“Methods And Systems For Anonymizing Genome Segments And Sequences And Associated Information” in Patent Application Approval Process (USPTO 20230124077): Patent Application

2023 MAY 08 (NewsRx) -- By a News Reporter-Staff News Editor at Insurance Daily News -- A patent application by the inventor Huang, Ethan (Cupertino, CA, US), filed on August 30, 2022, was made available online on April 20, 2023, according to news reporting originating from Washington, D.C., by NewsRx correspondents.

This patent application has not been assigned to a company or institution.

The following quote was obtained by the news editors from the background information supplied by the inventors: “The present (circa 2015) price of sequencing an individual’s genome may have dropped dramatically. Such individual genome sequencing may open a new era of genome-wide association studies (GWAS) (as well as other less than full genome genetic studies) based on a plurality of such individual’s sequenced genomes (or portions thereof), along with their associated information (e.g., medical records) stored in various databases. Such individual genome sequencing may open a new era of personalized medicine, in which preventive and/or therapeutic interventions for complex diseases may be tailored to individuals based on their specific and particular genetic information.

“However, because of a wealth of information that may be learned from or that inherently associates with the individual’s own sequenced genome, handling of such individual genome sequence information may carry inherent risks of certain abuses. For example, the individual’s genome sequence information itself may act as a unique “fingerprint” allowing the individual to be identified from their own genome sequence information. Thus, the handling of the individual’s genome sequence information may provide opportunities for privacy breaches and/or intrusion into the individual’s privacy. Some countries and/or states, by law, mandate that such sensitive and identifying information be managed, stored, transmitted, disclosed, published, processed, handled, and the like in particular manners that mitigate against such privacy abuses. For example, in the United States, there is a federal law known as the Health Insurance Portability and Accountability Act (HIPAA). HIPAA may establish standards for privacy and security of health information, as well as, standards for electronic data interchange (EDI) of such health information. HIPAA may specify a list of 18 identifiers as Protected Health Information (PHI) that must be encrypted by law, and must be stored only in encrypted form, and transmitted only through secure means. Biometric identifiers may be included in this list of 18 identifiers. Commonly, biometric identifiers may comprise an individual’s fingerprints. Biometric identifiers may also comprise an individual’s DNA sequences. For example, an example of using the individual’s DNA sequences to identify the individual may be depicted in the FIG. 2 and FIG. 3 figures as well as discussed in the disclosure discussing those figures. HIPAA has specified two different de-identification techniques to minimize re-identification of a given individual. In particular, a safe harbor method may require removal of all 18 identifiers so no actual knowledge, including possibly residual information, can identify an individual. Since the biometric identifier, one of the 18 identifiers, has to be removed, the safe harbor method is not suitable for genetic studies, such as, but not limited to, GWAS. On the other hand, an expert determination method may apply statistical, mathematical, and/or scientific principles such that treated health information may carry an appropriately very small risk to re-identify an individual. This may comprise various data cleansing and/or anonymizing methods to minimized re-identification of any given individual. One example may be of anonymizing a geographic location like an individual’s address to retain only the state of the address before transmission of such address information to others. However, HIPAA does not provide for explicit nor specific instructions for anonymizing the biometric identifier. Note, other nations, states, and/or regions may have laws similar to HIPAA, that may require certain results must be achieved when dealing with biometric identifiers in order to protect individuals privacy and minimize the potential for genetic abuse and/or genetic discrimination.

“There then is a need, by law, and from the individual’s perspective, for methods and/or systems for one or more of: managing, storing, transmitting, disclosing, publishing, processing, handling, and/or the like of genome sequence information such that an ability to learn the individual’s identify is minimized or mitigated against.

“In another example, the individual’s genome sequence information may provide a means to associate various predispositions and/or active phenotypes in that individual. And others (e.g., third parties, like employers, insurance carriers, educational institutions, and/or the like) may use such information to discriminate against the individual. For example, such discrimination could be in the employment context and/or in a context admission into various programs, schools, insurance coverage and/or the like. There then is a need to prevent, minimize, and/or mitigate against such discrimination.

