ArticleBMC genomics2017
The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Caribbean-Hispanic Alzheimer's disease brain transcriptome reveals ancestry-specific disease mechanisms.Neurobiology of disease · 2023Pooled it
- Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Predictors of response and rational combinations for the novel MCL-1 inhibitor MIK665 in acute myeloid leukemia.Molecular oncology · 2026Article
- Multiomics Profiling of T-cell Leukemia and Lymphoma Enables Targeted Therapeutic Discovery.Cancer research · 2026Article
- Comparison of automated and manual mRNA enrichment to automated rRNA depletion for whole-blood RNA-sequencing.Scientific reports · 2025Article
- Role of long noncoding RNAs in diabetes-associated peripheral arterial disease.Cardiovascular diabetology · 2024Review
- Comparison of RNA-Sequencing Methods for Degraded RNA.International journal of molecular sciences · 2024Article
- A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples.BMC genomics · 2023Review
- Article
- Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma.British journal of cancer · 2023Article
- OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data.STAR protocols · 2022Article
- Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia.Cancer discovery · 2022Article
- Aggressive Natural Killer Cell Leukemia in an Adolescent Patient: A Case Report and Literature Review.Frontiers in pediatrics · 2022Article
- FLT3-ITD allelic ratio and HLF expression predict FLT3 inhibitor efficacy in adult AML.Scientific reports · 2021Article
- Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.Cellular and molecular life sciences : CMLS · 2021Article
- HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection.Viruses · 2021Article
- Evaluating Targeted Therapies in Ovarian Cancer Metabolism: Novel Role for PCSK9 and Second Generation mTOR Inhibitors.Cancers · 2021Article
- Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma.Cancers · 2021Article
- CD73 contributes to anti-inflammatory properties of afferent lymphatic endothelial cells in humans and mice.European journal of immunology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient samples. Here, we applied two commonly used RNA-seq library preparation protocols to samples from acute leukemia patients to understand how poly-A-tailed mRNA selection (PA) and ribo-depletion (RD) based RNA-seq library preparation protocols affect gene fusion detection, variant calling, and gene expression profiling.
resultsOverall, the protocols produced similar results with consistent outcomes. Nevertheless, the PA protocol was more efficient in quantifying expression of leukemia marker genes and showed better performance in the expression-based classification of leukemia. Independent qRT-PCR experiments verified that the PA protocol better represented total RNA compared to the RD protocol. In contrast, the RD protocol detected a higher number of non-coding RNA features and had better alignment efficiency. The RD protocol also recovered more known fusion-gene events, although variability was seen in fusion gene predictions.
conclusionThe overall findings provide a framework for the use of RNA-seq in a precision medicine setting with limited number of samples and suggest that selection of the library preparation protocol should be based on the objectives of the analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.