Profiling Plasma MicroRNA in Nasopharyngeal Carcinoma with Deep Sequencing

Abstract BACKGROUND The goal of this study was to establish a plasma microRNA profile by use of next-generation sequencing that could aid in assessment of patient prognosis in nasopharyngeal carcinoma (NPC). METHODS Two panels of NPC patients and healthy controls (HCs) were recruited for this study. We used deep sequencing to screen plasma microRNAs. Differentially expressed microRNAs were verified by quantitative real-time PCR (qPCR). Kaplan–Meier survival analysis with the log-rank test was used to compare overall survival (OS) and progression-free survival (PFS) between groups. RESULTS Twenty-three plasma miRNAs with differential expression levels were selected for qPCR analysis on an independent set including 100 NPC patients and 55 HCs. NPC patients with low concentrations of miR-483–5p and miR-103 had better prognosis for 5-year OS than those with high concentrations (87.5% vs 55.8%, P < 0.001; 80.9% vs 62.3%, P = 0.031). Those with low concentrations of miR-29a and let-7c had poorer prognosis (54.8% vs 82.8%, P = 0.002; 56.3% vs 84.6%, P = 0.001). A 3-signature miRNA integrated with clinical stage was further identified in an independent set. We calculated a prognostic index score and classified patients into low-, medium-, and high-risk groups. Five-year OS among the 3 groups was significantly different (90.9%, 66.7%, and 23.8%; P < 0.001). By multivariate analysis, a high-risk score was the most significantly unfavorable prognostic factor independent of other clinical variables (P < 0.001, hazard ratio = 15.1, 95% CI = 5.2–43.9). CONCLUSIONS Differentially expressed plasma miRNAs as identified by next-generation sequencing can be helpful for predicting survival in NPC patients.

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Differentially expressed circRNA and functional pathways in the hippocampus of epileptic mice based on next‐generation sequencing

The Kaohsiung Journal of Medical Sciences ◽

10.1002/kjm2.12404 ◽

2021 ◽

Author(s):

Xian‐Qiu Liao ◽

Hai‐Chun Yu ◽

Li‐Mei Diao ◽

Ling Lu ◽

Huan Li ◽

...

Keyword(s):

Next Generation Sequencing ◽

Differentially Expressed ◽

Next Generation ◽

Functional Pathways ◽

Generation Sequencing

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Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion

Genes ◽

10.3390/genes12081113 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1113

Author(s):

Michael Schwabe ◽

Sven Griep ◽

Henrike Schmidtberg ◽

Rudy Plarre ◽

Alexander Goesmann ◽

...

Keyword(s):

Next Generation Sequencing ◽

Disulfide Bonds ◽

Differentially Expressed ◽

Intestinal Microbiome ◽

Sequencing Analysis ◽

High Quality ◽

Transcriptomic Data ◽

Next Generation Sequencing Analysis ◽

Generation Sequencing ◽

Tineola Bisselliella

The clothes moth Tineola bisselliella is one of a few insects that can digest keratin, leading to the destruction of clothing, textiles and artwork. The mechanism of keratin digestion is not yet fully understood, partly reflecting the lack of publicly available genomic and transcriptomic data. Here we present a high-quality gut transcriptome of T. bisselliella generated from larvae reared on keratin-rich and keratin-free diets. The overall transcriptome consists of 428,221 contigs that were functionally annotated and screened for candidate enzymes involved in keratin utilization. As a mechanism for keratin digestion, we identified cysteine synthases, cystathionine β-synthases and cystathionine γ-lyases. These enzymes release hydrogen sulfite, which may reduce the disulfide bonds in keratin. The dataset also included 27 differentially expressed contigs with trypsin domains, among which 20 were associated with keratin feeding. Finally, we identified seven collagenases that were upregulated on the keratin-rich diet. In addition to this enzymatic repertoire potentially involved in breaking down keratin, our analysis of poly(A)-enriched and poly(A)-depleted transcripts suggested that T. bisselliella larvae possess an unstable intestinal microbiome that may nevertheless contribute to keratin digestion.

