Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing
Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth. Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methyl...
Gespeichert in:
| Veröffentlicht in: | Nature methods 2015-03, Vol.12 (3), p.230-232 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 232 |
|---|---|
| container_issue | 3 |
| container_start_page | 230 |
| container_title | Nature methods |
| container_volume | 12 |
| creator | Ziller, Michael J Hansen, Kasper D Meissner, Alexander Aryee, Martin J |
| description | Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.
Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates. |
| doi_str_mv | 10.1038/nmeth.3152 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4344394</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A403450133</galeid><sourcerecordid>A403450133</sourcerecordid><originalsourceid>FETCH-LOGICAL-c612t-2f34809e907a50ce819d81ff1e1017e3038e0a90b41348ed18d6cee666a5ef033</originalsourceid><addsrcrecordid>eNqNkk1rFTEUhoMotlY3_gAZcFOUueZ7ZjZCufgFBTfqNuRmTuamZJKazFTuv2-mt62tdVGySDjnyct5Dy9CrwleEczaD2GEabtiRNAn6JAI3tYNweLpzRt35AC9yPkMY8Y4Fc_RARVMUibZIfq1jheQ9ABVAhPHEUKvJxdDrmxM1SK881eFSgftd9nlarOr_myjh3qAEEeoNi7P3roJqgy_ZwjGheElema1z_Dq-j5CPz9_-rH-Wp9-__JtfXJaG0noVFPLeIs76HCjBTbQkq5vibUECCYNsOIOsO7whpMCQk_aXhoAKaUWYIudI_Rxr3s-b0boDYQpaa_Okxt12qmonbrfCW6rhnihOOOcdbwIHF8LpFiGz5MaXTbgvQ4Q56yIbBvZFPYxqMSYdpSSgr79Bz2LcyoLXCjRNpTKRvylBu1BuWBjGdEsouqEY8YFJmyxuPoPVU4PozMxgHWlfu_Du_0Hk2LOCeztOghWS2DUVWDUEpgCv7m7wFv0JiEFeL8HcmmFAdIdKw_lLgGeospu</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1658722675</pqid></control><display><type>article</type><title>Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing</title><source>MEDLINE</source><source>SpringerLink Journals</source><source>Nature Journals Online</source><creator>Ziller, Michael J ; Hansen, Kasper D ; Meissner, Alexander ; Aryee, Martin J</creator><creatorcontrib>Ziller, Michael J ; Hansen, Kasper D ; Meissner, Alexander ; Aryee, Martin J</creatorcontrib><description>Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.
Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates.</description><identifier>ISSN: 1548-7091</identifier><identifier>EISSN: 1548-7105</identifier><identifier>DOI: 10.1038/nmeth.3152</identifier><identifier>PMID: 25362363</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/114/2415 ; 631/1647/2210/2213 ; Bioinformatics ; Biological Microscopy ; Biological Techniques ; Biomedical Engineering/Biotechnology ; Brain - physiology ; brief-communication ; CD4-Positive T-Lymphocytes - physiology ; CD8-Positive T-Lymphocytes - physiology ; Cellular biology ; CpG Islands ; Data Interpretation, Statistical ; Databases, Genetic ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA sequencing ; Embryonic Stem Cells - physiology ; Gene expression ; Genetic research ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Innovations ; Life Sciences ; Nucleotide sequencing ; Proteomics ; Sensitivity and Specificity ; Sequence Analysis, DNA - methods ; Sulfites</subject><ispartof>Nature methods, 2015-03, Vol.12 (3), p.230-232</ispartof><rights>Springer Nature America, Inc. 2014</rights><rights>COPYRIGHT 2015 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Mar 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c612t-2f34809e907a50ce819d81ff1e1017e3038e0a90b41348ed18d6cee666a5ef033</citedby><cites>FETCH-LOGICAL-c612t-2f34809e907a50ce819d81ff1e1017e3038e0a90b41348ed18d6cee666a5ef033</cites><orcidid>0000-0002-6848-1344 ; 0000000268481344</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nmeth.3152$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nmeth.3152$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,777,781,882,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25362363$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ziller, Michael J</creatorcontrib><creatorcontrib>Hansen, Kasper D</creatorcontrib><creatorcontrib>Meissner, Alexander</creatorcontrib><creatorcontrib>Aryee, Martin J</creatorcontrib><title>Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing</title><title>Nature methods</title><addtitle>Nat Methods</addtitle><addtitle>Nat Methods</addtitle><description>Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.
Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates.</description><subject>631/114/2415</subject><subject>631/1647/2210/2213</subject><subject>Bioinformatics</subject><subject>Biological Microscopy</subject><subject>Biological Techniques</subject><subject>Biomedical Engineering/Biotechnology</subject><subject>Brain - physiology</subject><subject>brief-communication</subject><subject>CD4-Positive T-Lymphocytes - physiology</subject><subject>CD8-Positive T-Lymphocytes - physiology</subject><subject>Cellular biology</subject><subject>CpG Islands</subject><subject>Data Interpretation, Statistical</subject><subject>Databases, Genetic</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA sequencing</subject><subject>Embryonic Stem Cells - physiology</subject><subject>Gene expression</subject><subject>Genetic research</subject><subject>Genome, Human</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Innovations</subject><subject>Life Sciences</subject><subject>Nucleotide sequencing</subject><subject>Proteomics</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Sulfites</subject><issn>1548-7091</issn><issn>1548-7105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkk1rFTEUhoMotlY3_gAZcFOUueZ7ZjZCufgFBTfqNuRmTuamZJKazFTuv2-mt62tdVGySDjnyct5Dy9CrwleEczaD2GEabtiRNAn6JAI3tYNweLpzRt35AC9yPkMY8Y4Fc_RARVMUibZIfq1jheQ9ABVAhPHEUKvJxdDrmxM1SK881eFSgftd9nlarOr_myjh3qAEEeoNi7P3roJqgy_ZwjGheElema1z_Dq-j5CPz9_-rH-Wp9-__JtfXJaG0noVFPLeIs76HCjBTbQkq5vibUECCYNsOIOsO7whpMCQk_aXhoAKaUWYIudI_Rxr3s-b0boDYQpaa_Okxt12qmonbrfCW6rhnihOOOcdbwIHF8LpFiGz5MaXTbgvQ4Q56yIbBvZFPYxqMSYdpSSgr79Bz2LcyoLXCjRNpTKRvylBu1BuWBjGdEsouqEY8YFJmyxuPoPVU4PozMxgHWlfu_Du_0Hk2LOCeztOghWS2DUVWDUEpgCv7m7wFv0JiEFeL8HcmmFAdIdKw_lLgGeospu</recordid><startdate>20150301</startdate><enddate>20150301</enddate><creator>Ziller, Michael J</creator><creator>Hansen, Kasper D</creator><creator>Meissner, Alexander</creator><creator>Aryee, Martin J</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><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>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7SS</scope><scope>7TK</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>7TM</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6848-1344</orcidid><orcidid>https://orcid.org/0000000268481344</orcidid></search><sort><creationdate>20150301</creationdate><title>Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing</title><author>Ziller, Michael J ; Hansen, Kasper D ; Meissner, Alexander ; Aryee, Martin J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c612t-2f34809e907a50ce819d81ff1e1017e3038e0a90b41348ed18d6cee666a5ef033</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/114/2415</topic><topic>631/1647/2210/2213</topic><topic>Bioinformatics</topic><topic>Biological Microscopy</topic><topic>Biological Techniques</topic><topic>Biomedical Engineering/Biotechnology</topic><topic>Brain - physiology</topic><topic>brief-communication</topic><topic>CD4-Positive T-Lymphocytes - physiology</topic><topic>CD8-Positive T-Lymphocytes - physiology</topic><topic>Cellular biology</topic><topic>CpG Islands</topic><topic>Data Interpretation, Statistical</topic><topic>Databases, Genetic</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA sequencing</topic><topic>Embryonic Stem Cells - physiology</topic><topic>Gene expression</topic><topic>Genetic research</topic><topic>Genome, Human</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Innovations</topic><topic>Life Sciences</topic><topic>Nucleotide sequencing</topic><topic>Proteomics</topic><topic>Sensitivity and Specificity</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Sulfites</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ziller, Michael J</creatorcontrib><creatorcontrib>Hansen, Kasper D</creatorcontrib><creatorcontrib>Meissner, Alexander</creatorcontrib><creatorcontrib>Aryee, Martin J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ziller, Michael J</au><au>Hansen, Kasper D</au><au>Meissner, Alexander</au><au>Aryee, Martin J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing</atitle><jtitle>Nature methods</jtitle><stitle>Nat Methods</stitle><addtitle>Nat Methods</addtitle><date>2015-03-01</date><risdate>2015</risdate><volume>12</volume><issue>3</issue><spage>230</spage><epage>232</epage><pages>230-232</pages><issn>1548-7091</issn><eissn>1548-7105</eissn><abstract>Results show the minimum sequencing depth required for the discovery of differentially methylated regions at desired sensitivity and specificity and the trade-off between adding more replicates versus increasing sequencing depth.
Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>25362363</pmid><doi>10.1038/nmeth.3152</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0002-6848-1344</orcidid><orcidid>https://orcid.org/0000000268481344</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1548-7091 |
| ispartof | Nature methods, 2015-03, Vol.12 (3), p.230-232 |
| issn | 1548-7091 1548-7105 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4344394 |
| source | MEDLINE; SpringerLink Journals; Nature Journals Online |
| subjects | 631/114/2415 631/1647/2210/2213 Bioinformatics Biological Microscopy Biological Techniques Biomedical Engineering/Biotechnology Brain - physiology brief-communication CD4-Positive T-Lymphocytes - physiology CD8-Positive T-Lymphocytes - physiology Cellular biology CpG Islands Data Interpretation, Statistical Databases, Genetic Deoxyribonucleic acid DNA DNA Methylation DNA sequencing Embryonic Stem Cells - physiology Gene expression Genetic research Genome, Human High-Throughput Nucleotide Sequencing Humans Innovations Life Sciences Nucleotide sequencing Proteomics Sensitivity and Specificity Sequence Analysis, DNA - methods Sulfites |
| title | Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-19T06%3A52%3A02IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Coverage%20recommendations%20for%20methylation%20analysis%20by%20whole-genome%20bisulfite%20sequencing&rft.jtitle=Nature%20methods&rft.au=Ziller,%20Michael%20J&rft.date=2015-03-01&rft.volume=12&rft.issue=3&rft.spage=230&rft.epage=232&rft.pages=230-232&rft.issn=1548-7091&rft.eissn=1548-7105&rft_id=info:doi/10.1038/nmeth.3152&rft_dat=%3Cgale_pubme%3EA403450133%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1658722675&rft_id=info:pmid/25362363&rft_galeid=A403450133&rfr_iscdi=true |