Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification : Proof of Concept
Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technolog...
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| Veröffentlicht in: | BioMed research international 2012-01, Vol.2012 (2012), p.1-7 |
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| description | Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs) from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety-six SNP loci, spanning the length of A. hypochondriacus linkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC). Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. Utilization of the Fluidigm Dynamic array platform allowed for the simultaneous PCR screening of 10,752 BAC pools for 96 SNP tag sites in less than three hours at a cost of ~$0.05 per reaction. |
| doi_str_mv | 10.1155/2012/405940 |
| format | Article |
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Ilyas</contributor><creatorcontrib>Maughan, Peter J. ; Smith, Scott M. ; Raney, Joshua A. ; Kamboh, M. Ilyas</creatorcontrib><description>Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs) from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety-six SNP loci, spanning the length of A. hypochondriacus linkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC). Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. 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Maughan et al.</rights><rights>Copyright © 2012 Peter J. Maughan et al. Peter J. Maughan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</rights><rights>Copyright © 2012 Peter J. Maughan et al. 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-8dc905c44d38cb295dcb269c1c318f31f2a12534a2d5585c870cc591147dda283</citedby><cites>FETCH-LOGICAL-c499t-8dc905c44d38cb295dcb269c1c318f31f2a12534a2d5585c870cc591147dda283</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/PMC3403795/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403795/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22910714$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kamboh, M. 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Ilyas</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification : Proof of Concept</atitle><jtitle>BioMed research international</jtitle><addtitle>J Biomed Biotechnol</addtitle><date>2012-01-01</date><risdate>2012</risdate><volume>2012</volume><issue>2012</issue><spage>1</spage><epage>7</epage><pages>1-7</pages><issn>1110-7243</issn><issn>2314-6133</issn><eissn>1110-7251</eissn><eissn>2314-6141</eissn><abstract>Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. 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| subjects | Amaranthus - genetics Amaranthus hypochondriacus Artificial chromosomes Biomedical research Chromosomes, Artificial, Bacterial - genetics Cloning Cloning, Molecular Deoxyribonucleic acid DNA Genetic Linkage Genetic Markers Genetic Testing Genetics Genomes Genomics Genotyping Techniques - methods High-Throughput Nucleotide Sequencing - methods Methodology Report Polymerase Chain Reaction Polymorphism, Single Nucleotide - genetics Reproducibility of Results Sequence Analysis, DNA |
| title | Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification : Proof of Concept |
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