In a session entitled, “Using DNA Sequence to Detect Variation Related to Human Disease: The Promises and Challenges of Medical Sequencing,” Richard Wilson, Ph.D., professor at Washington University School of Medicine, explored new technologies for medical sequencing and mutation discovery in cancer. He described the disadvantages of traditional technologies: for example, array-based experiments only identify variation in exonic regions, and PCR-based resequencing is expensive.
Dr. Wilson’s group has used Illumina’s next-generation sequencing platform to perform whole genome sequence analysis and to look for disease-linked variability in acute myeloid leukemia. The researchers identified eight validated somatic mutations, all of which were heterozygous, and two somatic insertions/deletions. The group is pursuing similar studies in glioblastoma.
Stacey Gabriel, Ph.D., director of the Genetic Analysis Platform at the Broad Institute, gave conference attendees an overview of the ongoing 1000 Genomes Project and described how GWAS are being used as an unbiased discovery tool for identifying rare mutations that may have value as novel drug targets. Dr. Gabriel’s group developed a scalable process for exome sequencing that uses hybrid selection and capture of hybridized regions on beads to pull out the exonic regions of the genome.
The 1000 Genomes Project will catalog all SNPs and CNVs with an allelic frequency >1% and make them available in a public database. The Project comprises three pilot programs: 4x genomic coverage of 180 people; 20x coverage of three case/parent trios; and 1,000 genes studied in 1,000 different people. One of the main challenges at present is how to integrate the disparate data derived from multiple different technology platforms and the development of hybrid platforms that can perform SNP and CNV genotyping on the same sample.
Richard Gibbs, from Baylor College of Medicine, focused on directed sequencing approaches for exploring disease genomics and described his group’s work using Roche’s NimbleGen’s “rebalanced” arrays to capture targeted regions of the genome and Roche 454’s next-generation sequencing technology. The combination has allowed for greater than 94% coverage of the genome at 10x, according to Dr. Gibbs. He outlined the advantages of using high-density arrays of the exome instead of GWAS for medical sequencing studies: there is less data to manage; the experimental design has greater flexibility; the process is more readily scalable; it is easier to map variants; and the cost is substantially lower.
Richard Lifton from Yale University, commented on the dramatic decrease in the cost of DNA sequencing over the past decade: from $100 per 1,000 high-quality bases in 1998 to less than $0.01 at present, using Illumina’s next-generation sequencing platform as an example.