Cambridge, U.K. and Foster City, CA. (OBBeC) – Researchers from The Wellcome Trust Sanger Institute and Applied Biosystems are working together to investigate the genetic underpinnings of cancer in the human genome.

The researchers are sequencing a cancer genome and normal DNA from the same individual to comprehensively detect and characterize the genetic changes that occur during the development of the disease.

The purpose of this research is to provide the highest resolution picture to date of genetic variation in the development of cancer. Preliminary scientific findings resulting from this collaboration will be presented at the Cold Spring Harbor Laboratory’s Biology of Genomes meeting in New York from May 6 – 10.

In this collaboration, scientists will use five Applied Biosystems SOLiD Systems in an effort to sequence the genomes of a small cell lung cancer cell line, and a non-cancerous cell line and comprehensively cover all of the genomic variations in both cell lines.

This project is expected to advance research recently carried out by The Sanger Institute’s Cancer Genome Project that examined low coverage of structural variation in cancerous and normal cell lines. Structural variants consist of gene copy-number variations, single-base duplications, inversions, translocations, insertions and deletions. In this project, by surveying both single-base changes – SNPs (single nucleotide polymorphisms) – and larger segments of genomic rearrangements, or structural variations, researchers expect to obtain more in-depth coverage of all types of genetic variation that contribute to cancer.

According to the announcement, the research will advance cancer research already accomplished as part of The Sanger Institute’s Cancer Genome Project. In that study, researchers found that the number of driver mutations – those that drive the development of cancer – is greater than previously thought, suggesting that many more genes contribute to cancer development. Researchers believe that the use of highly accurate, ultra-high throughput genomic analysis technologies will now help them to more thoroughly investigate how these mutations, including SNPs and structural variants, contribute to the development of cancer.

The use of genomic analysis sequencing technologies for cancer research could make possible the complete survey of cancer genomes within individuals. Scientists at The Sanger Institute have been using SOLiD Systems to employ a DNA sequencing technique known as deep-shotgun resequencing to obtain DNA sequence information of both cancerous and normal genomes from the same individual. Deep shotgun resequencing refers to the sequencing of an entire genome using very large numbers of small DNA fragments, such that every base is likely to be covered many times.

In this collaboration, scientists from both organizations plan to increase sequence coverage of both genomes by identifying one SNP for every 500,000 bases of DNA. They anticipate that such low frequency SNP detection will be made possible by the SOLiD System’s high accuracy, which includes 2-base encoding. The platform’s 2-base encoding chemistry discriminates random or systematic errors from true SNPs to reveal SNPs with greater than 99.94 percent sequencing accuracy.

One of the goals of this research is to generate 20-fold genome coverage of the cancer genome and 20-fold genome coverage of normal DNA using paired-end reads of a wide range of insert sizes, making use of the SOLiD System’s ability to analyze insert sizes of up to 10,000 base pairs from both cancer and normal DNA. Insert sizes are pairs of sequences separated by a known distance between them.

The scientists will use mate-pair analysis on the SOLiD System, a crucial technique which enables highly accurate sequence assembly and the detection of a comprehensive range of sequence variation. Scientists at The Sanger Institute have been using multiple mate-pair insert sizes ranging from 400 base pairs to 3,500 base pairs to help create a catalog of mutations in an individual cancer. This portrait of genetic variation will offer researchers the ability to lay the groundwork for a complete cataloging of the events that are required for the generation of individual cancers.
“The Wellcome Trust Sanger Institute Cancer Genome Project is dedicated to implementing sophisticated genomic analysis technologies in the study of somatic changes in cancer genomes,” said Professor Mike Stratton, co-leader of The Sanger Institute’s Cancer Genome Project. “We anticipate that the SOLiD System’s high-throughput capabilities will allow us to cost-effectively reduce the number of runs needed to achieve the 20-fold coverage we are seeking, and will enable us to identify and recognize single nucleotide polymorphisms and rearrangements more accurately.”

The SOLiD System is an end-to-end next-generation genomic 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 utilizes 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.

The SOLiD System can be scaled to support a higher density of sequence per slide through bead enrichment. Beads are an integral part of the SOLiD System’s open-slide format architecture, which enables the system to generate greater than 6 gigabases of sequence data per run. Moreover, the SOLiD System has demonstrated runs greater than 10 gigabases per run at customer locations. The combination of the open-slide format, bead enrichment, and software algorithms provide the infrastructure for allowing it to scale to even higher throughput, without significant changes to the platform’s current hardware or software.