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Data released on December 17, 2014

Supporting material for: "Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology".

Anantharaman, T; Andrews, W; Cao, D; Cao, H; Cao, H; Chan, S; Hastie, A, R; Huang, H; Huang, S; Krogh, A; Lam, E, T; Lin, L; Liu, X; Requa, M; Sun, Y; Tong, X; Xu, X; Yang, H (2014): Supporting material for: "Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology". GigaScience Database. http://dx.doi.org/10.5524/100097 RIS BibTeX Text

The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, automatically images fluorescently labeled DNA molecules in a massively parallel nanochannel array. This technology has previously been used to map the 4.7-Mb highly variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the highly complex Aegilops tauschii genome, lending great promise for use in complete genome sequence analysis.
Here, we apply this rapid and high-throughput genome mapping method to discern genome wide structural variations (SVs) as well as explore complex regions based on the YH (first Asian genome) cell line.
A structural variant (SV) is generally defined as a region of DNA 1 kb and larger in size that is changed with respect to another sample; examples include inversions, translocations, deletions, duplications and insertions. Deletions and duplications are also referred to as copy number variants (CNVs). Structural variants (SVs) are less common than single nucleotide polymorphisms (SNPs) or insertions/deletions (InDels) in the population but collectively account for a significant fraction of genetic polymorphism and diseases.
Utilizing Genome Mapping, we identified 725 SVs including InDels, inversions as well as SVs involved in N-base gap regions that are difficult to assess by current methods. The data presented here are the processed .tiff image files together with the interpreted .metrics file for each restriction map.

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Related manuscripts:

doi:10.1186/2047-217X-3-34

Related datasets:

doi:10.5524/100097 IsSupplementTo doi:10.5524/100038
doi:10.5524/100097 IsSupplementedBy doi:10.5524/100096

Genome-Mapping

http://gigadb.org/images/data/cropped/yh_bionano.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
YH_cell_line9606HumanhumanHomo sapiens
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
ReadmeTEXT7.43 KB2014-05-26
YH_cell_lineTabular dataTEXT422.72 MB2014-10-13
YH_cell_lineDirectoryUNKNOWN536.25 GB2014-10-13
Displaying 1-3 of 3 File(s).

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