CRoPS®
SNP Discovery
KeyGene offers a variety of techniques for the discovery and validation of Single Nucleotide Polymorphisms (SNPs):
- Re-sequencing of genomic DNA (CRoPS)
- Re-sequencing of EST sequences
- Single Feature Polymorphism (SFP) analysis - hybridization of genomic DNA on gene expression chips
- AFLP® – fingerprinting
How it works
Complexity Reduction of Polymorphic Sequences (CRoPS)
The CRoPS technology combines the power of AFLP® as a robust genome complexity reduction method with the power of new sequencing technologies, like the 454 Life Sciences technology highly parallel sequence analysis of DNA fragments.
- A discovery set of individuals/lines/species is selected and their DNA isolated.
- AFLP fragments are prepared according to the KeyGene AFLP protocol and extended with a 4 bp TAG sequence.
- These DNA fragments are then subjected to the Roche GS FLX Titanium protocol for emulsion PCR and sequence library preparation (see diagram).
Next the fragments are sequenced on the GS FLX Titanium sequencing instrument. One GS FLX Titanium run generates at least 400 Mb of sequence information, resulting in thousands of putative polymorphisms (SNPs, indels and SSRs) of which hundreds will be validated using SNP or SSR detection technologies (standard >80% conversion rates).
Benefits
- Sequence-based strategy to generate a large number of high-quality putative SNP’s in a short time frame;
- a high percentage of the putative SNP’s can be converted to SNP assays;
- automated pipeline for Illumina assay design available;
- CRoPS can be applied on between two and eight samples (strains, varieties, etc.) of an organism;
- sample choice will be determined in consultation with the customer;
- resulting sequence assemblies and putative polymorphic sequences are delivered within a two month period.
Deliverables
- List of putative polymorphisms (SNPs, SSRs, Indels) on CD/DVD;
- data sheet with sequence alignments;
- project report.