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Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling

Fabio Marroni, Sara Pinosio, Eleonara Di Centa, Irena Jurman, Wout Boerjan UGent, Nicoletta Felice, Federica Cattonaro and Michele Morgante (2011) PLANT JOURNAL. 67(4). p.736-745
abstract
Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DISCOVERY, POPULATIONS, CONSERVATION, DNA, LIGNIN BIOSYNTHESIS, DISEASE, SYSTEMS, POPULUS-TRICHOCARPA, SAMPLES, GENES, next-generation sequencing, SNP, rare variants, pooled multiplexed sequencing, lignin biosynthesis, populus nigra
journal title
PLANT JOURNAL
Plant J.
volume
67
issue
4
pages
736 - 745
Web of Science type
Article
Web of Science id
000293753800014
JCR category
PLANT SCIENCES
JCR impact factor
6.16 (2011)
JCR rank
8/189 (2011)
JCR quartile
1 (2011)
ISSN
0960-7412
DOI
10.1111/j.1365-313X.2011.04627.x
project
Biotechnology for a sustainable economy (Bio-Economy)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1893667
handle
http://hdl.handle.net/1854/LU-1893667
date created
2011-08-26 17:02:45
date last changed
2016-12-19 15:41:56
@article{1893667,
  abstract     = {Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.},
  author       = {Marroni, Fabio and Pinosio, Sara and Di Centa, Eleonara and Jurman, Irena and Boerjan, Wout and Felice, Nicoletta and Cattonaro, Federica and Morgante, Michele},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {DISCOVERY,POPULATIONS,CONSERVATION,DNA,LIGNIN BIOSYNTHESIS,DISEASE,SYSTEMS,POPULUS-TRICHOCARPA,SAMPLES,GENES,next-generation sequencing,SNP,rare variants,pooled multiplexed sequencing,lignin biosynthesis,populus nigra},
  language     = {eng},
  number       = {4},
  pages        = {736--745},
  title        = {Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2011.04627.x},
  volume       = {67},
  year         = {2011},
}

Chicago
Marroni, Fabio, Sara Pinosio, Eleonara Di Centa, Irena Jurman, Wout Boerjan, Nicoletta Felice, Federica Cattonaro, and Michele Morgante. 2011. “Large-scale Detection of Rare Variants via Pooled Multiplexed Next-generation Sequencing: Towards Next-generation Ecotilling.” Plant Journal 67 (4): 736–745.
APA
Marroni, F., Pinosio, S., Di Centa, E., Jurman, I., Boerjan, W., Felice, N., Cattonaro, F., et al. (2011). Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling. PLANT JOURNAL, 67(4), 736–745.
Vancouver
1.
Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, et al. Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling. PLANT JOURNAL. 2011;67(4):736–45.
MLA
Marroni, Fabio, Sara Pinosio, Eleonara Di Centa, et al. “Large-scale Detection of Rare Variants via Pooled Multiplexed Next-generation Sequencing: Towards Next-generation Ecotilling.” PLANT JOURNAL 67.4 (2011): 736–745. Print.