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Meander: visually exploring the structural variome using space-filling curves.

Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J - Nucleic Acids Res. (2013)

Bottom Line: An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases.With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference.The application was developed using Java version 1.6 and Processing.org and can be run on any platform.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering (ESAT/SCD), University of Leuven, Kasteelpark Arenberg 10, Box 2446, 3001 Leuven, Belgium. g.pavlopoulos@med.uoc.gr

ABSTRACT
The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander.

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Comparison of chromosome 1 between strain ICE153 from central Asia and strain ICE97 from southern Italy. (A) An example of a deletion and a tandem duplication supported by both pair-end and read-depth information. (B) The advantage of the Hilbert representation. Left: A tandem duplication that is not visible in the linear representation (1 pixel length) but very clear in the Hilbert representation as a bigger block. Right: The same tandem duplication at zoom level 5 supported both by read-depth and pair-end evidence.
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gkt254-F3: Comparison of chromosome 1 between strain ICE153 from central Asia and strain ICE97 from southern Italy. (A) An example of a deletion and a tandem duplication supported by both pair-end and read-depth information. (B) The advantage of the Hilbert representation. Left: A tandem duplication that is not visible in the linear representation (1 pixel length) but very clear in the Hilbert representation as a bigger block. Right: The same tandem duplication at zoom level 5 supported both by read-depth and pair-end evidence.

Mentions: Meander supports visualization of SVs based both on read-pair and pair-end data. In the linear representation, the bar height indicates the value of the log2(sample/reference) ratio. Negative ratios (red pixels) indicate possible deletions in the sample, whereas positive ratios (blue pixels) indicate possible duplications. Aberrantly, mapped pair-end data can indicate the presence of balanced as well as unbalanced variations. Meander, therefore, also links these together, both in the Hilbert and the linear views. Because the Hilbert curve only displays a single chromosome at a time, these links cannot be shown in cases where the partners of a paired-end lie on different chromosomes. To solve this issue, the whole genome split in chromosomes is schematically represented as a rectangle, wrapped around the main Hilbert plot, (see left part of Figure 3B), to allow direct linking between the position of the one paired end that corresponds to the loaded chromosome and the other paired end that corresponds to another chromosome of the same organism.Figure 3.


Meander: visually exploring the structural variome using space-filling curves.

Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, Voet T, Moreau Y, Aerts J - Nucleic Acids Res. (2013)

Comparison of chromosome 1 between strain ICE153 from central Asia and strain ICE97 from southern Italy. (A) An example of a deletion and a tandem duplication supported by both pair-end and read-depth information. (B) The advantage of the Hilbert representation. Left: A tandem duplication that is not visible in the linear representation (1 pixel length) but very clear in the Hilbert representation as a bigger block. Right: The same tandem duplication at zoom level 5 supported both by read-depth and pair-end evidence.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3675473&req=5

gkt254-F3: Comparison of chromosome 1 between strain ICE153 from central Asia and strain ICE97 from southern Italy. (A) An example of a deletion and a tandem duplication supported by both pair-end and read-depth information. (B) The advantage of the Hilbert representation. Left: A tandem duplication that is not visible in the linear representation (1 pixel length) but very clear in the Hilbert representation as a bigger block. Right: The same tandem duplication at zoom level 5 supported both by read-depth and pair-end evidence.
Mentions: Meander supports visualization of SVs based both on read-pair and pair-end data. In the linear representation, the bar height indicates the value of the log2(sample/reference) ratio. Negative ratios (red pixels) indicate possible deletions in the sample, whereas positive ratios (blue pixels) indicate possible duplications. Aberrantly, mapped pair-end data can indicate the presence of balanced as well as unbalanced variations. Meander, therefore, also links these together, both in the Hilbert and the linear views. Because the Hilbert curve only displays a single chromosome at a time, these links cannot be shown in cases where the partners of a paired-end lie on different chromosomes. To solve this issue, the whole genome split in chromosomes is schematically represented as a rectangle, wrapped around the main Hilbert plot, (see left part of Figure 3B), to allow direct linking between the position of the one paired end that corresponds to the loaded chromosome and the other paired end that corresponds to another chromosome of the same organism.Figure 3.

Bottom Line: An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases.With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference.The application was developed using Java version 1.6 and Processing.org and can be run on any platform.

View Article: PubMed Central - PubMed

Affiliation: Department of Electrical Engineering (ESAT/SCD), University of Leuven, Kasteelpark Arenberg 10, Box 2446, 3001 Leuven, Belgium. g.pavlopoulos@med.uoc.gr

ABSTRACT
The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander.

Show MeSH
Related in: MedlinePlus