“U.S. Pat. No. 8,019,620 issued to Miller et al. teaches an integrated platform for privacy management of electronic medical records, encompassing the entire life cycle of privacy management. U.S. Pat. No. 8,326,849 issued to El Emam et al. teaches a method, system and computer memory for optimally de-identifying a dataset of medical records where a lattice of information may be determined to define the anonymization strategies. U.S. Pat. No. 7,823,207 issued to Evenhaim teaches a privacy preserving data-mining protocol for querying privacy-sensitive micro-data. However, these platforms, systems, methods, and/or protocols were not specifically designed to manage nor process genome sequences and associated information. These platforms, systems, methods, and/or protocols are very poorly equipped to manage and/or process genome sequences and associated information in a way to achieve the desired goals. With about 3 million base pairs per individual of their own genome, portions of which may be of varying degrees of uniqueness, very specific methods and/or systems must be used to achieve the desired goals of preventing, minimizing, and/or mitigating against identification of a given individual; and/or of preventing, minimizing, and/or mitigating against discrimination.

“U.S. Pat. No. 8,589,437 issued to Khomenko et al. teaches a system for separating identifying data from personal data in which a set of mapping data is introduced to associate a first set of stored identifying data such as account data and a second set of stored personal data such as phenotype data and genotype data. U.S. Pat. No. 8,600,683 issued to George teaches methods and systems for obtaining, processing, and managing sequence data in which a unique identifier is used to store the original sequence in one database and the same unique identifier is used to index information for identifying the source of the sequence in another database. However, how to further separate and associate the genotype data has never been taught in these systems and methods.

“There is a need in the art for methods and/or systems for processing genome sequence information and associated information in a manner that achieves the desired goals of preventing, minimizing, and/or mitigating against identification of a given individual; and/or of preventing, minimizing, and/or mitigating against discrimination. Accordingly, methods and/or system for anonymizing at least a portion of a given genome sequence and/or at least a portion of associated information are required.

“It is to these ends that the present invention has been developed.”

In addition to the background information obtained for this patent application, NewsRx journalists also obtained the inventor’s summary information for this patent application: “To minimize the limitations in the prior art, and to minimize other limitations that will be apparent upon reading and understanding the present specification, the present invention describes various methods and systems for processing at least some of one or more genome sequences and at least some of associated information, for at least one individual. A purpose of such processing may be to prevent, minimize, and/or mitigate against identification of the at least one individual from the at least some of the one or more genome sequences and/or from associated information. For example, some such methods and/or systems may be compliant with HIPAA with respect to at least some biometric identifiers like genome sequence information. Another purpose of such processing may be to prevent, minimize, and/or mitigate against using the at least some of one or more genome sequences and/or associated information as a basis for discriminating against the individual. In some embodiments, such processing may comprise one or more of: (1) segmenting the at least some of one or more genome sequences for at least a purpose of anonymizing the at least some of one or more genome sequences; (2) using anchor segments for a purpose of minimizing storage space in storing of genetic sequence information; (3) generating at least one linkage record for accessing the at least some of one or more genome sequences and/or the at least some of associated information from storage, wherein the at least some of one or more genome sequences and/or the at least some of associated information may have been organized into various organizational units for storage in a manner that minimizes opportunity for identification and/or discrimination; (4) generating at least one anonymized linkage record, which may entail further processing (e.g., modifying and/or anonymizing) of at least some of the organizational units; (5) processing requests for genetic study results to be provided and providing those genetic study results in a manner that may not compromise anonymity; (6) processing genetic study results received; and/or (7) generating personalized information of interest pertaining to the individual pursuant to a request for such information.

“It is an objective of the present invention to prevent, minimize, and/or mitigate against identification of the at least one individual from the at least some of the one or more genome sequences and/or from associated information.

“It is another objective of the present invention to provide methods and/or systems which may be compliant with HIPAA with respect to at least some biometric identifiers such as, but not limited to, genome sequence information.

“It is another objective of the present invention to prevent, minimize, and/or mitigate against using the at least some of one or more genome sequences and/or associated information as a basis for discriminating against the individual.

“It is another objective of the present invention to provide methods and systems for processing the at least some of one or more genome sequences and the at least some of associated information, for the at least one individual.

