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A microarray-based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease
Objectives We describe a novel microarray‐based approach for the high‐throughput discovery of epigenetic biomarkers for use in the noninvasive detection of fetal genetic disease. Methods We combined a 215 060‐probe custom oligonucleotide microarray with a comprehensive library preparation method and...
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| Published in: | Prenatal diagnosis 2009-11, Vol.29 (11), p.1020-1030 |
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| container_end_page | 1030 |
| container_issue | 11 |
| container_start_page | 1020 |
| container_title | Prenatal diagnosis |
| container_volume | 29 |
| creator | Chu, Tianjiao Burke, Brian Bunce, Kimberly Surti, Urvashi Allen Hogge, W. Peters, David G. |
| description | Objectives
We describe a novel microarray‐based approach for the high‐throughput discovery of epigenetic biomarkers for use in the noninvasive detection of fetal genetic disease.
Methods
We combined a 215 060‐probe custom oligonucleotide microarray with a comprehensive library preparation method and novel statistical tools to compare DNA methylation patterns in chorionic villus samples (CVS) with gestational age‐matched maternal blood cell (MBC) samples. Our custom microarray was designed to provide high‐resolution coverage across human chromosomes 13, 18 and 21.
Results
We identified 6311 MspI/HpaII sites across all three chromosomes that displayed tissue‐specific differential CpG methylation patterns. To maximize the probability of identifying biomarkers that have clinical utility we filtered our data to identify MspI/HpaII sites that are within 150 bp of a highly polymorphic single nucleotide polymorphism (SNP) so that its allelic ratio may be determined for the detection of fetal aneuploidy. Our microarray design and the computational tools used for data analysis are available for download as is the entire data set.
Conclusions
This high‐resolution analysis of DNA methylation patterns in the human placenta during the first trimester of pregnancy identifies numerous potential biomarkers for the diagnosis of fetal aneuploidy on chromosomes 13, 18 and 21. Copyright © 2009 John Wiley & Sons, Ltd. |
| doi_str_mv | 10.1002/pd.2335 |
| format | article |
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We describe a novel microarray‐based approach for the high‐throughput discovery of epigenetic biomarkers for use in the noninvasive detection of fetal genetic disease.
Methods
We combined a 215 060‐probe custom oligonucleotide microarray with a comprehensive library preparation method and novel statistical tools to compare DNA methylation patterns in chorionic villus samples (CVS) with gestational age‐matched maternal blood cell (MBC) samples. Our custom microarray was designed to provide high‐resolution coverage across human chromosomes 13, 18 and 21.
Results
We identified 6311 MspI/HpaII sites across all three chromosomes that displayed tissue‐specific differential CpG methylation patterns. To maximize the probability of identifying biomarkers that have clinical utility we filtered our data to identify MspI/HpaII sites that are within 150 bp of a highly polymorphic single nucleotide polymorphism (SNP) so that its allelic ratio may be determined for the detection of fetal aneuploidy. Our microarray design and the computational tools used for data analysis are available for download as is the entire data set.
