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Mountain View, CA, United States

Complete Genomics is a life sciences company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis. This solution combines the company’s proprietary human genome sequencing technology with its informatics and data management software to provide finished variant reports and assemblies at Complete Genomics’ own commercial genome center in Mountain View, California. In March 2013 Complete Genomics was acquired by BGI-Shenzhen, the world’s largest genomics services company. BGI is a 4,000-person company headquartered in Shenzhen, China, that provides comprehensive sequencing and bioinformatics services for commercial science, medical, agricultural, and environmental applications. Wikipedia.

Drmanac R.,Complete Genomics
Science | Year: 2012

Individual whole-genome sequencing has the potential to greatly improve disease prevention, diagnosis, and treatment.

Tian C.,Perlegen Sciences | Stokowski R.P.,Perlegen Sciences | Kershenobich D.,National Autonomous University of Mexico | Ballinger D.G.,Perlegen Sciences | And 2 more authors.
Nature Genetics | Year: 2010

Two genome-wide association studies (GWAS) have described associations of variants in PNPLA3 with nonalcoholic fatty liver and plasma liver enzyme levels. We investigated the contributions of these variants to liver disease in Mestizo subjects with a history of alcohol dependence. We found that rs738409 in PNPLA3 is strongly associated with alcoholic liver disease and clinically evident alcoholic cirrhosis (unadjusted OR= 2.25, P=1.7 × 10-10 ancestry-adjusted OR=1.79, P=1.9 × 10 -5). © 2010 Nature America, Inc. All rights reserved.

Drmanac R.,Complete Genomics
Genetics in Medicine | Year: 2011

Rapid technological advances are decreasing DNA sequencing costs and making it practical to undertake complete human genome sequencing on a large scale for the first time. Disease studies that involve sequencing hundreds of patient genomes are underway. The all-inclusive sequencing price per genome is expected to reach $1000 over the next few years and will likely decline further in the following years. This dramatic price decline will herald widespread personal genome sequencing and lead to significant improvements in human health and reduced health care costs. Key to realizing these benefits will be medical genomics' and systems biology's success in providing increasing contextual interpretation of biological and medical effects of the detected sequence variants in a genome. Given the substantial potential benefits and the manageability of the health and discrimination risks involved with the possible misuse of this information, we propose that governments and insurance companies support or even require personal genome sequencing. Critical to the widespread acceptance of personal genome sequencing, however, will be the need to educate physicians and the public about the realistic benefits and risks of such an analysis to prevent overinterpretation and misuse of this valuable information. © 2011 Lippincott Williams & Wilkins.

Complete Genomics | Date: 2014-12-15

Methods, systems, and apparatuses are provided for creating and using a machine-leaning model to call a base at a position of a nucleic acid based on intensity values measured during a production sequencing run. The model can be trained using training data from training sequencing runs performed earlier. The model is trained using intensity values and assumed sequences that are determined as the correct output. The training data can be filtered to improve accuracy. The training data can be selected in a specific manner to be representative of the type of organism to be sequenced. The model can be trained to use intensity signals from multiple cycles and from neighboring nucleic acids to improve accuracy in the base calls.

Complete Genomics | Date: 2014-10-01

Long fragment read techniques can be used to identify deletions and resolve base calls by utilizing shared labels (e.g., shared aliquots) of a read with any reads corresponding to heterozygous loci (hets) of a haplotype. For example, the linking of a locus to a haplotype of multiple hets can increase the reads available at the locus for determining a base call for a particular haplotype. For a hemizygous deletion, a region can be linked to one or more hets, and the labels for a particular haplotype can be used to identify which reads in the region correspond to which haplotype. In this manner, since the reads for a particular haplotype can be identified, a hemizygous deletion can be determined. Further, a phasing rate of pulses can be used to identify large deletions. A deletion can be identified with the phasing rate is sufficiently low, and other criteria can be used.

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