Accurate and reliable high-throughput detection of copy number variation in the human genome
This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in...
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| Veröffentlicht in: | Genome Research 2006-12, Vol.16 (12), p.1566-1574 |
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| creator | Fiegler, Heike Redon, Richard Andrews, Dan Scott, Carol Andrews, Robert Carder, Carol Clark, Richard Dovey, Oliver Ellis, Peter Feuk, Lars French, Lisa Hunt, Paul Kalaitzopoulos, Dimitrios Larkin, James Montgomery, Lyndal Perry, George H Plumb, Bob W Porter, Keith Rigby, Rachel E Rigler, Diane Valsesia, Armand Langford, Cordelia Humphray, Sean J Scherer, Stephen W Lee, Charles Hurles, Matthew E Carter, Nigel P |
| description | This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method. |
| doi_str_mv | 10.1101/gr.5630906 |
| format | Article |
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We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.</description><identifier>ISSN: 1088-9051</identifier><identifier>EISSN: 1549-5477</identifier><identifier>DOI: 10.1101/gr.5630906</identifier><identifier>PMID: 17122085</identifier><language>eng</language><publisher>United States: Cold Spring Harbor Laboratory Press</publisher><subject>Algorithms ; Chromosome Mapping ; DNA - genetics ; DNA Fingerprinting ; Euchromatin - chemistry ; False Negative Reactions ; False Positive Reactions ; Gene Dosage ; Gene Expression Profiling ; Genetic Variation ; Genome, Human ; Humans ; Methods ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Reproducibility of Results</subject><ispartof>Genome Research, 2006-12, Vol.16 (12), p.1566-1574</ispartof><rights>Copyright © 2006, Cold Spring Harbor Laboratory Press 2006</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c376t-45f399dc3eeb6150e2b3ca452de8f68ecef286af714fe00e06e83b17045cc5943</citedby><cites>FETCH-LOGICAL-c376t-45f399dc3eeb6150e2b3ca452de8f68ecef286af714fe00e06e83b17045cc5943</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/PMC1665640/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665640/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17122085$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fiegler, Heike</creatorcontrib><creatorcontrib>Redon, Richard</creatorcontrib><creatorcontrib>Andrews, Dan</creatorcontrib><creatorcontrib>Scott, Carol</creatorcontrib><creatorcontrib>Andrews, Robert</creatorcontrib><creatorcontrib>Carder, Carol</creatorcontrib><creatorcontrib>Clark, Richard</creatorcontrib><creatorcontrib>Dovey, Oliver</creatorcontrib><creatorcontrib>Ellis, Peter</creatorcontrib><creatorcontrib>Feuk, Lars</creatorcontrib><creatorcontrib>French, Lisa</creatorcontrib><creatorcontrib>Hunt, Paul</creatorcontrib><creatorcontrib>Kalaitzopoulos, Dimitrios</creatorcontrib><creatorcontrib>Larkin, James</creatorcontrib><creatorcontrib>Montgomery, Lyndal</creatorcontrib><creatorcontrib>Perry, George H</creatorcontrib><creatorcontrib>Plumb, Bob W</creatorcontrib><creatorcontrib>Porter, Keith</creatorcontrib><creatorcontrib>Rigby, Rachel E</creatorcontrib><creatorcontrib>Rigler, Diane</creatorcontrib><creatorcontrib>Valsesia, Armand</creatorcontrib><creatorcontrib>Langford, Cordelia</creatorcontrib><creatorcontrib>Humphray, Sean J</creatorcontrib><creatorcontrib>Scherer, Stephen W</creatorcontrib><creatorcontrib>Lee, Charles</creatorcontrib><creatorcontrib>Hurles, Matthew E</creatorcontrib><creatorcontrib>Carter, Nigel P</creatorcontrib><title>Accurate and reliable high-throughput detection of copy number variation in the human genome</title><title>Genome Research</title><addtitle>Genome Res</addtitle><description>This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. 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Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.</description><subject>Algorithms</subject><subject>Chromosome Mapping</subject><subject>DNA - genetics</subject><subject>DNA Fingerprinting</subject><subject>Euchromatin - chemistry</subject><subject>False Negative Reactions</subject><subject>False Positive Reactions</subject><subject>Gene Dosage</subject><subject>Gene Expression Profiling</subject><subject>Genetic Variation</subject><subject>Genome, Human</subject><subject>Humans</subject><subject>Methods</subject><subject>Nucleic Acid Hybridization</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Reproducibility of Results</subject><issn>1088-9051</issn><issn>1549-5477</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkc1O3TAQhS3UCuiFTR8AedUFUug4_omzQUII2kpX6gZ2SJbjTBJXiX3rOEi8PQGuKF3NSOebM6M5hHxlcMEYsO99upCKQw3qgBwzKepCiqr6tPagdVGDZEfkyzz_AQAutD4kR6xiZQlaHpOHK-eWZDNSG1qacPS2GZEOvh-KPKS49MNuybTFjC77GGjsqIu7JxqWqcFEH23y9lXwgeZhnVwmG2iPIU54Qj53dpzxdF835P725u76Z7H9_ePX9dW2cLxSuRCy43XdOo7YKCYBy4Y7K2TZou6URoddqZXtKiY6BEBQqHnDKhDSOVkLviGXb767pZmwdRhysqPZJT_Z9GSi9eZ_JfjB9PHRMKWkErAafNsbpPh3wTmbyc8Ox9EGjMtslC6hrrRawfM30KU4zwm79yUMzEsYpk9mH8YKn3086x-6_z5_BjfAh3A</recordid><startdate>200612</startdate><enddate>200612</enddate><creator>Fiegler, Heike</creator><creator>Redon, Richard</creator><creator>Andrews, Dan</creator><creator>Scott, Carol</creator><creator>Andrews, Robert</creator><creator>Carder, Carol</creator><creator>Clark, Richard</creator><creator>Dovey, Oliver</creator><creator>Ellis, Peter</creator><creator>Feuk, Lars</creator><creator>French, Lisa</creator><creator>Hunt, Paul</creator><creator>Kalaitzopoulos, Dimitrios</creator><creator>Larkin, James</creator><creator>Montgomery, Lyndal</creator><creator>Perry, George H</creator><creator>Plumb, Bob W</creator><creator>Porter, Keith</creator><creator>Rigby, Rachel E</creator><creator>Rigler, Diane</creator><creator>Valsesia, Armand</creator><creator>Langford, Cordelia</creator><creator>Humphray, Sean J</creator><creator>Scherer, Stephen W</creator><creator>Lee, Charles</creator><creator>Hurles, Matthew E</creator><creator>Carter, Nigel P</creator><general>Cold Spring Harbor Laboratory Press</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>7X8</scope><scope>5PM</scope></search><sort><creationdate>200612</creationdate><title>Accurate and reliable high-throughput detection of copy number variation in the human genome</title><author>Fiegler, Heike ; 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We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. 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| ispartof | Genome Research, 2006-12, Vol.16 (12), p.1566-1574 |
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| subjects | Algorithms Chromosome Mapping DNA - genetics DNA Fingerprinting Euchromatin - chemistry False Negative Reactions False Positive Reactions Gene Dosage Gene Expression Profiling Genetic Variation Genome, Human Humans Methods Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Reproducibility of Results |
| title | Accurate and reliable high-throughput detection of copy number variation in the human genome |
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