The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants
Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-06-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00133/full |
| _version_ | 1818847904015581184 |
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| author | Fabio eMarroni Sara ePinosio Sara ePinosio Michele eMorgante |
| author_facet | Fabio eMarroni Sara ePinosio Sara ePinosio Michele eMorgante |
| author_sort | Fabio eMarroni |
| collection | DOAJ |
| description | Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, only three research groups working in plant sciences have exploited this potentiality. They showed that pooled NGS can provide results in excellent agreement with those obtained by individual Sanger sequencing. Aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method we will explain in detail the variations in study design and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled next generation sequencing can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity and Tajima’s D. Finally we will discuss applications and future perspectives of the multiplexed NGS approach. |
| first_indexed | 2024-12-19T06:08:51Z |
| format | Article |
| id | doaj.art-152c69ecf97c418c81b7411070eab36b |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-19T06:08:51Z |
| publishDate | 2012-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-152c69ecf97c418c81b7411070eab36b2022-12-21T20:33:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2012-06-01310.3389/fpls.2012.0013325116The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in PlantsFabio eMarroni0Sara ePinosio1Sara ePinosio2Michele eMorgante3Istituto di Genomica ApplicataIstituto di Genomica ApplicataCNRIstituto di Genomica ApplicataNext generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, only three research groups working in plant sciences have exploited this potentiality. They showed that pooled NGS can provide results in excellent agreement with those obtained by individual Sanger sequencing. Aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method we will explain in detail the variations in study design and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled next generation sequencing can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity and Tajima’s D. Finally we will discuss applications and future perspectives of the multiplexed NGS approach.http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00133/fullPlantspoolnext generation sequencingDNA polymeraserare variantsBarcode |
| spellingShingle | Fabio eMarroni Sara ePinosio Sara ePinosio Michele eMorgante The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants Frontiers in Plant Science Plants pool next generation sequencing DNA polymerase rare variants Barcode |
| title | The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants |
| title_full | The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants |
| title_fullStr | The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants |
| title_full_unstemmed | The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants |
| title_short | The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants |
| title_sort | quest for rare variants pooled multiplexed next generation sequencing in plants |
| topic | Plants pool next generation sequencing DNA polymerase rare variants Barcode |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2012.00133/full |
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