Clinical-Grade Genomes

Complete Genomics Announces New Technology Developed to Set Standard for Clinical-Grade Genomes

Long Fragment Read Technology Described in Nature Paper Provides Much Higher Accuracy Sequencing

MOUNTAIN VIEW, Calif. – July 11, 2012 – Complete Genomics, Inc. (NASDAQ: GNOM) today announced that its Long Fragment Read (LFR) technology for whole genome sequencing dramatically improves accuracy, enables fully-phased genomes, and significantly reduces the amount of DNA required for testing. Complete’s LFR technology should accelerate the use of whole genome sequencing by physicians to diagnose and treat their patients.

“We expect the introduction of this technological breakthrough to accelerate the move of whole genome sequencing into patient care, which in turn will begin to change the face of medicine,” said Dr. Clifford Reid, Complete Genomics’ chairman, president and CEO.

“The Nature paper by Peters et al. describes how our LFR technology uses ‘barcoded’ DNA to generate whole genome sequencing with approximately one error in 10 million base pairs, or just 600 errors in an entire human genome,” said Dr. Rade Drmanac, the company’s chief scientific officer and inventor of the LFR technology. “This represents a 10-fold increase in accuracy for Complete and is unmatched by any high-sensitivity method currently available.”

Until now, determining whether two disease-associated variants were on the same or different parental chromosomes was either impossible or required expensive, low-throughput technologies — an approach often infeasible in a clinical environment. Complete’s new LFR technology not only enables an accurate identification of mutations, but includes phasing that shows which mutations are in fact together on the same parental chromosome. Through phasing, a physician can determine whether a patient with two pathogenic variants in a gene including its regulatory regions is affected or merely a carrier of the trait. In addition, Complete’s LFR technology provides, for the first time, accurate whole-genome sequencing from as few as 10 to 20 cells (only 100 picograms of DNA), making it an ideal choice for small sample clinical sequencing applications including circulating tumor cells, fine needle aspirations, and pre-implantation genetic diagnostics.

“In the not-too-distant future, failure to use phasing when providing genomic diagnoses in patient care will be seen as unacceptably inaccurate,” said Dr. George Church, professor of genetics at Harvard Medical School and director of PersonalGenomes.org. “I also suspect that LFR will reveal surprising things we didn’t know were missing because we didn’t have a tool to see them.”

The U.S. Patent and Trademark Office has already issued Complete Genomics two separate patents on LFR technology, and additional patent applications, including miniaturization using nanodrops, are pending. Complete Genomics plans to incorporate the new technology into its sequencing offerings in early 2013.

About Complete Genomics

Through its pioneering sequencing-as-a-service model, Complete Genomics provides the most accurate whole human genomes generally available today. The ease of use and power of Complete’s advanced informatics and analysis systems provide genomic information needed to better understand the prevention, diagnosis, and treatment of diseases. Additional information can be found at http://www.completegenomics.com.

Forward-Looking Statement

Certain statements in this press release, including the incorporation of LFR technology into genomic sequencing and the potential future impact of LFR technology on medical care, are forward-looking statements that are subject to risks and uncertainties. These forward-looking statements are based on management’s current expectations, and actual results may differ materially from our expectations. The following factors, without limitation, could cause actual results to differ materially from those in our forward-looking statements: the timing of the company’s incorporation of LFR technology into its sequencing offerings and the pace of acceptance of human genome sequencing into patient care. More information on risk factors that could affect our results can be found in our Annual Report on Form 10-K filed with the SEC on March 9, 2012, and our Quarterly Report on Form 10-Q filed with the SEC on May 9, 2012, including those risks listed in those filings under the heading “Risk Factors.” We disclaim any obligation to update information contained in our forward-looking statements, whether as a result of new information, future events or otherwise.

Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10–20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications.

