Posted by: ctraderd | July 11, 2012

Complete Genomics, Inc: A Deeper Look

Introduction:

Complete Genomics, Inc. (GNOM) is the first company in the world to convey whole human genome sequencing and bioinformatics analysis as services. GNOM helps to free researchers from having to buy very expensive sequencing machines and having to operate them, so instead, the researchers can focus on making biological discoveries.

Stock Information:

Complete Genomics, Inc. (GNOM) has a market cap of $72.45 million and is currently trading 20.4% under its 200-day EMA (Exponential Moving Average) however, GNOM is also trading 39.7% above its 50-day EMA. As of March 31, 2012, Complete Genomics held $63.1 million in cash and had a burn rate of $20 million per quarter.

GNOM

On July 11, 2012, GNOM’s stock price opened at 2.03 and at the close of the market, the stock price was 2.93. Climbing +.89, for a total of +43.63%, what could have caused GNOM’s tremendous leap?

Researchers said they had developed a less expensive method of whole-genome sequencing that gives doctors a more complete picture of a person’s genetic makeup and requires only a small amount of DNA, potentially making the technique more available to patients.

Source: http://online.wsj.com/article/SB10001424052702303644004577520851224339844.html

After this news was released, there was a massive bull-raid sending the stock price through the roof.

GNOM’s biggest competitor in the genome industry is Rosetta Genomics, Ltd. (ROSG). On July 11, 2012, ROSG’s stock price opened at 10.39 and closed at 9.82 after the news came out, stating that GNOM had discovered a less costly method of whole-genome sequencing. ROSG fell for a total -.57, or -5.49%. On May 14, 2012 ROSG did a 1 for 15 reverse split in order to keep the $1.00 minimum bid price required to stay on the NASDAQ. This proves that GNOM’s competitor, ROSG, is in a worse financial state then GNOM . Rosetta Genomics is also behind Complete Genomics in development as well.

Current Developments:

Currently, Complete Genomics has no methods approved yet because they are not CILA (Clinical Laboratory Improvement Amendments) certified but that can soon change. Complete Genomics is has three potential applications of research for whole-genome sequencing. The areas of research are:

  • Cancer Research
  • Mendelian Disease Research
  • Rare Variant Disease Research

Complete Genomics is currently testing the Standard Sequencing Service.

Full Background of the Standard Sequencing Service:

Standard Sequencing Service

The Complete Genomics Standard Sequencing Service provides the most accurate whole human genome sequencing and analysis as a simple outsourced service. Customers send high-molecular weight DNA and in return, receive comprehensive sequence analysis results. All the library preparation, DNA sequencing, assembly and analysis are performed at Complete Genomics sequencing center in Mountain View, CA. Sequence data is processed using our comprehensive Analysis Pipeline that performs mapping, assembly, variant detection, scoring, and annotations across all variation types including SNPs, indels, copy number variations (CNVs), structural variations (SVs), and mobile element insertions (MEIs).The Standard Sequencing Service includes:

  • A choice of either >40x or >80x mapped reads sequenced across the reference genome
  • Complete diploid calls in > 90% of the reference genome
  • Variant calls (SNPs, indels, copy number variations (CNVs), structural variations (SVs), and mobile element insertions (MEIs))
  • Variant annotations (e.g. dbSNPs, RefSeq Genes, ncRNAs) allowing comparisons to known variants and for easier identification of genes and pathways modified in human diseases
  • Data summary reports with an overview of the results and data quality and also including coverage, library details, and variation call statistics as well as the full set of supporting data for these results (reads, scores and mappings)

Source: http://www.completegenomics.com/services/standard-sequencing/

Complete Genomics is also currently testing a Cancer Sequencing Service as well.

Full Background of The Cancer Sequencing Service:

Cancer Sequencing Service

Our Cancer Sequencing Service provides researchers with a valuable tool to further their understanding of cancer genomics. Samples are accepted as tumor-normal pairs or trios, reflecting how common cancer studies are designed. Algorithms in our Analysis Pipeline are tailored to handle the complexities of cancer samples, which are typically heterogeneous, aneuploid and include possible stromal contamination.

Each genome is compared to the reference genome and each tumor genome is also compared to its matched normal sample. All germline and somatic variants are called, facilitating a much greater understanding of the genetic basis of cancer.

The Cancer Sequencing Service includes:

  • A choice of either > 40x or >80x mapped reads sequenced across the reference genome
  • Complete diploid calls in > 90% of the reference genome
  • Germline and somatic variant calls (SNPs, indels, copy number variations (CNVs), structural variations (SVs), and mobile element insertions (MEIs))
  • Variant annotations (e.g. dbSNPs, RefSeq Genes, ncRNAs) allowing comparisons to known variants and for easier identification of genes and pathways modified in human diseases
  • Data summary reports with an overview of the results and data quality and also including coverage, library details, and variation call statistics as well as the full set of supporting data for these results (reads, scores and mappings)

Source: http://www.completegenomics.com/services/cancer/

Complete Genomics has also built one the first analysis platforms of it’s type named “The Complete Genomics Analysis Platform.” This platform helps conduct many genomic sequencing tests and is very accurate. Because of this, the potential for this company and it’s technology is very great.

