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Targeted interrogation of copy number variation using SCIMMkit
Troy Zerr1, Gregory M Cooper, Evan E Eichler
1Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. troyz@u.washington.edu
Bioinformatics (Oxford, England)
|October 23, 2009
Summary
SCIMMkit offers a robust solution for copy number variant (CNV) genotyping using SNP assays. This tool enhances the study of human genomic diversity and genotype-phenotype associations.
Area of Science:
- Genomics
- Human Genetics
Background:
- Copy number variants (CNVs) are significant contributors to human genomic diversity.
- Accurate and efficient CNV genotyping is crucial for understanding genotype-phenotype relationships.
Purpose of the Study:
- To introduce SCIMMkit, an integrated software package for CNV genotyping.
- To provide a robust implementation of validated algorithms for targeted CNV analysis.
Main Methods:
- SCIMMkit integrates three algorithms: SCIMM (SNP-Conditional Mixture Modeling), SCIMM-Search, and SCOUT (SNP-Conditional OUTlier detection).
- The tool is designed for use with Illumina Infinium II and GoldenGate SNP assays.
- Applicable to both standardized genome-wide SNP arrays and customized multiplexed SNP panels.
Main Results:
- SCIMMkit offers a flexible and efficient approach to CNV genotyping.
- The software provides accurate interrogation of CNVs.
Conclusions:
- SCIMMkit facilitates the exploration of human genotype-phenotype associations by enabling accurate CNV genotyping.
- The tool offers economy, efficiency, and flexibility in experimental design for genomic studies.
