Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing
Aim. To investigate the application of the Oxford Nanopore Technologies’ third generation sequencing for the genetic testing of hypertrophic cardiomyopathy.Material and methods. The study involved 12 patients with hypertrophic cardiomyopathy aged 18 to 67 years (women, 9; men, 3). Using the PCR barc...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | Russian |
| Published: |
«FIRMA «SILICEA» LLC
2021-11-01
|
| Series: | Российский кардиологический журнал |
| Subjects: | |
| Online Access: | https://russjcardiol.elpub.ru/jour/article/view/4673 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849689780119404544 |
|---|---|
| author | R. R. Salakhov M. V. Golubenko E. N. Pavlukova A. N. Kucher N. P. Babushkina N. R. Valiahmetov A. V. Markov E. O. Belyaeva A. F. Kanev M. S. Nazarenko |
| author_facet | R. R. Salakhov M. V. Golubenko E. N. Pavlukova A. N. Kucher N. P. Babushkina N. R. Valiahmetov A. V. Markov E. O. Belyaeva A. F. Kanev M. S. Nazarenko |
| author_sort | R. R. Salakhov |
| collection | DOAJ |
| description | Aim. To investigate the application of the Oxford Nanopore Technologies’ third generation sequencing for the genetic testing of hypertrophic cardiomyopathy.Material and methods. The study involved 12 patients with hypertrophic cardiomyopathy aged 18 to 67 years (women, 9; men, 3). Using the PCR barcoding amplicons (SQK-LSK109) protocol, DNA libraries were created which contained long-range PCR fragments of the MYH7, MYBPC3, TNNT2, TNNI3 and TPM1 genes. The sequencing was performed using the MinION system by Oxford Nanopore Technologies (UK). Bioinformatic algorithms for data analysis included Guppy v.5.0.7, Nanopolish and Clairvoyante. The identified genetic variants were confirmed by Sanger sequencing.Results. Data on the complete sequence of the five major sarcomeric genes for hypertrophic cardiomyopathy were obtained. We found eight potentially disease-causing sequence variants in MYH7, MYBPC3 and TNNT2 genes by monomolecular sequencing. However, only three mutations p.Arg243Cys, p.Tyr609Asn, p.Arg870His in the MYH7 gene, and one mutation p.Lys985Asn in the MYBPC3 were confirmed by Sanger sequencing. Cascade screening of pathogenic variant p.Arg870His in the MYH7 gene was performed. We found one asymptomatic carrier.Conclusion. It appears that monomolecular sequencing technology is a feasible approach to identify mutations in patients with hypertrophic cardiomyopathy. Although improvement in accuracy of DNA sequencing, as well as optimization and simplification of bioinformatic algorithms for identification of the genetic variants are needed. |
| format | Article |
| id | doaj-art-e925f8e52fef4d8abf3af1c55cd6cb45 |
| institution | DOAJ |
| issn | 1560-4071 2618-7620 |
| language | Russian |
| publishDate | 2021-11-01 |
| publisher | «FIRMA «SILICEA» LLC |
| record_format | Article |
| series | Российский кардиологический журнал |
| spelling | doaj-art-e925f8e52fef4d8abf3af1c55cd6cb452025-08-20T03:21:31Zrus«FIRMA «SILICEA» LLCРоссийский кардиологический журнал1560-40712618-76202021-11-01261010.15829/1560-4071-2021-46733368Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencingR. R. Salakhov0M. V. Golubenko1E. N. Pavlukova2A. N. Kucher3N. P. Babushkina4N. R. Valiahmetov5A. V. Markov6E. O. Belyaeva7A. F. Kanev8M. S. Nazarenko9Research Institute of Medical Genetics, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterCardiology Research Institute, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterCardiology Research Institute, Tomsk National Research Medical CenterResearch Institute of Medical Genetics, Tomsk National Research Medical CenterAim. To investigate the application of the Oxford Nanopore Technologies’ third generation sequencing for the genetic testing of hypertrophic cardiomyopathy.Material and methods. The study involved 12 patients with hypertrophic cardiomyopathy aged 18 to 67 years (women, 9; men, 3). Using the PCR barcoding amplicons (SQK-LSK109) protocol, DNA libraries were created which contained long-range PCR fragments of the MYH7, MYBPC3, TNNT2, TNNI3 and TPM1 genes. The sequencing was performed using the MinION system by Oxford Nanopore Technologies (UK). Bioinformatic algorithms for data analysis included Guppy v.5.0.7, Nanopolish and Clairvoyante. The identified genetic variants were confirmed by Sanger sequencing.Results. Data on the complete sequence of the five major sarcomeric genes for hypertrophic cardiomyopathy were obtained. We found eight potentially disease-causing sequence variants in MYH7, MYBPC3 and TNNT2 genes by monomolecular sequencing. However, only three mutations p.Arg243Cys, p.Tyr609Asn, p.Arg870His in the MYH7 gene, and one mutation p.Lys985Asn in the MYBPC3 were confirmed by Sanger sequencing. Cascade screening of pathogenic variant p.Arg870His in the MYH7 gene was performed. We found one asymptomatic carrier.Conclusion. It appears that monomolecular sequencing technology is a feasible approach to identify mutations in patients with hypertrophic cardiomyopathy. Although improvement in accuracy of DNA sequencing, as well as optimization and simplification of bioinformatic algorithms for identification of the genetic variants are needed.https://russjcardiol.elpub.ru/jour/article/view/4673hypertrophic cardiomyopathymonomolecular sequencingoxford nanopore technologymyh7mybpc3. |
| spellingShingle | R. R. Salakhov M. V. Golubenko E. N. Pavlukova A. N. Kucher N. P. Babushkina N. R. Valiahmetov A. V. Markov E. O. Belyaeva A. F. Kanev M. S. Nazarenko Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing Российский кардиологический журнал hypertrophic cardiomyopathy monomolecular sequencing oxford nanopore technology myh7 mybpc3. |
| title | Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing |
| title_full | Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing |
| title_fullStr | Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing |
| title_full_unstemmed | Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing |
| title_short | Experience in genetic testing of hypertrophic cardiomyopathy using nanopore DNA sequencing |
| title_sort | experience in genetic testing of hypertrophic cardiomyopathy using nanopore dna sequencing |
| topic | hypertrophic cardiomyopathy monomolecular sequencing oxford nanopore technology myh7 mybpc3. |
| url | https://russjcardiol.elpub.ru/jour/article/view/4673 |
| work_keys_str_mv | AT rrsalakhov experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT mvgolubenko experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT enpavlukova experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT ankucher experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT npbabushkina experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT nrvaliahmetov experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT avmarkov experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT eobelyaeva experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT afkanev experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing AT msnazarenko experienceingenetictestingofhypertrophiccardiomyopathyusingnanoporednasequencing |