| Tiling Array Probes (2008) | |||||||||||||
Abstract | |||||||||||||
| In this report we describe a rapid and cost effective comparative genomic strategy for mapping and identify single nucleotide polymorphisms, deletions and amplification across entire microbial genomes. The technique, called comparative genomic resequencing (CGR), is a two-step procedure that utilizes high-density oligonucleotide arrays to map the location of mutations, and then employs custom arrays to resequence these mapped mutations. Here we demonstrate the technique on the genome of the live attenuated typhoid vaccine, Salmonella enterica Ty21a. Four arrays were designed to tile 29mer probes every 7 base pairs across both strands of the sequenced S. enterica Ty2 reference genome. This array set was used in a comparative genomic hybridization strategy to fine-map mutations to within one probe length (29 nucleotides). A second custom two-array set was specifically designed to resequence across the putative mapped mutations, identifying the sequence. 511 single nucleotide polymorphisms were mapped and identified across the genome using only 10 microarrays. The CGR strategy was compared with traditional array-based resequencing (ABR), requiring 101 arrays to span the entire genome. The CGR approach resulted in a significantly higher accuracy than ABR, (99.9998 % for CGR vs. 99.998 % for ABR), identified 97 % of the total SNPs discovered in the sample, and required less than 10 % of microarrays needed for ABR (6 per strain for CGR vs. 101 for resequencing). | |||||||||||||
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