Conclusions
This high‐resolution analysis of DNA methylation patterns in the human placenta during the first trimester of pregnancy identifies numerous potential biomarkers for the diagnosis of fetal aneuploidy on chromosomes 13, 18 and 21. Copyright © 2009 John Wiley & Sons, Ltd.</description><identifier>ISSN: 0197-3851</identifier><identifier>ISSN: 1097-0223</identifier><identifier>EISSN: 1097-0223</identifier><identifier>DOI: 10.1002/pd.2335</identifier><identifier>PMID: 19650061</identifier><identifier>CODEN: PRDIDM</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>Aneuploidy ; Biological and medical sciences ; biomarkers ; Biomarkers - metabolism ; Blood cells ; Case-Control Studies ; Chorionic Villi Sampling ; chromosome 13 ; Chromosomes ; Chromosomes, Human, Pair 13 ; Chromosomes, Human, Pair 18 ; Chromosomes, Human, Pair 21 ; Computer applications ; CpG islands ; Data processing ; Delivery. Postpartum. Lactation ; DNA ; DNA Methylation ; Epigenesis, Genetic - genetics ; epigenetics ; Female ; fetal ; Fetal Diseases - diagnosis ; Fetal Diseases - genetics ; Fetuses ; Fundamental and applied biological sciences. Psychology ; Gene Expression Profiling ; Genetics of eukaryotes. Biological and molecular evolution ; Gynecology. Andrology. Obstetrics ; High-Throughput Screening Assays - methods ; Humans ; Medical sciences ; Models, Biological ; Molecular and cellular biology ; Oligonucleotide Array Sequence Analysis - methods ; Oligonucleotides ; Placenta ; plasma ; Pregnancy ; Prenatal diagnosis ; Prenatal Diagnosis - methods ; Single-nucleotide polymorphism ; Statistics ; Villus</subject><ispartof>Prenatal diagnosis, 2009-11, Vol.29 (11), p.1020-1030</ispartof><rights>Copyright © 2009 John Wiley & Sons, Ltd.</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4825-fe5bb83c8869b9c2ff9a44156234f96dbd686169f5c58d0d998a906e865e28f33</citedby><cites>FETCH-LOGICAL-c4825-fe5bb83c8869b9c2ff9a44156234f96dbd686169f5c58d0d998a906e865e28f33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22087712$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19650061$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chu, Tianjiao</creatorcontrib><creatorcontrib>Burke, Brian</creatorcontrib><creatorcontrib>Bunce, Kimberly</creatorcontrib><creatorcontrib>Surti, Urvashi</creatorcontrib><creatorcontrib>Allen Hogge, W.</creatorcontrib><creatorcontrib>Peters, David G.</creatorcontrib><title>A microarray-based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease</title><title>Prenatal diagnosis</title><addtitle>Prenat. Diagn</addtitle><description>Objectives
We describe a novel microarray‐based approach for the high‐throughput discovery of epigenetic biomarkers for use in the noninvasive detection of fetal genetic disease.
Methods
We combined a 215 060‐probe custom oligonucleotide microarray with a comprehensive library preparation method and novel statistical tools to compare DNA methylation patterns in chorionic villus samples (CVS) with gestational age‐matched maternal blood cell (MBC) samples. Our custom microarray was designed to provide high‐resolution coverage across human chromosomes 13, 18 and 21.
Results
We identified 6311 MspI/HpaII sites across all three chromosomes that displayed tissue‐specific differential CpG methylation patterns. To maximize the probability of identifying biomarkers that have clinical utility we filtered our data to identify MspI/HpaII sites that are within 150 bp of a highly polymorphic single nucleotide polymorphism (SNP) so that its allelic ratio may be determined for the detection of fetal aneuploidy. Our microarray design and the computational tools used for data analysis are available for download as is the entire data set.
