Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples

Field, Lori A.; Jordan, Rick; Hadix, Jennifer A.; Dunn, Michael A.; Shriver, Craig D.; Ellsworth, Rachel E.; Ellsworth, Darrell L.

doi:10.1016/j.clinbiochem.2007.01.004

Cited by 43 publications

(55 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, abundant transcripts in abundant cell types may conceal the more interesting less abundant transcripts from less abundant cell types. Particularly, the presence of globin transcripts originating from reticulocytes in whole blood samples may limit the sensitivity of gene expression profiling experiments [14], since globin transcripts can constitute up to 70% of the total whole blood mRNA population [17]. While in microarray experiments the presence of globin transcripts may reduce the amount of fluorescent label available for other transcripts but otherwise just results in a saturated spot on the microarray, the high abundance of globin transcripts is more of a concern in sequencing-based expression profiling studies.…”

Section: Introductionmentioning

confidence: 99%

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

et al. 2012

View full text Add to dashboard Cite

BackgroundTranscriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides robust, comparable and highly informative expression profiling data, with several million of tags per blood sample, reticulocyte globin transcripts can constitute up to 76% of total mRNA compromising the detection of low abundant transcripts. We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression.ResultsGlobin tags comprised 52-76% of total tags in our samples. Out of 21,633 genes only 87 genes were detected at significantly lower levels in the globin reduced samples. In contrast, 11,338 genes were detected at significantly higher levels in the globin reduced samples. Removing globin transcripts allowed us to also identify 2112 genes that could not be detected in the non-globin reduced samples, with roles in cell surface receptor signal transduction, G-protein coupled receptor protein signalling pathways and neurological processes.ConclusionsThe reduction of globin transcripts in whole blood samples constitutes a reproducible and reliable method that can enrich data obtained from next generation sequencing-based expression profiling.

show abstract

Section: Introductionmentioning

confidence: 99%

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Reduced sensitivity of RNA derived from PAXgene tubes and an overall increase in variability have been noted for RNA expression assays using microarrays [28]. Procedures that reduce the globin transcript levels may allow the detection of low abundance transcripts and improve the limit of detection of minimal residual disease [29,30].…”

Section: Limit Of Detectionmentioning

confidence: 98%

Chronic Myelogenous Leukemia: Monitoring Response to Therapy

Branford

Prime

2011

Curr Hematol Malig Rep

View full text Add to dashboard Cite

Molecular monitoring is a key component of the management of patients with chronic myeloid leukemia. The current recommendation is that molecular monitoring be performed in place of cytogenetic assessment when a major molecular response (MMR) is achieved. With the more potent kinase inhibitors nilotinib and dasatinib now approved as front-line therapy, more patients will achieve an MMR and will benefit from molecular monitoring. There is a strong correlation between certain BCR-ABL1 levels and the cytogenetic response, which means that molecular monitoring may act as a surrogate for cytogenetic response, but only if the BCR-ABL1 values are converted to the international reporting scale. Furthermore, improvements in the limit of BCR-ABL1 detection and reduction of intra-assay variability are ongoing issues of importance for molecular monitoring. Standardization of molecular methods to accurately assess the patient response also remains a challenge, despite the recent certification of international scale reference materials.

show abstract

“…Therefore, the quality and accuracy of gene expression profiles obtained from peripheral blood is highly reliant on the effectiveness of globin reduction carried out prior to microarray probe generation. Technologies available to reduce globin mRNA have been shown to efficiently increase the sensitivity of transcript detection (Field et al 2007; Li et al 2008; Liu et al 2006) but can also reduce the signal intensities achieved for some genes (Field et al 2007). Importantly, methods of globin reduction have also been shown to introduce changes in the transcriptome profile observed (Feezor et al 2004; Liu et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene™ Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

et al. 2008

View full text Add to dashboard Cite

Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene™ RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2™ enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene™ blood samples also advocate a short, fixed room temperature storage time for all PAXgene™ blood samples collected for the purposes of global transcriptional profiling in clinical studies.

show abstract

Functional identity of genes detectable in expression profiling assays following globin mRNA reduction of peripheral blood samples

Cited by 43 publications

References 13 publications

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA

Chronic Myelogenous Leukemia: Monitoring Response to Therapy

Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene™ Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

Contact Info

Product

Resources

About