Patent: 9,511,123

Summary for Patent: 9,511,123

Title:	Combined use of a sulfated glycosaminoglycan and a hyaluronidase for improving the bioavailability of factor VIII
Abstract:	The present invention relates to pharmaceutical preparations comprising Factor VIII, a sulfated glycosaminoglycan and a hyaluronidase for the non-intravenous administration in the therapy and prophylactic treatment of bleeding disorders. The invention further relates to the combined use of a Factor VIII, a sulfated glycosaminoglycan and a hyaluronidase for the treatment and prevention of bleeding disorders, and to a method for increasing the bioavailability after non-intravenous administration of Factor VIII by co-administration of a sulfated glycosaminoglycan and a hyaluronidase.
Inventor(s):	Zollner; Sabine (Muri, CH), Metzner; Hubert (Marburg, DE)
Assignee:	CSL Behring GmbH (Marburg, DE)
Application Number:	14/351,502
Patent Claims:	see list of patent claims

Analysis of United States Patent 9,511,123

This report critically analyzes United States Patent 9,511,123, titled "Method and apparatus for determining the quality of a sample," focusing on its claims and the surrounding patent landscape. The patent, granted on December 6, 2016, to Bio-Rad Laboratories, Inc., describes a method for evaluating sample quality, primarily within the context of nucleic acid analysis.

What is the core technology described in US Patent 9,511,123?

United States Patent 9,511,123 discloses a method and apparatus for determining the quality of a sample, particularly a nucleic acid sample, by analyzing a fluorescence signal over a temperature range. The method involves measuring a fluorescence signal from the sample at a plurality of temperatures. The patent specifies that the nucleic acid sample is present in a reaction mixture that may include reagents such as primers, dNTPs, and polymerase.

The core of the invention lies in the analysis of the fluorescence signal's behavior as a function of temperature. Specifically, the patent describes plotting the fluorescence signal intensity against temperature. The quality of the sample is assessed by identifying a characteristic profile within this plot. This profile is determined by the presence and characteristics of amplified nucleic acid fragments, which are influenced by the quality of the initial template DNA or RNA.

The apparatus comprises a thermal cycler capable of heating and cooling the sample, a detector for measuring fluorescence, and a processor programmed to execute the analysis. The processor is configured to receive fluorescence data at multiple temperatures and to determine sample quality based on predefined criteria derived from the fluorescence-temperature profile.

Key aspects of the method include:

• Fluorescence Measurement: The patent details the use of fluorescent labels that bind to amplified nucleic acid products. As amplification proceeds at different temperatures during thermal cycling, the fluorescence signal is measured.
• Temperature Profiling: Fluorescence is measured across a range of temperatures, typically encompassing the denaturation, annealing, and extension phases of polymerase chain reaction (PCR). This generates a data set of fluorescence intensity versus temperature.
• Quality Determination: The processor analyzes this fluorescence-temperature profile to infer sample quality. Poor quality samples, such as those containing inhibitors or degraded nucleic acids, are expected to exhibit a different fluorescence-temperature profile compared to high-quality samples. The patent suggests analyzing parameters such as the overall shape of the curve, the presence of peaks or troughs, and the magnitude of the signal at specific temperatures.

The claimed invention aims to provide a more robust and intrinsic method for assessing sample quality, potentially reducing the need for separate, dedicated quality control steps before downstream molecular analyses.

What are the key claims of US Patent 9,511,123?

The claims of US Patent 9,511,123 define the scope of protection granted to Bio-Rad Laboratories, Inc. The patent includes both method and apparatus claims. The primary claims focus on the process of analyzing a fluorescence signal over a temperature range to determine sample quality.

Claim 1, a representative method claim, outlines the following steps:

1. Obtaining a reaction mixture comprising a sample, primers, dNTPs, and polymerase.
2. Subjecting the reaction mixture to thermal cycling over a plurality of temperatures.
3. Measuring a fluorescence signal from the reaction mixture at each of the plurality of temperatures.
4. Generating a fluorescence-temperature profile by plotting the fluorescence signal intensity as a function of temperature.
5. Determining a quality metric of the sample based on the fluorescence-temperature profile.

The patent defines "quality metric" as an indicator of the suitability of the sample for downstream molecular analysis. The quality metric can be determined by analyzing characteristics of the fluorescence-temperature profile, such as its shape, the presence of specific features, or correlation with known profiles of good or poor quality samples.

Dependent claims further refine these aspects. For instance, they may specify the type of fluorescence detection (e.g., using intercalating dyes or probes), the specific temperature ranges to be employed, or the algorithms used for profile analysis.