Conclusions
This high‐resolution analysis of DNA methylation patterns in the human placenta during the first trimester of pregnancy identifies numerous potential biomarkers for the diagnosis of fetal aneuploidy on chromosomes 13, 18 and 21. Copyright © 2009 John Wiley & Sons, Ltd.</description><subject>Aneuploidy</subject><subject>Biological and medical sciences</subject><subject>biomarkers</subject><subject>Biomarkers - metabolism</subject><subject>Blood cells</subject><subject>Case-Control Studies</subject><subject>Chorionic Villi Sampling</subject><subject>chromosome 13</subject><subject>Chromosomes</subject><subject>Chromosomes, Human, Pair 13</subject><subject>Chromosomes, Human, Pair 18</subject><subject>Chromosomes, Human, Pair 21</subject><subject>Computer applications</subject><subject>CpG islands</subject><subject>Data processing</subject><subject>Delivery. Postpartum. Lactation</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>Epigenesis, Genetic - genetics</subject><subject>epigenetics</subject><subject>Female</subject><subject>fetal</subject><subject>Fetal Diseases - diagnosis</subject><subject>Fetal Diseases - genetics</subject><subject>Fetuses</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Profiling</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Gynecology. Andrology. Obstetrics</subject><subject>High-Throughput Screening Assays - methods</subject><subject>Humans</subject><subject>Medical sciences</subject><subject>Models, Biological</subject><subject>Molecular and cellular biology</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Oligonucleotides</subject><subject>Placenta</subject><subject>plasma</subject><subject>Pregnancy</subject><subject>Prenatal diagnosis</subject><subject>Prenatal Diagnosis - methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Statistics</subject><subject>Villus</subject><issn>0197-3851</issn><issn>1097-0223</issn><issn>1097-0223</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNqF0c9rFDEUB_Agit1W8T-QuYiFMjW_JzmWqlVc1ENF6CVkkpc2OjszJrPV9a9vlh22p-op4fHJe-R9EXpB8CnBmL4Z_SllTDxCC4J1U2NK2WO0wKTcmRLkAB3m_KNARXXzFB0QLQXGkizQ37NqFV0abEp2U7c2g6_sOJaCu6nCkKrpBqrooZ9iiM5OceirIVQwxmvoYYquauOwsuknpLz3_dDH_tbmeAuVj_a6H3LM22cBJtuVUoYy6Bl6EmyX4fl8HqFv799dnn-ol18uPp6fLWvHFRV1ANG2ijmlpG61oyFoyzkRkjIetPStl0oSqYNwQnnstVZWYwlKCqAqMHaEXu_6ll_9WkOezCpmB11nexjW2WjMeSM5kf-VDeOE4oaRIo__KQmmWDGFC943LVvOOUEwY4plY5uCzDY8M3qzDa_Il3PTdbsCf-_mtAp4NQObne1Csr2Lee9omdk0hBZ3snO_Ywebh-aZr2_nsfVOxzzBn70umRrZsEaY758vDMeXRC-vrswndgdJOr41</recordid><startdate>200911</startdate><enddate>200911</enddate><creator>Chu, Tianjiao</creator><creator>Burke, Brian</creator><creator>Bunce, Kimberly</creator><creator>Surti, Urvashi</creator><creator>Allen Hogge, W.</creator><creator>Peters, David G.</creator><general>John Wiley & Sons, Ltd</general><general>Wiley</general><scope>BSCLL</scope><scope>IQODW</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>7TM</scope><scope>7X8</scope></search><sort><creationdate>200911</creationdate><title>A microarray-based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease</title><author>Chu, Tianjiao ; Burke, Brian ; Bunce, Kimberly ; Surti, Urvashi ; Allen Hogge, W. ; Peters, David G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4825-fe5bb83c8869b9c2ff9a44156234f96dbd686169f5c58d0d998a906e865e28f33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Aneuploidy</topic><topic>Biological and medical sciences</topic><topic>biomarkers</topic><topic>Biomarkers - metabolism</topic><topic>Blood cells</topic><topic>Case-Control Studies</topic><topic>Chorionic Villi Sampling</topic><topic>chromosome 13</topic><topic>Chromosomes</topic><topic>Chromosomes, Human, Pair 13</topic><topic>Chromosomes, Human, Pair 18</topic><topic>Chromosomes, Human, Pair 21</topic><topic>Computer applications</topic><topic>CpG islands</topic><topic>Data processing</topic><topic>Delivery. Postpartum. Lactation</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>Epigenesis, Genetic - genetics</topic><topic>epigenetics</topic><topic>Female</topic><topic>fetal</topic><topic>Fetal Diseases - diagnosis</topic><topic>Fetal Diseases - genetics</topic><topic>Fetuses</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Profiling</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Gynecology. Andrology. Obstetrics</topic><topic>High-Throughput