Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors
Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methy...
Gespeichert in:
| Veröffentlicht in: | PloS one 2011-07, Vol.6 (7), p.e21332 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 7 |
| container_start_page | e21332 |
| container_title | PloS one |
| container_volume | 6 |
| creator | Herrmann, Alexander Haake, Andrea Ammerpohl, Ole Martin-Guerrero, Idoia Szafranski, Karol Stemshorn, Kathryn Nothnagel, Michael Kotsopoulos, Steve K Richter, Julia Warner, Jason Olson, Jeff Link, Darren R Schreiber, Stefan Krawczak, Michael Platzer, Matthias Nürnberg, Peter Siebert, Reiner Hampe, Jochen |
| description | Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer. |
| doi_str_mv | 10.1371/journal.pone.0021332 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1305137348</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A476886390</galeid><doaj_id>oai_doaj_org_article_f7bb46aa1a8e40d1a7494bd4cbdc0594</doaj_id><sourcerecordid>A476886390</sourcerecordid><originalsourceid>FETCH-LOGICAL-c691t-87c751ae2d4b991388937ff707f871c0f6804945018df68258062291d74fb3423</originalsourceid><addsrcrecordid>eNqNkl1rFDEUhgdRbK3-A9GAIHgxazLJTDI3Qln8WCi01I_bkJk52U3NTqZJprb_3qw7LTugILlIOHnOe8KbN8teErwglJP3V270vbKLwfWwwLgglBaPsmNS0yKvCkwfH5yPsmchXGFcUlFVT7OjgvAScyyOs9sLM4A1PSDtPLLKryEPrbKAtqb1rvNusBBRY8JotYmALpaXeaMCdCjA9Qh9a_o1Uta6XwHFDaDoVftzV3MabWAw8W4ABDfOjtG4HpkexXHrfHiePdHKBngx7SfZ908fvy2_5Gfnn1fL07O8rWoSc8FbXhIFRceauiZUiJpyrTnmWnDSYl0JzGpWYiK6dC5KgauiqEnHmW4oK-hJ9nqvO1gX5GRakITiMtlImUjEak90Tl3JwZut8nfSKSP_FJxfS-WjaS1IzZuGVUoRJYDhjiieZjcda5uuxWXNktaHadrYbKFroU9-2Jno_KY3G7l2N5KmB2GKk8CbScC7ZG-I_3jyRK3TT0nTa7ezfWtCK08Zr4SoaL3TWvyFSquD9LkpNtqk-qzh3awhMRFu41qNIcjV18v_Z89_zNm3B-wGlI2bMCUizEG2B1P0QvCgH5wjWO5Sf--G3KVeTqlPba8OXX9ouo85_Q1JB_2v</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1305137348</pqid></control><display><type>article</type><title>Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS)</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Herrmann, Alexander ; Haake, Andrea ; Ammerpohl, Ole ; Martin-Guerrero, Idoia ; Szafranski, Karol ; Stemshorn, Kathryn ; Nothnagel, Michael ; Kotsopoulos, Steve K ; Richter, Julia ; Warner, Jason ; Olson, Jeff ; Link, Darren R ; Schreiber, Stefan ; Krawczak, Michael ; Platzer, Matthias ; Nürnberg, Peter ; Siebert, Reiner ; Hampe, Jochen</creator><contributor>Tao, Qian</contributor><creatorcontrib>Herrmann, Alexander ; Haake, Andrea ; Ammerpohl, Ole ; Martin-Guerrero, Idoia ; Szafranski, Karol ; Stemshorn, Kathryn ; Nothnagel, Michael ; Kotsopoulos, Steve K ; Richter, Julia ; Warner, Jason ; Olson, Jeff ; Link, Darren R ; Schreiber, Stefan ; Krawczak, Michael ; Platzer, Matthias ; Nürnberg, Peter ; Siebert, Reiner ; Hampe, Jochen ; Tao, Qian</creatorcontrib><description>Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0021332</identifier><identifier>PMID: 21750708</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aged ; Aging ; Analysis ; Arabidopsis ; Biological evolution ; Biology ; Bisulfite ; Brain cancer ; Cancer ; Chromosomes ; Colonic Neoplasms - genetics ; Colorectal cancer ; Colorectal carcinoma ; Cytosine ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA sequencing ; DNA, Neoplasm - chemistry ; DNA, Neoplasm - genetics ; Epigenetic inheritance ; Epigenetics ; Evolution ; Female ; Fibroblast growth factor 6 ; Fibroblast Growth Factor 6 - genetics ; Gene expression ; Gene sequencing ; Genes ; Genetic aspects ; Genetic Predisposition to Disease - classification ; Genetic Predisposition to Disease - genetics ; Genetics ; Genome, Human - genetics ; Genome-Wide Association Study - methods ; Genomes ; Genomics ; Haplotypes ; Health informatics ; Humans ; Internal medicine ; Lymphoma ; Lymphoma, Follicular - genetics ; Male ; Medicine ; Methylation ; Middle Aged ; Neoplasms - genetics ; Nervous system ; Non-Hodgkin's lymphomas ; Nucleotide sequence ; Nucleotide sequencing ; Phylogeny ; Plastic foam ; Polymerase chain reaction ; Polymerase Chain Reaction - methods ; Polymorphism, Single Nucleotide ; Prostate ; Pyrimidines ; Sequence Analysis, DNA - methods ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; snRNP