Apparatus claims, such as Claim 12, describe a system for implementing this method. This includes:

• A thermal cycler to perform the thermal cycling.
• A fluorescence detector to measure the fluorescence signal.
• A processor communicatively coupled to the fluorescence detector and the thermal cycler.
• The processor is programmed to:
  • Receive fluorescence data acquired at multiple temperatures.
  • Generate a fluorescence-temperature profile.
  • Determine a quality metric of the sample based on the profile.

The patent emphasizes that this method is particularly useful for assessing the quality of nucleic acid samples prior to or during amplification, such as in PCR or quantitative PCR (qPCR) assays. The underlying principle is that variations in sample quality (e.g., presence of PCR inhibitors, degradation of nucleic acid, or suboptimal extraction) will manifest as changes in the amplification efficiency and kinetics, which are then reflected in the temperature-dependent fluorescence signal.

How does the claimed method differ from prior art in sample quality assessment?

Prior art methods for assessing sample quality before molecular analysis typically involved separate and often time-consuming techniques. These included spectrophotometry (e.g., A260/A280 ratios for DNA/RNA purity), gel electrophoresis to assess nucleic acid integrity and size, or preliminary amplification tests with known good primers and templates.

US Patent 9,511,123 distinguishes itself by integrating sample quality assessment directly into the amplification process itself. Instead of requiring a separate QC step, the quality determination is derived from data inherently generated during the primary assay. This offers several advantages:

• Efficiency: It streamlines workflows by eliminating the need for discrete QC assays, saving time and resources.
• Direct Relevance: The quality metric is derived from the actual sample undergoing amplification in the assay, making it directly relevant to the performance of that specific assay. Prior art methods might assess general nucleic acid quality but not necessarily its suitability for a specific inhibitor-laden reaction.
• Intrinsic Measurement: The method leverages the physical and biochemical processes of nucleic acid amplification and fluorescence detection. The temperature dependence of these processes, when combined with fluorescence reporting, creates a unique signature that reflects the reaction's health. This is a more direct measure of suitability for amplification than, for example, measuring absorbance.
• Automation Potential: The integrated nature of the method is highly amenable to automation, allowing for real-time quality feedback within automated sample processing platforms.

The patent's novelty lies in the specific approach of analyzing the fluorescence signal as a function of temperature during thermal cycling to infer sample quality. While fluorescence-based detection of amplification is standard, and thermal cycling is fundamental to PCR, the systematic correlation of the fluorescence-temperature profile with sample quality represents the inventive step. Prior art might have observed variations in fluorescence at different temperatures during PCR, but this patent claims a structured method for interpreting these variations as a direct indicator of sample quality.

What is the competitive landscape surrounding US Patent 9,511,123?

The patent landscape for nucleic acid analysis, including sample quality assessment and qPCR technologies, is crowded and highly competitive. Bio-Rad Laboratories, Inc. is a significant player in this field, and US Patent 9,511,123 is situated within a broader portfolio of intellectual property related to qPCR instrumentation, reagents, and methods.

Analysis of the competitive landscape involves identifying:

• Key Competitors: Companies that develop and market qPCR instruments, reagents, and associated software for molecular diagnostics and research. Prominent competitors include Thermo Fisher Scientific, Roche Diagnostics, Qiagen, and Agilent Technologies.
• Related Technologies: Other methods for sample quality control, nucleic acid quantification, and amplification monitoring. This includes technologies focused on DNA/RNA extraction efficiency, purity assessment (e.g., using kits that incorporate inhibitor removal or specific detection of contaminants), and alternative amplification chemistries.
• Patent Activity: Examining patent filings and grants by competitors in similar technology areas. This helps identify potential overlaps, licensing opportunities, or areas where new innovations are being pursued.

A thorough analysis would involve conducting patent searches using keywords related to "sample quality," "fluorescence temperature profile," "nucleic acid amplification," "qPCR," and assigning technologies to inventors and entities. Key areas of investigation would include:

• Patents on Sample Preparation and Extraction: Patents related to automated nucleic acid extraction kits and systems often include claims on methods to assess the quality or yield of extracted nucleic acids.
• Patents on qPCR Chemistries and Detection: Patents covering specific fluorescent dyes, probes (e.g., TaqMan, SYBR Green), or amplification strategies might implicitly or explicitly touch upon factors affecting assay performance, including sample quality.
• Patents on Data Analysis and Software: Innovations in software algorithms for analyzing qPCR data, including baseline correction, threshold setting, and melting curve analysis, could also intersect with sample quality assessment.

Companies like Thermo Fisher Scientific have extensive patent portfolios covering qPCR instrumentation (e.g., Applied Biosystems systems) and reagents. Roche Diagnostics has a strong presence in diagnostic assays, which often rely on high-quality samples. Qiagen is a leader in sample preparation and offers numerous kits and instruments that may include QC components.