Screening Assays - methods</topic><topic>Humans</topic><topic>Medical sciences</topic><topic>Models, Biological</topic><topic>Molecular and cellular biology</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>Oligonucleotides</topic><topic>Placenta</topic><topic>plasma</topic><topic>Pregnancy</topic><topic>Prenatal diagnosis</topic><topic>Prenatal Diagnosis - methods</topic><topic>Single-nucleotide polymorphism</topic><topic>Statistics</topic><topic>Villus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chu, Tianjiao</creatorcontrib><creatorcontrib>Burke, Brian</creatorcontrib><creatorcontrib>Bunce, Kimberly</creatorcontrib><creatorcontrib>Surti, Urvashi</creatorcontrib><creatorcontrib>Allen Hogge, W.</creatorcontrib><creatorcontrib>Peters, David G.</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Prenatal diagnosis</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chu, Tianjiao</au><au>Burke, Brian</au><au>Bunce, Kimberly</au><au>Surti, Urvashi</au><au>Allen Hogge, W.</au><au>Peters, David G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A microarray-based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease</atitle><jtitle>Prenatal diagnosis</jtitle><addtitle>Prenat. Diagn</addtitle><date>2009-11</date><risdate>2009</risdate><volume>29</volume><issue>11</issue><spage>1020</spage><epage>1030</epage><pages>1020-1030</pages><issn>0197-3851</issn><issn>1097-0223</issn><eissn>1097-0223</eissn><coden>PRDIDM</coden><abstract>Objectives
We describe a novel microarray‐based approach for the high‐throughput discovery of epigenetic biomarkers for use in the noninvasive detection of fetal genetic disease.
Methods
We combined a 215 060‐probe custom oligonucleotide microarray with a comprehensive library preparation method and novel statistical tools to compare DNA methylation patterns in chorionic villus samples (CVS) with gestational age‐matched maternal blood cell (MBC) samples. Our custom microarray was designed to provide high‐resolution coverage across human chromosomes 13, 18 and 21.
Results
We identified 6311 MspI/HpaII sites across all three chromosomes that displayed tissue‐specific differential CpG methylation patterns. To maximize the probability of identifying biomarkers that have clinical utility we filtered our data to identify MspI/HpaII sites that are within 150 bp of a highly polymorphic single nucleotide polymorphism (SNP) so that its allelic ratio may be determined for the detection of fetal aneuploidy. Our microarray design and the computational tools used for data analysis are available for download as is the entire data set.
Conclusions
This high‐resolution analysis of DNA methylation patterns in the human placenta during the first trimester of pregnancy identifies numerous potential biomarkers for the diagnosis of fetal aneuploidy on chromosomes 13, 18 and 21. Copyright © 2009 John Wiley & Sons, Ltd.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>19650061</pmid><doi>10.1002/pd.2335</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Aneuploidy Biological and medical sciences biomarkers Biomarkers - metabolism Blood cells Case-Control Studies Chorionic Villi Sampling chromosome 13 Chromosomes Chromosomes, Human, Pair 13 Chromosomes, Human, Pair 18 Chromosomes, Human, Pair 21 Computer applications CpG islands Data processing Delivery. Postpartum. Lactation DNA DNA Methylation Epigenesis, Genetic - genetics epigenetics Female fetal Fetal Diseases - diagnosis Fetal Diseases - genetics Fetuses Fundamental and applied biological sciences. Psychology Gene Expression Profiling Genetics of eukaryotes. Biological and molecular evolution Gynecology. Andrology. Obstetrics High-Throughput Screening Assays - methods Humans Medical sciences Models, Biological Molecular and cellular biology Oligonucleotide Array Sequence Analysis - methods Oligonucleotides Placenta plasma Pregnancy Prenatal diagnosis Prenatal Diagnosis - methods Single-nucleotide polymorphism Statistics Villus |
| title | A microarray-based approach for the identification of epigenetic biomarkers for the noninvasive diagnosis of fetal disease |
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