The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems
Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining...
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| Veröffentlicht in: | Journal of applied genetics 2024-09, Vol.65 (3), p.559-563 |
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| creator | Daca-Roszak, Patrycja Fiedorowicz, Joanna Jankowski, Maciej Ciesielka, Marzanna Teresiński, Grzegorz Lipska-Zietkiewicz, Beata Zietkiewicz, Ewa Grzybowski, Tomasz Skonieczna, Katarzyna |
| description | Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (
Nextera XT DNA Library Preparation Kit
and
Nextera DNA Flex Library Preparation Kit
) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems. |
| doi_str_mv | 10.1007/s13353-023-00821-4 |
| format | Article |
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Nextera XT DNA Library Preparation Kit
and
Nextera DNA Flex Library Preparation Kit
) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.</description><identifier>ISSN: 1234-1983</identifier><identifier>EISSN: 2190-3883</identifier><identifier>DOI: 10.1007/s13353-023-00821-4</identifier><identifier>PMID: 38110828</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Biomedical and Life Sciences ; DNA libraries ; DNA sequencing ; DNA, Mitochondrial - genetics ; Gene Library ; Gene sequencing ; Genome, Mitochondrial - genetics ; Heteroplasmy ; Heteroplasmy - genetics ; High-Throughput Nucleotide Sequencing - methods ; Human Genetics ; Human Genetics • Short Communication ; Humans ; Life Sciences ; Medical research ; Microbial Genetics and Genomics ; Mitochondrial DNA ; mitochondrial genome ; Nucleotide sequence ; nucleotide sequences ; Plant Genetics and Genomics ; Platforms ; Sensitivity analysis ; Sequence Analysis, DNA - methods</subject><ispartof>Journal of applied genetics, 2024-09, Vol.65 (3), p.559-563</ispartof><rights>The Author(s) 2023. corrected publication 2024</rights><rights>2023. The Author(s).</rights><rights>The Author(s) 2023. corrected publication 2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c403t-22f353ddc15f116308ab3f95f8e7ccdfbd508084db09447fea9b8542be1703e53</cites><orcidid>0000-0001-5788-9398</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s13353-023-00821-4$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s13353-023-00821-4$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>314,778,782,27907,27908,41471,42540,51302</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38110828$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Daca-Roszak, Patrycja</creatorcontrib><creatorcontrib>Fiedorowicz, Joanna</creatorcontrib><creatorcontrib>Jankowski, Maciej</creatorcontrib><creatorcontrib>Ciesielka, Marzanna</creatorcontrib><creatorcontrib>Teresiński, Grzegorz</creatorcontrib><creatorcontrib>Lipska-Zietkiewicz, Beata</creatorcontrib><creatorcontrib>Zietkiewicz, Ewa</creatorcontrib><creatorcontrib>Grzybowski, Tomasz</creatorcontrib><creatorcontrib>Skonieczna, Katarzyna</creatorcontrib><title>The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems</title><title>Journal of applied genetics</title><addtitle>J Appl Genetics</addtitle><addtitle>J Appl Genet</addtitle><description>Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (
Nextera XT DNA Library Preparation Kit
and
Nextera DNA Flex Library Preparation Kit
) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.</description><subject>Animal Genetics and Genomics</subject><subject>Biomedical and Life Sciences</subject><subject>DNA libraries</subject><subject>DNA sequencing</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Gene Library</subject><subject>Gene sequencing</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Heteroplasmy</subject><subject>Heteroplasmy - genetics</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Human Genetics</subject><subject>Human Genetics • Short Communication</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Medical research</subject><subject>Microbial Genetics and Genomics</subject><subject>Mitochondrial DNA</subject><subject>mitochondrial genome</subject><subject>Nucleotide sequence</subject><subject>nucleotide sequences</subject><subject>Plant Genetics and Genomics</subject><subject>Platforms</subject><subject>Sensitivity analysis</subject><subject>Sequence Analysis, DNA - methods</subject><issn>1234-1983</issn><issn>2190-3883</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc1u1DAUhS0EokPhBVggS2y6CfgvE3tZlb9KFWzK2nKc644rJx7spGjehwftnaaAxIKFZVv-zrnX9xDymrN3nLHufeVStrJhAhfTgjfqCdkIblgjtZZPyYYLqRputDwhL2q9ZUxq1Ynn5ERqzlGhN-TX9Q4ohAB-pjnQFPviyoHuC-xdcXPME57znH1OFM_zSkcfYfKHo2IHM5S8T66OBzrgxT-I4kTHiLJdnoYSXaIfvp7Tpcbphs4_Mx1drfEOElbCMilBohV-LGh6JC5TWsY4OVoPdYaxviTPgksVXj3up-T7p4_XF1-aq2-fLy_OrxqvmJwbIQLOYxg8bwPnW8m062UwbdDQeT-EfmiZZloNPTNKdQGc6XWrRA-8YxJaeUrOVl_8MjZTZzvG6iElN0FeqpW8lZ0S0mwRffsPepuXMmF3VjLDjNgabpASK-VLrrVAsPsSRxyw5cweM7RrhhYztA8ZWoWiN4_WSz_C8EfyOzQE5ApUfJpuoPyt_R_be2WrqtI</recordid><startdate>20240901</startdate><enddate>20240901</enddate><creator>Daca-Roszak, Patrycja</creator><creator>Fiedorowicz, Joanna</creator><creator>Jankowski, Maciej</creator><creator>Ciesielka, Marzanna</creator><creator>Teresiński, Grzegorz</creator><creator>Lipska-Zietkiewicz, Beata</creator><creator>Zietkiewicz, Ewa</creator><creator>Grzybowski, Tomasz</creator><creator>Skonieczna, Katarzyna</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0001-5788-9398</orcidid></search><sort><creationdate>20240901</creationdate><title>The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems</title><author>Daca-Roszak, Patrycja ; Fiedorowicz, Joanna ; Jankowski, Maciej ; Ciesielka, Marzanna ; Teresiński, Grzegorz ; Lipska-Zietkiewicz, Beata ; Zietkiewicz, Ewa ; Grzybowski, Tomasz ; Skonieczna, Katarzyna</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c403t-22f353ddc15f116308ab3f95f8e7ccdfbd508084db09447fea9b8542be1703e53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biomedical and Life Sciences</topic><topic>DNA libraries</topic><topic>DNA sequencing</topic><topic>DNA, Mitochondrial - genetics</topic><topic>Gene Library</topic><topic>Gene sequencing</topic><topic>Genome, Mitochondrial - genetics</topic><topic>Heteroplasmy</topic><topic>Heteroplasmy - genetics</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Human Genetics</topic><topic>Human Genetics • Short Communication</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Medical research</topic><topic>Microbial Genetics and Genomics</topic><topic>Mitochondrial DNA</topic><topic>mitochondrial genome</topic><topic>Nucleotide sequence</topic><topic>nucleotide sequences</topic><topic>Plant Genetics and Genomics</topic><topic>Platforms</topic><topic>Sensitivity analysis</topic><topic>Sequence Analysis, DNA - methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Daca-Roszak, Patrycja</creatorcontrib><creatorcontrib>Fiedorowicz, Joanna</creatorcontrib><creatorcontrib>Jankowski, Maciej</creatorcontrib><creatorcontrib>Ciesielka, Marzanna</creatorcontrib><creatorcontrib>Teresiński, Grzegorz</creatorcontrib><creatorcontrib>Lipska-Zietkiewicz, Beata</creatorcontrib><creatorcontrib>Zietkiewicz, Ewa</creatorcontrib><creatorcontrib>Grzybowski, Tomasz</creatorcontrib><creatorcontrib>Skonieczna, Katarzyna</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Journal of applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Daca-Roszak, Patrycja</au><au>Fiedorowicz, Joanna</au><au>Jankowski, Maciej</au><au>Ciesielka, Marzanna</au><au>Teresiński, Grzegorz</au><au>Lipska-Zietkiewicz, Beata</au><au>Zietkiewicz, Ewa</au><au>Grzybowski, Tomasz</au><au>Skonieczna, Katarzyna</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems</atitle><jtitle>Journal of applied genetics</jtitle><stitle>J Appl Genetics</stitle><addtitle>J Appl Genet</addtitle><date>2024-09-01</date><risdate>2024</risdate><volume>65</volume><issue>3</issue><spage>559</spage><epage>563</epage><pages>559-563</pages><issn>1234-1983</issn><eissn>2190-3883</eissn><abstract>Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (
Nextera XT DNA Library Preparation Kit
and
Nextera DNA Flex Library Preparation Kit
) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>38110828</pmid><doi>10.1007/s13353-023-00821-4</doi><tpages>5</tpages><orcidid>https://orcid.org/0000-0001-5788-9398</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1234-1983 |
| ispartof | Journal of applied genetics, 2024-09, Vol.65 (3), p.559-563 |
| issn | 1234-1983 2190-3883 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Animal Genetics and Genomics Biomedical and Life Sciences DNA libraries DNA sequencing DNA, Mitochondrial - genetics Gene Library Gene sequencing Genome, Mitochondrial - genetics Heteroplasmy Heteroplasmy - genetics High-Throughput Nucleotide Sequencing - methods Human Genetics Human Genetics • Short Communication Humans Life Sciences Medical research Microbial Genetics and Genomics Mitochondrial DNA mitochondrial genome Nucleotide sequence nucleotide sequences Plant Genetics and Genomics Platforms Sensitivity analysis Sequence Analysis, DNA - methods |
| title | The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems |
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