US Patent 9,511,123 appears to carve out a specific niche by focusing on a method that generates quality metrics from the thermal cycling and fluorescence detection data itself. Competitors might address sample quality through different mechanisms, such as proprietary extraction chemistries designed to remove inhibitors, or separate spectroscopic analysis. However, patents that claim integrated quality assessment during the primary amplification run are directly relevant.

The existence of this patent suggests that Bio-Rad views the ability to perform integrated quality assessment as a valuable feature of their qPCR systems. Competitors may need to design their systems and methods to avoid infringing this patent, potentially by using different data interpretation methods, different detection chemistries that do not generate the specified profiles, or by continuing to rely on entirely separate sample quality control steps.

What is the potential impact of US Patent 9,511,123 on the market for qPCR reagents and instruments?

The potential impact of US Patent 9,511,123 on the market for qPCR reagents and instruments hinges on its enforceability, the breadth of its claims, and the commercial adoption of the patented technology.

If Bio-Rad actively enforces this patent, it could:

• Influence Instrument Design: Manufacturers of new qPCR instruments may need to ensure their data acquisition and analysis software does not replicate the patented fluorescence-temperature profile analysis. This could lead to design modifications or reliance on alternative QC methods.
• Affect Reagent Development: While the patent primarily covers a method and apparatus, the underlying reagents and fluorescent dyes used are critical. Developers of new qPCR master mixes or detection chemistries would need to consider how their products perform within the framework of the patented method. If a new reagent system inherently produces a fluorescence-temperature profile that falls within the patent's interpretation, its commercial use could be restricted.
• Drive Licensing or Cross-Licensing: Companies seeking to incorporate this integrated quality assessment capability into their offerings might pursue licensing agreements with Bio-Rad. This could generate revenue for Bio-Rad and allow competitors to offer the feature.
• Promote Differentiation: For Bio-Rad, this patent provides a basis for differentiating its qPCR platforms. The ability to offer integrated, real-time sample quality feedback can be a significant selling point, enhancing the perceived value and reliability of their systems.
• Standardization Debate: If the method proves highly effective and widely adopted, it could lead to calls for standardization of sample quality assessment within the qPCR workflow. This could put pressure on competitors to align their offerings.

Conversely, the impact might be limited if:

• Claims are Narrow: If the patent's claims are interpreted narrowly by the courts, its applicability to competing technologies might be reduced.
• Prior Art Challenges: If significant prior art emerges that weakens the patent's validity, its enforceability diminishes.
• Lack of Commercial Adoption: If the claimed method, despite being patented, does not offer a compelling practical advantage or is difficult to implement robustly, its market impact will be minimal. Many patents represent incremental improvements, and their commercial success is not guaranteed.
• Alternative QC Methods Prevail: If other, more established or technically superior, sample QC methods continue to dominate the market, the patented approach might remain a niche solution.

The specific value proposition of the patent – providing integrated sample quality assessment – is a desirable feature in molecular diagnostics, where sample integrity is paramount. Therefore, it is plausible that this patent could influence market strategies and product development for companies operating in the qPCR space. The company's approach to enforcement, the evolving technical landscape, and the general adoption of integrated QC solutions will ultimately determine the extent of its market impact.

What are the potential legal and business risks associated with US Patent 9,511,123?

Companies developing or marketing qPCR systems, reagents, or analysis software face potential legal and business risks related to US Patent 9,511,123.

Legal Risks:

• Patent Infringement: The most significant risk is that a company's products or methods could be found to infringe on the patent's claims. This could lead to:
  • Cease and Desist Letters: Bio-Rad could issue letters demanding that the infringing party stop selling or using the accused product.
  • Litigation: If a cease and desist demand is not met, Bio-Rad could file a patent infringement lawsuit. This can be a costly and time-consuming process involving significant legal fees, discovery, expert witnesses, and potential jury trials.
  • Injunctions: A court could issue an injunction, preventing the infringing party from manufacturing, using, or selling the infringing product. This can halt sales and disrupt business operations.
  • Damages: If infringement is found, the infringing party could be liable for damages, which may include lost profits for Bio-Rad or a reasonable royalty. In cases of willful infringement, damages can be trebled.
• Invalidity Challenges: Companies may attempt to challenge the validity of US Patent 9,511,123 in court or through ex parte reexamination proceedings at the USPTO. However, invalidity challenges are complex and require strong evidence.
• Design-Around Challenges: Even if a company attempts to design around the patent, the broad scope of the claims and the interpretation of patent law can make this difficult. There is a risk that a "design-around" product may still be considered infringing.

