The $60,000 genome

Source: Applied Biosystems

Scientists from Applied Biosystems have sequenced a human genome using its next-generation genetic analysis platform for less than $60,000.

The cost of the sequencing project - calculated from the cost of all of the reagents required - is less than the $100,000 milestone set forth by the industry for the new generation of DNA sequencing technologies, the company said.

The sequence data provides a high-resolution, whole-genome view of the structural variants in a human genome, making it one of the most in-depth analyses of any human genome sequence.

Applied Biosystems is making this information available to the scientific community through a public database hosted by the US National Center for Biotechnology Information (NCBI).

Under the direction of Kevin McKernan, Applied Biosystems' senior director of scientific operations, the scientists resequenced a human DNA sample that was included in the International HapMap Project.

The team used the company's SOLiD System to generate 36 gigabases of sequence data in seven runs of the system, achieving throughput up to nine gigabases per run, which is the highest throughput reported by any of the providers of DNA sequencing technology.

The 36 gigabases includes DNA sequence data generated from covering the contents of the human genome more than 12 times, which helped the scientists to determine the precise order of DNA bases and to confidently identify the millions of single-base variations (SNPs) present in a human genome.

The team also analysed the areas of the human genome that contain the structural variation between individuals. These regions of structural variation were revealed by greater than 100-fold physical coverage, which shows positions of larger segments of the genome that may vary relative to the human reference genome.

"We believe this project validates the promise of next-generation sequencing technologies, which is to lower the cost and increase the speed and accuracy of analysing human genomic information," McKernan said.

"With each technological milestone, we are moving closer to realizing the promise of personalised medicine."

McKernan's team used the SOLiD System's ultra-high-throughput capabilities to obtain deep sequence coverage of the genome of an anonymous African male of the Yoruba people of Ibadan, Nigeria, who participated in the International HapMap Project.

The scientists were able to perform an in-depth analysis of structural variants by creating multiple paired-end libraries of genomic sequence that included a wide range of insert sizes. Most inserts exceeded 1000 bases.

The SOLiD System has the ability to analyse paired-end libraries with large insert sizes. For the millions of SNPs identified in the project, the SOLiD System's two-base encoding chemistry discriminated random or systematic errors from true SNPs to reveal these SNPs with greater than 99.94 percent sequencing accuracy.

The SOLiD System is an end-to-end next-generation genetic analysis solution comprised of the sequencing unit, chemistry, a computing cluster and data storage. The platform is based on sequencing by oligonucleotide ligation and detection.

Unlike polymerase sequencing approaches, the SOLiD System utilises a proprietary technology called stepwise ligation, which generates high-quality data for applications including: whole genome sequencing, chromatin immunoprecipitation (ChIP), microbial sequencing, digital karyotyping, medical sequencing, genotyping, gene expression, and small RNA discovery, among others.

Applied Biosystems is also making an analysis tool available through the SOLiD System Software Development Community, which is expected to help independent software providers to interpret the subsets of data.

To access the human sequence data released by Applied Biosystems, please visit the SOLiD Software Development Community at: http://info.appliedbiosystems.com/solidsoftwarecommunity.

The data have also been deposited at the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov), which is part of the National Library of Medicine, National Institutes of Health (Bethesda MD USA).

At NCBI, the human sequence data can be located at ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/SRA000272 or by the project name, SOLiD Human HapMap Sample NA18507 Whole Genome Sequence under accession number SRA000272.