Complete Background of “The Complete Genomics Analysis Platform”:

Complete Genomics Analysis Platform

Our sequencing service uses a proprietary custom-built sequencing platform developed by Complete Genomics. This platform is a result of technological advancements in DNA library manufacturing, DNA nanoarrays, sequencing chemistry, instrumentation and software (Drmanac, et al., Science 2010). The accuracy of Complete Genomics’ novel sequencing chemistry, combined with advanced algorithms for mapping and assembly, provides high-quality data (99.9998% accurate) ready for biological interpretation, and at a much lower cost than the total cost of purchasing and operating DNA sequencing instruments.

Our Novel Array and Read Technology

There are two primary components of our sequencing technology: DNA nanoball arrays, or DNB™ arrays, and combinatorial probe-anchor ligation reads, or cPAL™, reads.

I. DNB Nanoball Arrays

We have developed a novel approach to preparing fragmented DNA which can be packed onto a silicon chip very efficiently. Each DNA fragment is then reproduced in a manner that connects all copies together in a head-to-tail configuration, forming a long single molecule of connected nucleotides. Proprietary techniques developed by Complete Genomics cause each long single molecule to consolidate, or ball up, into a small particle of DNA that we call a DNA nanoball, or DNB. The DNBs are approximately 200 nanometers in diameter. Each DNB contains hundreds of copies of the 70 bases of DNA we are seeking to read in each fragment.

The patterned DNB arrays, due to their small size and biochemical characteristics, enable us to pack DNA very efficiently on a silicon chip. A proprietary process has been developed that causes the DNA to adhere to desired spots on the chip, while conversely preventing the DNA from adhering to the area between these spots. This enables us to affix individual particles of DNA to over 90% of these spots, leading to increased efficiency in nanoarray assembly.

II. cPAL Technology (Combinatorial Probe Anchor-Ligation)

We have also developed a unique and highly accurate cPAL technology that allows the sequence of each DNB to be read very efficiently on our sequencing platform. A ligase enzyme is used that attaches fluorescent molecules to the individual nucleotides in each DNB, corresponding to each single nucleotide base. By imaging the fluorescence, we can subsequently determine the sequence of nucleotides in each DNB.

A key characteristic of our cPAL technology is its high accuracy of reading short 5-base sequences of DNA. Another proprietary technique for preparing the DNA fragments has been developed so that we can read seven 5-base segments from each of the two ends of each DNA fragment, for a total of 70 bases from each fragment. Our proprietary assembly software accurately reconstructs over 90% of the whole human genomes from these 70 base reads from each fragment.

Advanced Informatics and Data Management Software

Sequencing whole human genomes generates considerable amounts of data that must be managed, stored and analyzed. In response to this need, we have built a genomics data processing facility with computing infrastructure and storage for managing both small and large-scale sequencing projects.

There are two major components of our Complete Genomics Analysis Pipeline: assembly and analysis software.

  • Assembly. Assembly is the process of organizing all of the overlapping 70-base nucleotide sequences to reconstruct the whole human genome. Our proprietary assembly software uses advanced data analysis algorithms and statistical modeling techniques to accurately reconstruct over 90% of the whole human genome from approximately two billion 70-base reads.
  • Analysis. Post assembly, our analysis software identifies key differences, or variants, in each genome. Detected variants include single nucleotide polymorphisms (SNPs), indels, substitutions, copy number variants (CNVs), structural variants (SVs), and mobile element insertions (MEIs). We then access publicly available databases of variants and genomic information to annotate each variant in the genome that is described in these databases. For the Cancer Sequencing Service, we identify somatic variants based on paired tumor-normal comparison, in addition to the variants detected by comparing each genome to the human genome reference. By using our service and open source analytical tools, our customers can significantly reduce their investments in computing and data storage infrastructure.

A comprehensive data file that lists all the variant calls, annotations, evidence for calls, and the calls and underlying reads and mappings are delivered as the final output. Genomic data is assembled and analyzed in Complete Genomics’ data center and then is securely transferred over a dedicated network to Amazon Web Services (AWS) for delivery to customers either by shipping hard disk drives or electronically.

By broadly enabling researchers to conduct large-scale whole human genome studies, we have helped revolutionize the scale and significance of these studies, and have helped researchers expand their understanding of complex diseases.

Source: http://www.completegenomics.com/services/technology/

Conclusion:

Overall, GNOM was the first company in the world to offer whole-human genome sequencing and bioinformatics analysis  as services. The company has a very strong research pipeline and only needs CILA certification before it can try their products before the FDA. We shall see what is around the corner for this company!

Disclosure: I am long GNOM.

CTraderD

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