“It is another objective of the present invention to provide methods and systems for segmenting the at least some of one or more genome sequences for at least a purpose of anonymizing the at least some of one or more genome sequences.

“It is another objective of the present invention to provide methods and systems for using anchor segments for the purpose of minimizing storage space in storing of genetic sequence information.

“It is another objective of the present invention to provide methods and systems for generating the at least one linkage record for accessing the at least some of one or more genome sequences and/or the at least some of associated information from storage, wherein the at least some of one or more genome sequences and/or the at least some of associated information may have been organized into the various organizational units for storage in a manner that minimizes opportunity for identification and/or discrimination.

“It is another objective of the present invention to provide methods and systems for generating the at least one anonymized linkage record, which may entail further processing (e.g., modifying and/or anonymizing) of the at least some of the organizational units.

“It is another objective of the present invention to provide methods and systems for processing the requests for the genetic study results to be provided and providing those genetic study results in a manner that may not compromise anonymity.

“It is another objective of the present invention to provide methods and systems for processing genetic study results received.

“It is yet another objective of the present invention to provide methods and systems for generating personalized information of interest pertaining to the individual pursuant to a request for such information.

“These and other advantages and features of the present invention are described herein with specificity so as to make the present invention understandable to one of ordinary skill in the art, both with respect to how to practice the present invention and how to make the present invention.

“Note, the subject matter of the various embodiments, including both method and system embodiments, of the present invention are not abstract ideas under 35 USC 101 as presently (circa 2015) understood by Alice Corp. Pty. Ltd. v. CLS Bank Int’l et al., 134 S.Ct. 2347, No. 13-298 (2014) and its progeny. For example, US patent law presently understand mathematical algorithms in isolation executed on a generic computer, and some fundamental economic and conventional business practices are abstract ideas and thus not patent eligible subject matter under 35 USC 101. See DDR HOLDINGS, LLC v. Hotels.com, LP, 773 F. 3d 1245 (Fed. Cir. 2014). In DDR asserted claims in a U.S. Pat. No. 7,818,399 patent were upheld as patent eligible subject matter under 35 USC 101. Id. These DDR claims do not recite a mathematical algorithm, nor do they recite a fundamental economic nor longstanding commercial practice; however those claims do address a business challenge and involve both a computer and the internet. Id. But the DDR claims “stand apart because they do not merely recite the performance of some business practice known from the pre-Internet world along with the requirement to perform it on the Internet. Instead, the claimed solution is necessarily rooted in computer technology in order to overcome a problem specifically arising in the realm of computer networks.” Id. Likewise, the subject matter herein, that of methods and systems for anonymizing genome sequences, segments, and associated information for purposes of protecting identity and minimizing discrimination also not do exclusively employ mathematical algorithms, nor claim fundamental economic nor longstanding commercial practices; and because of the sheer amount of information conveyed in such sequences of nucleotides, including how such sequence information gets transcribed, translated and regulated to produce various phenotypes, similarly requires computers and/or computer systems to function. And the problems of compromised identity and/or of being discriminated against because of one’s genome is a new problem that is only now manifesting as genetic studies mature and come to fruition, at least with respect to mapping, such as the Human Genome Project. Furthermore, such anonymization methods and systems must balance the desired purposes of identity protection and minimizing likelihood of discrimination with genetic researchers and medical community needs that prefer genetic data to be non-anonymized, as anonymization may result in some loss of information.”

There is additional summary information. Please visit full patent to read further.”

The claims supplied by the inventors are:

“1. A method for processing genetic study results, wherein the method comprises steps of: (a) receiving at least one result; wherein the at least one result once received is at least one received result; wherein the at least one received result comprises results-information; (b) cataloging the results-information into cataloged-results-information; and © non-transitorily storing the cataloged-results-information in one or more databases, repositories, or storage units.

“2. The method according to claim 1, wherein the results-information comprises one or more of: at least one genome sequence from at least one individual, at least one segment of the at least one individual, at least one marked allele of the at least one individual, or information-of-interest.

“3. The method according to claim 2, wherein the information-of-interest comprises one or more of: associated information, phenotype information, medical record information, personal information, a disease of interest, a genetic condition of interest, treatment results of interest per the at least one individual, or results of a given genetic study.

