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Complete Genomics Launches $12K Cancer Genome Sequencing Service

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Complete Genomics this week launched a cancer sequencing service, adding to its existing human whole-genome sequencing service.

The service will address "substantial challenges inherent in sequencing cancer genomes," such as tumor heterogeneity, contamination of tumors with normal tissue, and increased copy number changes.

The company will charge $12,000 for sequencing a tumor/normal sample and $18,000 for a trio, such as a tumor, metastasis, and normal sample from the same individual, according to Jay Kaufman, Complete's vice president of product management.

Kaufman told Clinical Sequencing News at the American Society of Human Genetics annual meeting this week that going forward, the company expects a significant number of its customers to come from translational medicine.

For the new service, Complete has made improvements to its algorithms for calling structural variations, copy number variants, and gene fusions. It has developed an analysis pipeline that can handle aneuploidy and accounts for the fact that alleles in tumors are not always present at a 50/50 ratio. Customers will also be able to specify the stringency with which variants are called.

Complete reports somatic and germline variants, including SNPs, insertions, deletions, structural variations, copy number changes, and mobile element insertions. It also annotates theses variants functionally.

Each sample will be sequenced to a minimum depth of 80X — twice the company's standard coverage of 40X — in order to be able to detect rare variants.

Company representatives did not say what the lower detection limit for rare variants will be, but CSO Rade Drmanac said the service would be able to detect at least 95 percent of alleles present at a frequency of 30 percent.

Already, Complete has sequenced more than 650 tumor-normal pairs, according to CEO Cliff Reid, and has orders for more. Cancer sequencing projects are for basic, translational, and clinical research, with customers from pharmaceutical and biotechnology companies.

By the end of the month, the company plans to release sequence data for two tumor-normal pairs — well-characterized cell lines from the American Type Culture Collection that are derived from breast cancer patients.

It will also release an update of the 69 genomes it released earlier this year, generated with the new analysis pipeline.

With the launch of the cancer sequencing service, the firm is also updating its Complete Genomics Analysis Tools, a suite of open-source software that includes multigenome comparison tools.

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