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Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing.

Liu Q, Shen E, Min Q, Li X, Wang X, Li X, Sun ZS, Wu J - BMC Genomics (2012)

Bottom Line: Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits.The identified candidate disease-related genetic variations can be annotated according to their sample features.In summary, by exploring exome sequencing data, Exome-assistant can provide researchers with detailed biological insights into genetic variation events and permits the identification of potential genetic causes of human diseases and related traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China.

ABSTRACT

Background: Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits. Compared with whole-genome sequencing of complex samples, exome sequencing serves as an alternative option because of its dramatically reduced cost. In fact, exome sequencing has been successfully applied to identify the cause of several Mendelian disorders, such as Miller and Schinzel-Giedio syndrome. However, there remain great challenges in handling the huge data generated by exome sequencing and in identifying potential disease-related genetic variations.

Results: In this study, Exome-assistant (http://122.228.158.106/exomeassistant), a convenient tool for submitting and annotating single nucleotide polymorphisms (SNPs) and insertion/deletion variations (InDels), was developed to rapidly detect candidate disease-related genetic variations from exome sequencing projects. Versatile filter criteria are provided by Exome-assistant to meet different users' requirements. Exome-assistant consists of four modules: the single case module, the two cases module, the multiple cases module, and the reanalysis module. The two cases and multiple cases modules allow users to identify sample-specific and common variations. The multiple cases module also supports family-based studies and Mendelian filtering. The identified candidate disease-related genetic variations can be annotated according to their sample features.

Conclusions: In summary, by exploring exome sequencing data, Exome-assistant can provide researchers with detailed biological insights into genetic variation events and permits the identification of potential genetic causes of human diseases and related traits.

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Related in: MedlinePlus

Screenshot of Exome-assistant.
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Figure 2: Screenshot of Exome-assistant.

Mentions: Exome-assistant provides flexible and intuitive windows for convenient analysis and viewing of the results. In addition, all the results, including the input list, intermediate annotation results and the last results can be downloaded in a gzip-compressed format from the results webpage. A typical result of a single case analysis contains three parts for SNPs/InDels: the summary information of input variations, the distribution of variation annotation and the detailed annotation of each variation (Figure‚ÄČ2).


Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing.

Liu Q, Shen E, Min Q, Li X, Wang X, Li X, Sun ZS, Wu J - BMC Genomics (2012)

Screenshot of Exome-assistant.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539923&req=5

Figure 2: Screenshot of Exome-assistant.
Mentions: Exome-assistant provides flexible and intuitive windows for convenient analysis and viewing of the results. In addition, all the results, including the input list, intermediate annotation results and the last results can be downloaded in a gzip-compressed format from the results webpage. A typical result of a single case analysis contains three parts for SNPs/InDels: the summary information of input variations, the distribution of variation annotation and the detailed annotation of each variation (Figure‚ÄČ2).

Bottom Line: Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits.The identified candidate disease-related genetic variations can be annotated according to their sample features.In summary, by exploring exome sequencing data, Exome-assistant can provide researchers with detailed biological insights into genetic variation events and permits the identification of potential genetic causes of human diseases and related traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou 325035, China.

ABSTRACT

Background: Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits. Compared with whole-genome sequencing of complex samples, exome sequencing serves as an alternative option because of its dramatically reduced cost. In fact, exome sequencing has been successfully applied to identify the cause of several Mendelian disorders, such as Miller and Schinzel-Giedio syndrome. However, there remain great challenges in handling the huge data generated by exome sequencing and in identifying potential disease-related genetic variations.

Results: In this study, Exome-assistant (http://122.228.158.106/exomeassistant), a convenient tool for submitting and annotating single nucleotide polymorphisms (SNPs) and insertion/deletion variations (InDels), was developed to rapidly detect candidate disease-related genetic variations from exome sequencing projects. Versatile filter criteria are provided by Exome-assistant to meet different users' requirements. Exome-assistant consists of four modules: the single case module, the two cases module, the multiple cases module, and the reanalysis module. The two cases and multiple cases modules allow users to identify sample-specific and common variations. The multiple cases module also supports family-based studies and Mendelian filtering. The identified candidate disease-related genetic variations can be annotated according to their sample features.

Conclusions: In summary, by exploring exome sequencing data, Exome-assistant can provide researchers with detailed biological insights into genetic variation events and permits the identification of potential genetic causes of human diseases and related traits.

Show MeSH
Related in: MedlinePlus