Core Proteins - genetics ; Sulfites ; Sulfites - chemistry ; Sulfotransferases - genetics ; Tumors</subject><ispartof>PloS one, 2011-07, Vol.6 (7), p.e21332</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Herrmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Herrmann et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c691t-87c751ae2d4b991388937ff707f871c0f6804945018df68258062291d74fb3423</citedby><cites>FETCH-LOGICAL-c691t-87c751ae2d4b991388937ff707f871c0f6804945018df68258062291d74fb3423</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130030/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3130030/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21750708$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Tao, Qian</contributor><creatorcontrib>Herrmann, Alexander</creatorcontrib><creatorcontrib>Haake, Andrea</creatorcontrib><creatorcontrib>Ammerpohl, Ole</creatorcontrib><creatorcontrib>Martin-Guerrero, Idoia</creatorcontrib><creatorcontrib>Szafranski, Karol</creatorcontrib><creatorcontrib>Stemshorn, Kathryn</creatorcontrib><creatorcontrib>Nothnagel, Michael</creatorcontrib><creatorcontrib>Kotsopoulos, Steve K</creatorcontrib><creatorcontrib>Richter, Julia</creatorcontrib><creatorcontrib>Warner, Jason</creatorcontrib><creatorcontrib>Olson, Jeff</creatorcontrib><creatorcontrib>Link, Darren R</creatorcontrib><creatorcontrib>Schreiber, Stefan</creatorcontrib><creatorcontrib>Krawczak, Michael</creatorcontrib><creatorcontrib>Platzer, Matthias</creatorcontrib><creatorcontrib>Nürnberg, Peter</creatorcontrib><creatorcontrib>Siebert, Reiner</creatorcontrib><creatorcontrib>Hampe, Jochen</creatorcontrib><title>Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.</description><subject>Aged</subject><subject>Aging</subject><subject>Analysis</subject><subject>Arabidopsis</subject><subject>Biological evolution</subject><subject>Biology</subject><subject>Bisulfite</subject><subject>Brain cancer</subject><subject>Cancer</subject><subject>Chromosomes</subject><subject>Colonic Neoplasms - genetics</subject><subject>Colorectal cancer</subject><subject>Colorectal carcinoma</subject><subject>Cytosine</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA sequencing</subject><subject>DNA, Neoplasm - chemistry</subject><subject>DNA, Neoplasm - genetics</subject><subject>Epigenetic inheritance</subject><subject>Epigenetics</subject><subject>Evolution</subject><subject>Female</subject><subject>Fibroblast growth factor 6</subject><subject>Fibroblast Growth Factor 6 - genetics</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Predisposition to Disease - classification</subject><subject>Genetic Predisposition to Disease - genetics</subject><subject>Genetics</subject><subject>Genome, Human - genetics</subject><subject>Genome-Wide Association Study - methods</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Haplotypes</subject><subject>Health informatics</subject><subject>Humans</subject><subject>Internal medicine</subject><subject>Lymphoma</subject><subject>Lymphoma, Follicular - genetics</subject><subject>Male</subject><subject>Medicine</subject><subject>Methylation</subject><subject>Middle Aged</subject><subject>Neoplasms - genetics</subject><subject>Nervous system</subject><subject>Non-Hodgkin's lymphomas</subject><subject>Nucleotide sequence</subject><subject>Nucleotide sequencing</subject><subject>Phylogeny</subject><subject>Plastic foam</subject><subject>Polymerase chain reaction</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Prostate</subject><subject>Pyrimidines</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>snRNP Core Proteins - genetics</subject><subject>Sulfites</subject><subject>Sulfites - chemistry</subject><subject>Sulfotransferases - genetics</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</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><sourceid>DOA</sourceid><recordid>eNqNkl1rFDEUhgdRbK3-A9GAIHgxazLJTDI3Qln8WCi01I_bkJk52U3NTqZJprb_3qw7LTugILlIOHnOe8KbN8teErwglJP3V270vbKLwfWwwLgglBaPsmNS0yKvCkwfH5yPsmchXGFcUlFVT7OjgvAScyyOs9sLM4A1PSDtPLLKryEPrbKAtqb1rvNusBBRY8JotYmALpaXeaMCdCjA9Qh9a_o1Uta6XwHFDaDoVftzV3MabWAw8W4ABDfOjtG4HpkexXHrfHiePdHKBngx7SfZ908fvy2_5Gfnn1fL07O8rWoSc8FbXhIFRceauiZUiJpyrTnmWnDSYl0JzGpWYiK6dC5KgauiqEnHmW4oK-hJ9nqvO1gX5GRakITiMtlImUjEak90Tl3JwZut8nfSKSP_FJxfS-WjaS1IzZuGVUoRJYDhjiieZjcda5uuxWXNktaHadrYbKFroU9-2Jno_KY3G7l2N5KmB2GKk8CbScC7ZG-I_3jyRK3TT0nTa7ezfWtCK08Zr4SoaL3TWvyFSquD9LkpNtqk-qzh3awhMRFu41qNIcjV18v_Z89_zNm3B-wGlI2bMCUizEG2B1P0QvCgH5wjWO5Sf--G3KVeTqlPba8OXX9ouo85_Q1JB_2v</recordid><startdate>20110705</startdate><enddate>20110705</enddate><creator>Herrmann, Alexander</creator><creator>Haake, Andrea</creator><creator>Ammerpohl, Ole</creator><creator>Martin-Guerrero, Idoia</creator><creator>Szafranski, Karol</creator><creator>Stemshorn, Kathryn</creator><creator>Nothnagel, Michael</creator><creator>Kotsopoulos, Steve K</creator><creator>Richter, Julia</creator><creator>Warner, Jason</creator><creator>Olson, Jeff</creator><creator>Link, Darren R</creator><creator>Schreiber, Stefan</creator><creator>Krawczak, Michael</creator><creator>Platzer, Matthias</creator><creator>Nürnberg, Peter</creator><creator>Siebert, Reiner</creator><creator>Hampe, Jochen</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</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>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>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20110705</creationdate><title>Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors</title><author>Herrmann, Alexander ; Haake, Andrea ; Ammerpohl, Ole ; Martin-Guerrero, Idoia ; Szafranski, Karol ; Stemshorn, Kathryn ; Nothnagel, Michael ; Kotsopoulos, Steve K ; Richter, Julia ; Warner, Jason ; Olson, Jeff ; Link, Darren R ; Schreiber, Stefan ; Krawczak, Michael ; Platzer, Matthias ; Nürnberg, Peter ; Siebert, Reiner ; Hampe, Jochen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c691t-87c751ae2d4b991388937ff707f871c0f6804945018df68258062291d74fb3423</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Aged</topic><topic>Aging</topic><topic>Analysis</topic><topic>Arabidopsis</topic><topic>Biological evolution</topic><topic>Biology</topic><topic>Bisulfite</topic><topic>Brain cancer</topic><topic>Cancer</topic><topic>Chromosomes</topic><topic>Colonic Neoplasms - genetics</topic><topic>Colorectal cancer</topic><topic>Colorectal carcinoma</topic><topic>Cytosine</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA sequencing</topic><topic>DNA, Neoplasm - chemistry</topic><topic>DNA, Neoplasm - genetics</topic><topic>Epigenetic inheritance</topic><topic>Epigenetics</topic><topic>Evolution</topic><topic>Female</topic><topic>Fibroblast growth factor 6</topic><topic>Fibroblast Growth Factor 6 - genetics</topic><topic>Gene expression</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic Predisposition to Disease - classification</topic><topic>Genetic Predisposition to Disease - genetics</topic><topic>Genetics</topic><topic>Genome, Human - genetics</topic><topic>Genome-Wide Association Study - methods</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Haplotypes</topic><topic>Health informatics</topic><topic>Humans</topic><topic>Internal medicine</topic><topic>Lymphoma</topic><topic>Lymphoma, Follicular - genetics</topic><topic>Male</topic><topic>Medicine</topic><topic>Methylation</topic><topic>Middle Aged</topic><topic>Neoplasms - genetics</topic><topic>Nervous system</topic><topic>Non-Hodgkin's lymphomas</topic><topic>Nucleotide sequence</topic><topic>Nucleotide sequencing</topic><topic>Phylogeny</topic><topic>Plastic foam</topic><topic>Polymerase chain reaction</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Prostate</topic><topic>Pyrimidines</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>snRNP Core Proteins - genetics</topic><topic>Sulfites</topic><topic>Sulfites - chemistry</topic><topic>Sulfotransferases - genetics</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Herrmann, Alexander</creatorcontrib><creatorcontrib>Haake, Andrea</creatorcontrib><creatorcontrib>Ammerpohl, Ole</creatorcontrib><creatorcontrib>Martin-Guerrero, Idoia</creatorcontrib><creatorcontrib>Szafranski, Karol</creatorcontrib><creatorcontrib>Stemshorn, Kathryn</creatorcontrib><creatorcontrib>Nothnagel, Michael</creatorcontrib><creatorcontrib>Kotsopoulos, Steve