA-sequencing for Analysis of Circulating miRNAs: Benchmark Study 94%
- Comparative Analysis of Gene Expression Analysis Methods for RNA In Situ Hybridization Images 93%
- Evaluating discordant somatic calls across mutation discovery approaches to minimize false negative drug-resistant findings 91%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.