AluScan: a method for genome-wide scanning of sequence variations in the human genome

Background To complement next-generation sequencing technologies, there is pressing need for pre-sequencing capture methods to target genomic regions of interest, thereby reducing costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they can conveniently facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. Results Here we report on the use of multiplex inter-Alu PCR coupled with next-generation sequencing, to obtain an Alu-anchored scan, or ‘AluScan’, of DNA sequences between Alu transposons. The inter-Alu PCR capture approach utilized combinations of Alu consensus sequence-based ‘H-type’ primers that undergo extension outward from the head of an Alu element together with ‘T-type’ primers extending from the poly-A containing tail to amplify intervening sequences between Alu elements genome-wide. To showcase the method, a glioma tissue was compared with white blood cell control of the same patient by AluScan, the resultant over 10 Mb sequences, including that obtained from over 8,000 genes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a genetic variation discovery tool was demonstrated by the finding of 274 somatic SNVs, and seven high-frequency somatic SNV clusters, in the glioma DNA. Conclusions AluScan implemented with just a small number of PCR primers provides an effective method for genome-wide sequence analysis. AluScan enables an examination of gene-rich regions containing exons, introns and intergenic sequences with modest capture and sequencing costs, modest computation workload and submicrogram DNA sample requirement. AluScan is expected to accelerate not only the discovery of somatic mutations, but also the examination of disease-predisposing germline polymorphisms, in which cost-effective genome-wide sequence analysis of large human cohorts is essential.