The extraordinary advancements made in DNA sequencing technologies over the past few years have led to the elucidation of ~10,000 (refs 1–13) individual human genomes (30× or greater base coverage) from different ethnicities and using different technologies2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and at a fraction of the cost10 of sequencing the original human reference genome14, 15. Although this is a monumental achievement, the vast majority of these genomes have excluded a very important element of human genetics. Individual human genomes are diploid in nature, with half of the homologous chromosomes being derived from each parent. The context in which variations occur on each individual chromosome can have profound effects on the expression and regulation of genes and other transcribed regions of the genome16. Furthermore, determining whether two potentially detrimental mutations occur within one or both alleles of a gene is of paramount clinical importance.

Almost all recent human genome sequencing has been performed on short read length (

At present, four personal genomes—J. Craig Venter19, a Gujarati Indian (HapMap sample NA20847)11, and two Europeans (Max Planck One13 and HapMap Sample NA12878 (ref. 20))—have been sequenced and assembled as diploid. All have involved cloning long DNA fragments in a process similar to that used for the construction of the human reference genome14, 15. Although these processes generate long-phased contigs (N50 values (50% of the covered bases are found within contigs longer than this number) of 350 kb19, 386 kb11 and 1 megabase (Mb)13, and full-chromosome haplotypes in combination with parental genotypes20) they require a large amount of initial DNA, extensive library processing, and are currently too expensive11 to use in a routine clinical environment. Furthermore, several reports have recently demonstrated whole chromosome haplotyping through direct isolation of metaphase chromosomes21, 22, 23, 24. These methods have yet to be used for whole-genome sequencing and require preparation and isolation of whole metaphase chromosomes, which can be challenging for some clinical samples. Here we introduce long fragment read (LFR) technology, a process that enables genome sequencing and haplotyping at a clinically relevant cost, quality and scale.

The LFR approach can generate long-range phased variants because it is conceptually similar to single-molecule sequencing of fragments 10–1,000 kb25 in length. This is achieved by the stochastic separation of corresponding long parental DNA fragments into physically distinct pools followed by subsequent fragmentation to generate shorter sequencing templates (Fig. 1). The same principles are used in aliquoting fosmid clones11, 13. As the fraction of the genome in each pool decreases to less than a haploid genome, the statistical likelihood of having a corresponding fragment from both parental chromosomes in the same pool markedly diminishes25. For example, 0.1 genome equivalents (300 Mb) per well yields an approximately 10% chance that two fragments will overlap, and a 50% chance that those fragments will be derived from separate parental chromosomes. The end result is a roughly 5% overall chance that a particular well will be uninformative for a given fragment. Likewise, the more individual pools interrogated the greater the number of times a fragment from the maternal and paternal homologues will be analysed in separate pools. The current version of LFR uses a 384-well plate with 10–20% of a haploid genome in each well, yielding a theoretical 19–38× physical coverage of both the maternal and paternal alleles of each fragment (see Supplementary Materials and Supplementary Table 1 for an explanation of how this amount of material was selected). This high initial DNA redundancy of 19–38× versus recently described strategies using fosmid pools of 3× (ref. 11) or 6× (ref. 13) ensures complete genome coverage and higher variant calling and phasing accuracy.

Figure 1: The LFR technology.

An overview of the LFR technology and controlled random enzymatic fragmenting is shown. (i) First, 100–130 pg of high molecular mass (HMM) DNA is physically separated into 384 distinct wells; (ii) through several steps, all within the same well without intervening purifications, the genomic DNA is amplified, fragmented and ligated to unique barcode adapters; (iii) all 384 wells are combined, purified and introduced into the sequencing platform of Complete Genomics10; (iv) mate-paired reads are mapped to the genome using a custom alignment program and barcode sequences are used to group tags into haplotype contigs; and (v) the final result is a diploid genome sequence.

Source : http://www.completegenomics.com/news-events/press-releases/Complete-Genomics-Announces-New-Technology-Developed-to-Set-Standard-for-Clinical-Grade-Genomes-161946595.html

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