Jun 10, 2010

A statistical method for the detection of variants from next-generation resequencing of DNA pools

Bioinformatics
Vikas Bansal

Abstract

Next-generation sequencing technologies have enabled the sequencing of several human genomes in their entirety. However, the routine resequencing of complete genomes remains infeasible. The massive capacity of next-generation sequencers can be harnessed for sequencing specific genomic regions in hundreds to thousands of individuals. Sequencing-based association studies are currently limited by the low level of multiplexing offered by sequencing platforms. Pooled sequencing represents a cost-effective approach for studying rare variants in large populations. To utilize the power of DNA pooling, it is important to accurately identify sequence variants from pooled sequencing data. Detection of rare variants from pooled sequencing represents a different challenge than detection of variants from individual sequencing. We describe a novel statistical approach, CRISP [Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms (SNPs) from Pooled sequencing] that is able to identify both rare and common variants by using two approaches: (i) comparing the distribution of allele counts across multiple pools using contingency tables and (ii) evaluating the probability of observing multiple non-reference base calls du...Continue Reading

  • References24
  • Citations100
  • References24
  • Citations100

Citations

Mentioned in this Paper

Genome
DNA Resequencing
Genomics
Sequencing
Data Interpretation, Statistical
Massively-Parallel Sequencing
Sequence Determinations, DNA
Alleles
Genetic Polymorphism
Single Nucleotide Polymorphism

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