K</creatorcontrib><creatorcontrib>Richter, Julia</creatorcontrib><creatorcontrib>Warner, Jason</creatorcontrib><creatorcontrib>Olson, Jeff</creatorcontrib><creatorcontrib>Link, Darren R</creatorcontrib><creatorcontrib>Schreiber, Stefan</creatorcontrib><creatorcontrib>Krawczak, Michael</creatorcontrib><creatorcontrib>Platzer, Matthias</creatorcontrib><creatorcontrib>Nürnberg, Peter</creatorcontrib><creatorcontrib>Siebert, Reiner</creatorcontrib><creatorcontrib>Hampe, Jochen</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids 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>ProQuest Pharma Collection</collection><collection>Public Health Database</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>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>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</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>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</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>Materials Science Collection</collection><collection>Publicly Available Content Database</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>Genetics Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Herrmann, Alexander</au><au>Haake, Andrea</au><au>Ammerpohl, Ole</au><au>Martin-Guerrero, Idoia</au><au>Szafranski, Karol</au><au>Stemshorn, Kathryn</au><au>Nothnagel, Michael</au><au>Kotsopoulos, Steve K</au><au>Richter, Julia</au><au>Warner, Jason</au><au>Olson, Jeff</au><au>Link, Darren R</au><au>Schreiber, Stefan</au><au>Krawczak, Michael</au><au>Platzer, Matthias</au><au>Nürnberg, Peter</au><au>Siebert, Reiner</au><au>Hampe, Jochen</au><au>Tao, Qian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-07-05</date><risdate>2011</risdate><volume>6</volume><issue>7</issue><spage>e21332</spage><pages>e21332-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into "hepitypes" and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21750708</pmid><doi>10.1371/journal.pone.0021332</doi><tpages>e21332</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2011-07, Vol.6 (7), p.e21332 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1305137348 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS); EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aged Aging Analysis Arabidopsis Biological evolution Biology Bisulfite Brain cancer Cancer Chromosomes Colonic Neoplasms - genetics Colorectal cancer Colorectal carcinoma Cytosine Deoxyribonucleic acid DNA DNA Methylation DNA sequencing DNA, Neoplasm - chemistry DNA, Neoplasm - genetics Epigenetic inheritance Epigenetics Evolution Female Fibroblast growth factor 6 Fibroblast Growth Factor 6 - genetics Gene expression Gene sequencing Genes Genetic aspects Genetic Predisposition to Disease - classification Genetic Predisposition to Disease - genetics Genetics Genome, Human - genetics Genome-Wide Association Study - methods Genomes Genomics Haplotypes Health informatics Humans Internal medicine Lymphoma Lymphoma, Follicular - genetics Male Medicine Methylation Middle Aged Neoplasms - genetics Nervous system Non-Hodgkin's lymphomas Nucleotide sequence Nucleotide sequencing Phylogeny Plastic foam Polymerase chain reaction Polymerase Chain Reaction - methods Polymorphism, Single Nucleotide Prostate Pyrimidines Sequence Analysis, DNA - methods Single nucleotide polymorphisms Single-nucleotide polymorphism snRNP Core Proteins - genetics Sulfites Sulfites - chemistry Sulfotransferases - genetics Tumors |
| title | Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-11T22%3A26%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Pipeline%20for%20large-scale%20microdroplet%20bisulfite%20PCR-based%20sequencing%20allows%20the%20tracking%20of%20hepitype%20evolution%20in%20tumors&rft.jtitle=PloS%20one&rft.au=Herrmann,%20Alexander&rft.date=2011-07-05&rft.volume=6&rft.issue=7&rft.spage=e21332&rft.pages=e21332-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0021332&rft_dat=%3Cgale_plos_%3EA476886390%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1305137348&rft_id=info:pmid/21750708&rft_galeid=A476886390&rft_doaj_id=oai_doaj_org_article_f7bb46aa1a8e40d1a7494bd4cbdc0594&rfr_iscdi=true |