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Open Access Research article

Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method

Ye Du1, Hui Jiang1, Ying Chen1, Cong Li12, Meiru Zhao1, Jinghua Wu1, Yong Qiu1, Qibin Li1 and Xiuqing Zhang1*

Author Affiliations

1 BGI_shenzhen, Shenzhen 518000, China

2 Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, 430071, China

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BMC Genomics 2012, 13:77  doi:10.1186/1471-2164-13-77

Published: 16 February 2012

Abstract

Background

Restriction Enzyme-based Reduced Representation Library (RRL) method represents a relatively feasible and flexible strategy used for Single Nucleotide Polymorphism (SNP) identification in different species. It has remarkable advantage of reducing the complexity of the genome by orders of magnitude. However, comprehensive evaluation for actual efficacy of SNP identification by this method is still unavailable.

Results

In order to evaluate the efficacy of Restriction Enzyme-based RRL method, we selected Tsp 45I enzyme which covers 266 Mb flanking region of the enzyme recognition site according to in silico simulation on human reference genome, then we sequenced YH RRL after Tsp 45I treatment and obtained reads of which 80.8% were mapped to target region with an 20-fold average coverage, about 96.8% of target region was covered by at least one read and 257 K SNPs were identified in the region using SOAPsnp software.

Compared with whole genome resequencing data, we observed false discovery rate (FDR) of 13.95% and false negative rate (FNR) of 25.90%. The concordance rate of homozygote loci was over 99.8%, but that of heterozygote were only 92.56%. Repeat sequences and bases quality were proved to have a great effect on the accuracy of SNP calling, SNPs in recognition sites contributed evidently to the high FNR and the low concordance rate of heterozygote. Our results indicated that repeat masking and high stringent filter criteria could significantly decrease both FDR and FNR.

Conclusions

This study demonstrates that Restriction Enzyme-based RRL method was effective for SNP identification. The results highlight the important role of bias and the method-derived defects represented in this method and emphasize the special attentions noteworthy.