Development of an AmpliSeq (TM) Panel for Next-Generation Sequencing of a Set of Genetic Predictors of Persisting Pain
| Autor: | Kringel, D., Kaunisto, M.A., Lippmann, C., Kalso, E., Lötsch, J. |
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| Přispěvatelé: | Institute for Molecular Medicine Finland, University of Helsinki, Doctoral Programme in Clinical Research, Doctoral Programme Brain & Mind, Doctoral Programme in Drug Research, Eija Kalso / Principal Investigator, Clinicum, Anestesiologian yksikkö, Department of Diagnostics and Therapeutics, HUS Perioperative, Intensive Care and Pain Medicine, Zanger, Ulrich M., Publica |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
Pharmacology
METHYLTRANSFERASE COMT GENE DORSAL-ROOT GANGLIA SICKLE-CELL-DISEASE GAIN-OF-FUNCTION knowledge discovery NEUROPATHIC PAIN OPIOID RECEPTOR GENE next generation sequencing (NGS) 3126 Surgery anesthesiology intensive care radiology RHEUMATOID-ARTHRITIS 317 Pharmacy SINGLE NUCLEOTIDE POLYMORPHISMS BREAST-CANCER Pharmacology (medical) pain ddc:610 data science GENOME-WIDE ASSOCIATION functional genomics |
| Popis: | Background: Many gene variants modulate the individual perception of pain and possibly also its persistence. The limited selection of single functional variants is increasingly being replaced by analyses of the full coding and regulatory sequences of pain-relevant genes accessible by means of next generation sequencing (NGS). Methods: An NGS panel was created for a set of 77 human genes selected following different lines of evidence supporting their role in persisting pain. To address the role of these candidate genes, we established a sequencing assay based on a custom AmpliSeq (TM) panel to assess the exomic sequences in 72 subjects of Caucasian ethnicity. To identify the systems biology of the genes, the biological functions associated with these genes were assessed by means of a computational over-representation analysis. Results: Sequencing generated a median of 2.85 . 10(6) reads per run with a mean depth close to 200 reads, mean read length of 205 called bases and an average chip loading of 71%. A total of 3,185 genetic variants were called. A computational functional genomics analysis indicated that the proposed NGS gene panel covers biological processes identified previously as characterizing the functional genomics of persisting pain. Conclusion: Results of the NGS assay suggested that the produced nucleotide sequences are comparable to those earned with the classical Sanger sequencing technique. The assay is applicable for small to large-scale experimental setups to target the accessing of information about any nucleotide within the addressed genes in a study cohort. |
| Databáze: | OpenAIRE |
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