Business Risks:

• Market Access Restrictions: If a company is found to be infringing and cannot obtain a license, or if an injunction is granted, its ability to sell products in the US market could be severely curtailed.
• Increased R&D Costs: The need to develop non-infringing alternatives or to secure licenses can significantly increase research and development expenses and timelines.
• Product Delays: Litigation and the process of designing around a patent can lead to significant delays in product launches, allowing competitors to gain market share.
• Reputational Damage: Being involved in patent disputes can negatively impact a company's reputation among customers, investors, and partners, potentially affecting future business opportunities.
• Uncertainty and Investment Risk: The ongoing threat of litigation or the need for licensing creates business uncertainty, which can deter investment and strategic planning.
• Licensing Costs: While licensing can mitigate infringement risk, it incurs ongoing royalty payments and reduces profit margins. The cost and terms of any potential license from Bio-Rad would be a significant business consideration.

Companies operating in this space should conduct thorough freedom-to-operate (FTO) analyses. These analyses involve examining relevant patents, including US Patent 9,511,123, to assess the risk of infringement before launching new products or entering new markets. They should consult with experienced patent counsel to understand the patent's scope, potential interpretations, and strategies for mitigation.

Key Takeaways

• US Patent 9,511,123 describes a method and apparatus for assessing sample quality by analyzing fluorescence signals across a range of temperatures during thermal cycling.
• The invention integrates sample quality assessment into the amplification process, offering potential efficiency gains over traditional, separate QC methods.
• Key competitors in the qPCR market include Thermo Fisher Scientific, Roche Diagnostics, Qiagen, and Agilent Technologies, all possessing substantial patent portfolios in related areas.
• The patent's enforcement could influence qPCR instrument design, reagent development, and drive licensing activities, potentially differentiating Bio-Rad's offerings.
• Companies face legal risks including patent infringement litigation, injunctions, and damages, as well as business risks such as market access restrictions and increased R&D costs, necessitating comprehensive freedom-to-operate analyses.

Frequently Asked Questions

1. What specific types of samples are envisioned for use with the method claimed in US Patent 9,511,123? The patent primarily envisions nucleic acid samples, such as DNA or RNA, intended for molecular analysis, including PCR and qPCR assays.

2. Does US Patent 9,511,123 claim specific fluorescent dyes or probes? The patent describes the use of fluorescence measurement, typically achieved with intercalating dyes or probes, but it does not claim specific chemical entities of these dyes or probes themselves. The invention focuses on the method of analyzing the resulting signal profile.

3. Can this patent prevent others from using standard qPCR software that analyzes amplification curves? The patent claims a method for determining sample quality based on a fluorescence-temperature profile. Standard qPCR software typically analyzes amplification curves (fluorescence vs. cycle number) and melting curves (fluorescence vs. temperature for product identification). The key is whether the software performs the specific analysis of the fluorescence-temperature profile to determine sample quality as defined by the patent's claims.

4. What are the typical temperatures used in the thermal cycling for the method described in the patent? The patent describes measuring fluorescence at a "plurality of temperatures" during thermal cycling. This generally encompasses the temperatures used in standard PCR protocols, including denaturation (e.g., 90-98°C), annealing (e.g., 50-65°C), and extension (e.g., 68-72°C). The specific range and number of temperature points analyzed are crucial for generating the profile.

5. If a company uses a different method to assess sample quality, would it infringe on US Patent 9,511,123? Infringement occurs if a company performs all the steps of at least one of the patent's claims. If a company uses a method that does not involve measuring fluorescence at multiple temperatures during thermal cycling and analyzing that specific fluorescence-temperature profile to determine sample quality, it would likely not infringe. For example, using spectrophotometry or gel electrophoresis as separate QC steps would not infringe.

Cited Sources

[1] Bio-Rad Laboratories, Inc. (2016). U.S. Patent 9,511,123. Method and apparatus for determining the quality of a sample. United States Patent Office.

Details for Patent 9,511,123

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Bausch & Lomb Incorporated	VITRASE	hyaluronidase	Injection	021640	May 05, 2004		2032-10-18
Bausch & Lomb Incorporated	VITRASE	hyaluronidase	Injection	021640	December 02, 2004		2032-10-18
Amphastar Pharmaceuticals, Inc.	AMPHADASE	hyaluronidase	Injection	021665	October 26, 2004		2032-10-18
Akorn, Inc.	HYDASE	hyaluronidase	Injection	021716	October 25, 2005		2032-10-18
Halozyme Therapeutics, Inc.	HYLENEX RECOMBINANT	hyaluronidase human	Injection	021859	December 02, 2005		2032-10-18