CRISP

CRISP identifies rare and common single nucleotide polymorphisms (SNPs) from pooled next-generation sequencing datasets to enable accurate variant discovery across large populations.

Key Features:

• Variant Identification: CRISP detects rare and common single nucleotide polymorphisms (SNPs) from pooled sequencing data.
• Statistical Approach: It compares allele counts across multiple pools using contingency tables and evaluates the probability of observing non-reference base calls to distinguish true variants from sequencing errors.
• Data Integration: The method incorporates distribution of reads between forward and reverse strands and uses pool size information to filter false positives.
• Validation and Performance: Validation on two pooled sequencing datasets generated using the Illumina Genome Analyzer demonstrated detection of 80-85% of SNPs identified by individual sequencing and a false discovery rate of 3-5%.
• Comparative Advantage: Compared with previous pooled SNP detection methods, CRISP exhibits significantly lower false positive and false negative rates.

Scientific Applications:

• Population-scale variant screening: Enables cost-effective analysis of large populations using pooled sequencing.
• Rare variant discovery: Facilitates identification of rare genetic variants for studies of genetic diversity and population genetics.
• Disease association studies: Supports pooled sequencing–based association studies to detect variant-disease correlations.

Methodology:

Computational methods include contingency table analysis to compare allele frequencies across pools; assessment of the probability of sequencing errors underlying observed non-reference base calls; and use of strand-distribution and pool-size information to filter false positives.