“4. The method according to claim 3, wherein the at least one result comprises a plurality of results of a plurality of individuals.

“5. The method according to claim 2, wherein the at least one genome sequence is selected from one or more of: one or more genome sequences, one or more segments of nucleic acid sequences derived from the one or more genome sequences, modified-genome-sequences derived from the one or more genome sequences, or modified-segments derived from the one or more segments of nucleic acid sequences.

“6. The method according to claim 2, wherein the at least one genome sequence from the at least one individual or the at least one segment of the at least one individual is marked at at least one locus; wherein this marking of the at least one locus indicates that one or more of a disease of interest, a genetic condition of interest, or a phenotype of interest associates with the at least one locus.

“7. The method according to claim 2, wherein after the step of receiving the at least one result, but before the step of cataloging the results-information, the method further comprises a step of associating the at least one marked allele with at least one relevant segment; wherein the at least one relevant segment is relevant if the at least one segment comprises an allele or some nucleic acid sequence that matches the at least one marked allele.

“8. The method according to claim 7, wherein the step of associating comprises marking the at least one relevant segment at at least one locus on the at least one relevant segment that indicates a location of the allele or of the some nucleic acid sequence on the at least one relevant segment that matches the at least one marked allele.

“9. The method according to claim 8, wherein the marking of the at least one relevant segment is facilitated by using an align sequence to align the at least one marked allele with the at least one relevant segment.

“10. The method according to claim 9, wherein the align segment and the at least one relevant segment are the same segment.

“11. The method according to claim 1, wherein the step of cataloging the results-information further comprises scanning the results-information for information that compromises anonymity of at least one individual.

“12. The method according to claim 11, wherein if at least some of the information scanned reveals an anonymity problem, then the method proceeds to anonymize the at least some of the information.

“13. The method according to claim 1, periodically, after the step of non-transitorily storing the cataloged-results-information, the method further comprises scanning the cataloged-results-information for information that comprises anonymity of at least one individual.

“14. The method according to claim 13, wherein if at least some of the information scanned reveals an anonymity problem, then the method proceeds to anonymize the at least some of the information.

“15. The method according to claim 1, wherein after receiving the at least one result, but before the step of non-transitory storing, the method checks the results-information for anonymity, and if the results-information are not anonymous then the method one or more of anonymizes the results-information producing anonymized results-information and then proceeds with the step of step of non-transitory storing, or sends a warning of a lack of anonymity in the results-information; and if the results-information is anonymized then the method proceeds with the step of non-transitory storing.

“16. The method according to claim 15, wherein checking if the results-information are anonymous comprises analyzing the results-information to determine if any given individual is identifiable from the results-information.

“17. The method according to claim 14, wherein anonymizing the at least some of the information comprises creating an anonymized linkage record from the results-information.

“18. The method according to claim 14, wherein anonymizing the at least some of the information comprises one or more of: modifying one or more genome sequences into modified-genome-sequences, modifying one or more segments into modified-segments, modifying organizational units into modified-organizational units, dividing fields into subfields, generalizing fields into subfields, categorizing fields into categories, modifying subfields into modified-subfields, modifying categories into modified-categories, or modifying different-subfields into modified-different-subfields.

“19. The method according to claim 18, wherein the modifying of the one or more genome sequences or of the one or more segments is done by one or more of: deleting, inserting, appending, or replacing one or more nucleotides, or by using a nucleotide nomenclature system to specify sequences of nucleotides.

“20. The method according to claim 18, wherein the modifying of the one or more of the organizational units, the subfields, the categories, or the different subfields is done by one or more of: deleting, inserting, appending, or replacing some of the data in the results-information.”

URL and more information on this patent application, see: Huang, Ethan. Methods And Systems For Anonymizing Genome Segments And Sequences And Associated Information. U.S. Patent Application Number 20230124077, filed August 30, 2022 and posted April 20, 2023. Patent URL (for desktop use only): https://ppubs.uspto.gov/pubwebapp/external.html?q=(20230124077)&db=US-PGPUB&type=ids

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