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Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome

BioMed Research International ◽

10.1155/2018/8989252 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Thomas G. Nührenberg ◽

Marco Cederqvist ◽

Federico Marini ◽

Christian Stratz ◽

Björn A. Grüning ◽

...

Keyword(s):

Diabetes Mellitus ◽

Next Generation Sequencing ◽

Platelet Reactivity ◽

Platelet Rich Plasma ◽

Expression Profiles ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Major Influence ◽

Next Generation ◽

Generation Sequencing

Background. Diabetes mellitus (DM) has been associated with increased platelet reactivity as well as increased levels of platelet RNAs in plasma. Here, we sought to evaluate whether the platelet transcriptome is altered in the presence of uncontrolled DM. Methods. Next-generation sequencing (NGS) was performed on platelet RNA for 5 patients with uncontrolled DM (HbA1c 9.0%) and 5 control patients (HbA1c 5.5%) with otherwise similar clinical characteristics. RNA was isolated from leucocyte-depleted platelet-rich plasma. Libraries of platelet RNAs were created separately for long RNAs after ribosomal depletion and for small RNAs from total RNA, followed by next-generation sequencing. Results. Platelets in both groups demonstrated RNA expression profiles characterized by absence of leukocyte-specific transcripts, high expression of well-known platelet transcripts, and in total 6,343 consistently detectable transcripts. Extensive statistical bioinformatic analysis yielded 12 genes with consistently differential expression at a lenient FDR < 0.1, thereof 8 protein-coding genes and 2 genes with known expression in platelets (MACF1 and ITGB3BP). Three of the four differentially expressed noncoding genes were YRNAs (RNY1, RNY3, and RNY4) which were all downregulated in DM. 23 miRNAs were differentially expressed between the two groups. Of the 13 miRNAs with decreased expression in the diabetic group, 8 belonged to the DLK1–DIO3 gene region on chromosome 14q32.2. Conclusions. In this study, uncontrolled DM had a remote impact on different components of the platelet transcriptome. Increased expression of MACF1, together with supporting predicted mRNA-miRNA interactions as well as reduced expression of RNYs in platelets, may reflect subclinical platelet activation in uncontrolled DM.

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Enabling rapid and efficient selection of Next generation sequencing algorithms to align sequences to predict differentially expressed genes in cancer

Canadian Journal of Biotechnology ◽

10.24870/cjb.2017-a10 ◽

2017 ◽

Vol 1 (Special Issue) ◽

pp. 22-22

Author(s):

Maheswari L. Patil ◽

Shivakumar B. Madagi ◽

C.N. Prashantha

Keyword(s):

Next Generation Sequencing ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Next Generation ◽

Efficient Selection ◽

Generation Sequencing ◽

Selection Of

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Integrative genomic analysis reveals cancer-associated mutations at diagnosis of CML in patients with high-risk disease

Blood ◽

10.1182/blood-2018-02-832253 ◽

2018 ◽

Vol 132 (9) ◽

pp. 948-961 ◽

Cited By ~ 41

Author(s):

Susan Branford ◽

Paul Wang ◽

David T. Yeung ◽

Daniel Thomson ◽

Adrian Purins ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Risk ◽

Genomic Analysis ◽

Kinase Domain ◽

Cancer Genes ◽

High Risk Disease ◽

Key Points ◽

Kinase Domain Mutations ◽

Poor Outcomes ◽

Generation Sequencing

Key Points Next-generation sequencing revealed variants in cancer-associated genes at diagnosis of CML more frequently in patients with poor outcomes. All patients at BC had mutated cancer genes, including fusions, that predated BCR-ABL1 kinase domain mutations in a majority.

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Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02474-17 ◽

2018 ◽

Vol 62 (4) ◽

pp. e02474-17 ◽

Cited By ~ 20

Author(s):

Eldin Talundzic ◽

Shashidhar Ravishankar ◽

Julia Kelley ◽

Dhruviben Patel ◽

Mateusz Plucinski ◽

...

Keyword(s):

Drug Resistance ◽

Next Generation Sequencing ◽

Deep Sequencing ◽

Artemisinin Resistance ◽

The United States ◽

Imported Malaria ◽

Chloroquine Resistance ◽

Next Generation ◽

Content Type ◽

Generation Sequencing

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.

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