Next-generation tag sequencing for cancer gene expression profiling

Morrissy, A. Sorana; Morin, Ryan D.; Delaney, Allen; Zeng, Thomas; McDonald, Helen; Jones, Steven J.M.; Zhao, Yongjun; Hirst, Martin; Marra, Marco A.

doi:10.1101/gr.094482.109

Cited by 295 publications

(267 citation statements)

References 44 publications

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“…These 17 nt 'tags' are sequenced in a high-throughput manner and the number of occurrences of each unique tag is counted, resulting in digital gene expression profiles where tag counts reflect expression levels of the corresponding transcript. 34 A total of 20 288 unique gene transcripts with a tag count greater than 1 were identified. The transcripts showing a median count equal to zero across all samples were filtered out.…”

Section: Biomarker Identificationmentioning

confidence: 99%

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer

Nichita

Ciarloni

Monnier-Benoit³

et al. 2014

Aliment Pharmacol Ther

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These authors are regarded as joint first authors, having contributed equally to the manuscript. SUMMARY BackgroundEarly detection and treatment of colorectal adenomatous polyps (AP) and colorectal cancer (CRC) is associated with decreased mortality for CRC. However, accurate, non-invasive and compliant tests to screen for AP and early stages of CRC are not yet available. A blood-based screening test is highly attractive due to limited invasiveness and high acceptance rate among patients.

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Section: Biomarker Identificationmentioning

confidence: 99%

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer

Nichita

Ciarloni

Monnier-Benoit³

et al. 2014

Aliment Pharmacol Ther

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“…We used digital gene expression (Morrissy et al 2009) to identify genes that are misregulated in sd E3 mutants and genes showing evidence of allelic imbalance in SAM/ORE "hybrids." This approach is similar to RNA-seq, but the cDNA is treated with a restriction enzyme (NlaIII) during library preparation, causing all sequence reads to begin at a restriction site.…”

Section: Digital Gene Expressionmentioning

confidence: 99%

Causes and Consequences of Genetic Background Effects Illuminated by Integrative Genomic Analysis

et al. 2014

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The phenotypic consequences of individual mutations are modulated by the wild-type genetic background in which they occur. Although such background dependence is widely observed, we do not know whether general patterns across species and traits exist or about the mechanisms underlying it. We also lack knowledge on how mutations interact with genetic background to influence gene expression and how this in turn mediates mutant phenotypes. Furthermore, how genetic background influences patterns of epistasis remains unclear. To investigate the genetic basis and genomic consequences of genetic background dependence of the scalloped E3 allele on the Drosophila melanogaster wing, we generated multiple novel genome-level datasets from a mapping-byintrogression experiment and a tagged RNA gene expression dataset. In addition we used whole genome resequencing of the parental lines-two commonly used laboratory strains-to predict polymorphic transcription factor binding sites for SD. We integrated these data with previously published genomic datasets from expression microarrays and a modifier mutation screen. By searching for genes showing a congruent signal across multiple datasets, we were able to identify a robust set of candidate loci contributing to the background-dependent effects of mutations in sd. We also show that the majority of background-dependent modifiers previously reported are caused by higher-order epistasis, not quantitative noncomplementation. These findings provide a useful foundation for more detailed investigations of genetic background dependence in this system, and this approach is likely to prove useful in exploring the genetic basis of other traits as well. GENETICISTS often strictly control their organisms' wildtype genetic backgrounds when experimentally dissecting genetic pathways. Although this tight control is necessary to avoid faulty inferences caused by confounding variables (e.g., Burnett et al. 2011), it can often paint an incomplete or even incorrect picture; no genetic pathway or network exists in a vacuum. Instead, these networks occur in the context of all the alleles in the genome, which usually vary among individuals. There is substantial evidence that wild-type genetic background almost always modulates the phenotypic effects of mutations (e.g., McKenzie et al. 1982;Threadgill et al. 1995;Atallah et al. 2004;Milloz et al. 2008;Chandler 2010;Dowell et al. 2010;Gerke et al. 2010). The influence of wild-type genetic backgrounds also extends to interactions among mutations (Remold and Lenski 2004;Dworkin et al. 2009;Wang et al. 2013b), altering patterns of epistasis, and these complex interactions are likely widespread . Alleles that influence many mutant phenotypes segregate in most natural populations, representing a potential source of cryptic genetic variation Félix 2007;Vaistij et al. 2013). In many cases, this cryptic variation has been described phenomenologically, or via the partitioning of genetic variance components (Gibson et al. 1999;Dworkin et al. 2003;McGuigan e...

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“…The tag number of each contig was counted and normalized by the TPM algorithm (Morrissy et al, 2009). Results showed that the cloned IbPP2A1 was ubiquitously expressed in all of the seven tissues, although expression levels varied (Figure 4).…”

Section: Spatial Expression Patterns Analysesmentioning

confidence: 99%

“…The number of mapped tags were counted, and TPM values (transcripts per million clean tags) (Morrissy et al, 2009) were calculated and used for the quantification of each transcript in the different sweet potato samples.…”

Section: Expression Pattern Analyses Based On Dge Profilingmentioning

confidence: 99%

Cloning and characterization of a serine/threonine protein phosphatase2A-encoding gene IbPP2A1 from Ipomoea batatas (L.) Lam.

Xu¹,

Yong²,

Shao³

et al. 2017

Turk J Biol

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Sweet potato is one of the most important food crops with strong environmental adaptability. Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that plays crucial roles in hormone signal transduction and abiotic stress response. Characterization of PP2A can elucidate the mechanisms of stress resistance in this crop. In this study, a total of 15 PP2A transcripts, including nine regulatory subunit-encoding sequences and six catalytic subunit-encoding sequences, were identified from sweet potato and found to be expressed at varying levels. Only one contained a complete open reading frame and encoded a B regulatory subunit (termed IbPP2A1). Ten polymorphic sites were distributed in the coding region of this gene, but most did not result in amino acid change. RNA sequencing-based digital gene expression profiling showed that this PP2A gene was primarily expressed in fibrous roots and developing tuberous roots under natural conditions. After drought, salinity, and alkaline stress treatment, the expression of IbPP2A1 was obviously upregulated in stems and tuberous roots at 2 days, whereas the expression of IbPP2A1 in leaves was only upregulated by drought stress at 2 days. However, heterogeneous expression of IbPP2A1 did not enhance abiotic stress tolerance in recombinant Saccharomyces cerevisiae. The results described here indicate that IbPP2A1 is an abiotic stress-responsive gene, but it could not work alone in vitro. This study provides a preliminary but global insight into PP2A proteins in sweet potato for further investigations on improving stress tolerance in this crop.

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Next-generation tag sequencing for cancer gene expression profiling

Cited by 295 publications

References 44 publications

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer

Causes and Consequences of Genetic Background Effects Illuminated by Integrative Genomic Analysis

Cloning and characterization of a serine/threonine protein phosphatase2A-encoding gene IbPP2A1 from Ipomoea batatas (L.) Lam.

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