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| author |
Stokowy, Tomasz |
| author2 |
Eszlinger, Markus, Świerniak, Michał, Fujarewicz, Krzysztof, Jarząb, Barbara, Paschke, Ralf, Krohn, Kurt |
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Stokowy, Tomasz, Eszlinger, Markus, Świerniak, Michał, Fujarewicz, Krzysztof, Jarząb, Barbara, Paschke, Ralf, Krohn, Kurt |
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Stokowy, Tomasz |
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Library A |
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BMC Research Notes 2014, 7:144 doi:10.1186/1756-0500-7-144 |
| contents |
Background; Methods; Results; Discussion; Conclusions, Background: Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods: We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results: High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions: Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail. |
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610 |
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600 - Technology (Applied sciences) |
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610 - Medicine and health |
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610 |
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610 |
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3610 |
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610 - Medicine and health |
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Online, Free |
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medicine |
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Journal |
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Article, E-Article |
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Article, E-Article |
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E-Article |
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BMC Research Notes 2014, 7:144 doi:10.1186/1756-0500-7-144 |
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22-15-qucosa-144393 |
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Not Illustrated |
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Warsaw, Medical University of Warsaw, 2014 |
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Online-Ausg.: 2014 |
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DE-105, DE-Gla1, DE-Brt1, DE-D161, DE-540, DE-Pl11, DE-Rs1, DE-Bn3, DE-Zi4, DE-Zwi2, DE-D117, DE-Mh31, DE-D275, DE-Ch1, DE-15, DE-D13, DE-L242, DE-L229, DE-L328 |
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2024-04-29T03:07:58.667Z |
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2014 |
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2014 |
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Medical University of Warsaw |
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Stokowy, Tomasz, Analysis options for high-throughput sequencing in miRNA expression profiling, Warsaw Medical University of Warsaw 2014, Online-Ausg. 2014 Online-Ressource (Text) Universitätsbibliothek Leipzig, Background; Methods; Results; Discussion; Conclusions, Background: Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods: We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results: High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions: Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail., Hochdurchsatz-Sequenzierung, Follikuläres Schilddrüsenkarzinom, Microrna, Microarray, High-Throughput Sequencing, Follicular Thyroid Cancer, Mirna Expression, Eszlinger, Markus, Świerniak, Michał, Fujarewicz, Krzysztof, Jarząb, Barbara, Paschke, Ralf, Krohn, Kurt, BMC Research Notes 2014, 7:144 doi:10.1186/1756-0500-7-144, text/html https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa-144393 Online-Zugriff |
| spellingShingle |
Stokowy, Tomasz, Analysis options for high-throughput sequencing in miRNA expression profiling, Background; Methods; Results; Discussion; Conclusions, Background: Recently high-throughput sequencing (HTS) using next generation sequencing techniques became useful in digital gene expression profiling. Our study introduces analysis options for HTS data based on mapping to miRBase or counting and grouping of identical sequence reads. Those approaches allow a hypothesis free detection of miRNA differential expression. Methods: We compare our results to microarray and qPCR data from one set of RNA samples. We use Illumina platforms for microarray analysis and miRNA sequencing of 20 samples from benign follicular thyroid adenoma and malignant follicular thyroid carcinoma. Furthermore, we use three strategies for HTS data analysis to evaluate miRNA biomarkers for malignant versus benign follicular thyroid tumors. Results: High correlation of qPCR and HTS data was observed for the proposed analysis methods. However, qPCR is limited in the differential detection of miRNA isoforms. Moreover, we illustrate a much broader dynamic range of HTS compared to microarrays for small RNA studies. Finally, our data confirm hsa-miR-197-3p, hsa-miR-221-3p, hsa-miR-222-3p and both hsa-miR-144-3p and hsa-miR-144-5p as potential follicular thyroid cancer biomarkers. Conclusions: Compared to microarrays HTS provides a global profile of miRNA expression with higher specificity and in more detail. Summarizing of HTS reads as isoform groups (analysis pipeline B) or according to functional criteria (seed analysis pipeline C), which better correlates to results of qPCR are promising new options for HTS analysis. Finally, data opens future miRNA research perspectives for HTS and indicates that qPCR might be limited in validating HTS data in detail., Hochdurchsatz-Sequenzierung, Follikuläres Schilddrüsenkarzinom, Microrna, Microarray, High-Throughput Sequencing, Follicular Thyroid Cancer, Mirna Expression |
| title |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_auth |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_full |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_fullStr |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_full_unstemmed |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_in_hierarchy |
|
| title_short |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| title_sort |
analysis options for high-throughput sequencing in mirna expression profiling |
| title_unstemmed |
Analysis options for high-throughput sequencing in miRNA expression profiling |
| topic |
Hochdurchsatz-Sequenzierung, Follikuläres Schilddrüsenkarzinom, Microrna, Microarray, High-Throughput Sequencing, Follicular Thyroid Cancer, Mirna Expression |
| topic_facet |
Hochdurchsatz-Sequenzierung, Follikuläres Schilddrüsenkarzinom, Microrna, Microarray, High-Throughput Sequencing, Follicular Thyroid Cancer, Mirna Expression |
| url |
https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa-144393 |
| urn |
urn:nbn:de:bsz:15-qucosa-144393 |
| work_keys_str_mv |
AT stokowytomasz analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT eszlingermarkus analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT swierniakmichał analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT fujarewiczkrzysztof analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT jarzabbarbara analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT paschkeralf analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling, AT krohnkurt analysisoptionsforhighthroughputsequencinginmirnaexpressionprofiling |
