Concealing Information Present Within Nucleic Acids

Content Provider	The Lens
Abstract	Methods related to concealment of genetic information present within nucleic acid sequences, wherein individual nucleic acid molecules are barcoded. In some embodiments barcoding occurs before, after, or during enrichment. Barcoded nucleic acids are then combined with control barcoded nucleic acids. Different methods are provided for barcoding and pooling to conceal different types of genetic information present within nucleic acids.
Related Links	https://www.lens.org/lens/patent/011-054-265-198-036/frontpage
Language	English
Publisher Date	2019-08-01
Access Restriction	Open
Content Type	Text
Resource Type	Patent
Jurisdiction	United States of America
Date Applied	2017-10-24
Applicant	Geneinfosec Inc
Application No.	201716344004
Claim	A method for concealing information that may be present within nucleic acids, the method comprising: (a) securely generating barcodes; (b) affixing the barcodes to nucleic acids to create barcoded nucleic acids; (c) pooling the barcoded nucleic acids with other nucleic acids; wherein the secure generation of barcodes is done in a facility that generates a number of sets of barcodes along with a table of the barcodes present in each set; wherein the barcodes and the table of barcodes are sealed in a container that indicate when the seal is broken; wherein the barcodes are affixed to nucleic acid molecules such that barcodes are not entirely identical between different nucleic acids with the same individual sample of nucleic acids; wherein the pooling of the barcoded nucleic acids with other barcoded nucleic acids conceals information present in the nucleic acids. The method of claim 1 , wherein nucleic acids are provided with which nucleic acids of interest to the consumer can be barcoded and pooled. The method of claim 2 , wherein the nucleic acids that are provided are barcoded in the secure facility. The method of claim 3 , wherein a table of barcodes that have been added to the nucleic acids are provided to the consumer. The method of claim 1 , wherein barcodes are added to nucleic acids before or during an enrichment step. The method of claim 5 , wherein the barcodes are chosen and added during or before an enrichment step to alter the relative amounts of nucleic acids with different barcodes. The method of claim 1 , wherein the barcodes are added to nucleic acids using sticky-end ligation. The method of claim 7 , wherein the barcodes are added to nucleic acids using TA ligation. The method of claim 7 , wherein the nucleic acids are digested with restriction enzymes. The method of claim 9 , wherein the barcodes contain sticky-ends that correspond to the sticky-ends generated by the restriction enzymes, and these sticky-ends are used to ligate barcodes to nucleic acids. The method of claim 9 , wherein digestion with restriction enzymes is used to reduce the size of the oligonucleotides. The method of claim 9 , wherein digestion with restriction enzymes is used to unlink variants in the nucleic acids from each other prior to analyses. The method of claim 1 , wherein barcodes are added during a step that would normally occur for preparation of nucleic acids for sequence analysis. The method of claim 1 , wherein some barcodes added to nucleic acids share identical sequences with other barcodes added to other nucleic acids. The method of claim 1 , wherein advice is given to the consumer about how they may pool nucleic acids to conceal information that the nucleic acids may contain. The method of claim 1 , wherein barcoded nucleic acids are pooled with other barcoded nucleic acids that share some similarity. The method of claim 1 , wherein barcoded nucleic acids are pooled with other barcoded nucleic acids that share a similar origin. The method of claim 1 , wherein barcoded nucleic acids are chosen to be pooled with other barcoded nucleic acids in a manner that controls the predictions that can be made about traits present in the sources of the nucleic acids. The method of claim 1 , wherein barcoded nucleic acids are pooled so that the identity of the sources of the nucleic acids are concealed. The method of claim 1 , wherein barcoded nucleic acids are pooled so that information about traits present in some of the sources the nucleic acids is concealed. The method of claim 1 , wherein barcoded nucleic acids are pooled so that breeders may conceal the traits present in their breeds. The method of claim 1 , wherein barcoded nucleic acids are pooled so that breeders may conceal methods used in their breeding program. The method of claim 1 , wherein barcoded nucleic acids that contain data are pooled to conceal the data that they contain. A method for preparing a target nucleic acid sequence for analysis comprising: a. generating a set of barcodes comprising nucleic acids; b. affixing the barcodes of step (a) to the target nucleic acid sequence to be analyzed; and c. combining or pooling the barcoded target nucleic acid sequence to be analyzed with a control or decoy nucleic acid sequence comprising a barcode. The method of claim 24 , wherein the barcodes of step (a) are generated randomly by computer. The method of claim 24 , wherein the barcodes are affixed to the target nucleic acid sequence by ligation. The method of claim 24 , wherein the control or decoy nucleic acid sequence is selected from the group consisting of a sequence that shares a similar origin as the target nucleic acid sequence, a sequence known to correlate to a specific genetic trait, and a sequence known to correlate to a specific disease state. The method of claim 24 , wherein the barcoded target nucleic acid sequence is concealed when combined with the control or decoy nucleic acid sequence. A method for anonymizing a target nucleic acid sequence, the method comprising: a. generating a set of barcodes comprising nucleic acids; b. affixing the barcodes of step (a) to the target nucleic acid sequence; and c. combining or pooling the barcoded target nucleic acid sequence with a control or decoy nucleic acid sequence comprising a barcode, wherein the combination of the barcoded target nucleic acid sequence with the control or decoy nucleic acid sequence anonymizes the target nucleic acid sequence. The method of claim 1 , wherein the barcodes are randomly generated. The method of claim 1 , wherein not all nucleic acids receive a barcode. The method of claim 1 , wherein barcoded nucleic acids are randomly pooled. The method of claim 1 , wherein intrinsically random analyses are utilized for concealment. The method of claim 6 , wherein the rates of enrichment for different nucleic acids are randomly varied. The method of claim 9 , wherein sonication is used to unlink variants in the nucleic acids from each other prior to analyses.
CPC Classification	MICROORGANISMS OR ENZYMES;COMPOSITIONS THEREOF;PROPAGATING; PRESERVING; OR MAINTAINING MICROORGANISMS;MUTATION OR GENETIC ENGINEERING;CULTURE MEDIA Combinatorial Chemistry;Libraries; E.G. Chemical Libraries MEASURING OR TESTING PROCESSES INVOLVING ENZYMES; NUCLEIC ACIDS OR MICROORGANISMS ;COMPOSITIONS OR TEST PAPERS THEREFOR;PROCESSES OF PREPARING SUCH COMPOSITIONS;CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
Extended Family	011-054-265-198-036 054-730-364-098-509 002-441-525-057-410 041-237-557-629-811 055-102-440-945-335 034-033-588-827-070 081-643-573-759-012 063-637-502-476-134 145-789-839-256-829 156-007-455-864-470 008-882-675-773-078 072-124-002-636-456 022-932-549-397-171 053-737-708-628-40X 097-027-295-647-986
Patent ID	20190233877
Inventor/Author	Sawaya Sterling
IPC	C12Q1/6806 C12N15/11
Status	Active
Owner	Geneinfosec Inc
Simple Family	011-054-265-198-036 054-730-364-098-509 002-441-525-057-410 041-237-557-629-811 055-102-440-945-335 034-033-588-827-070 081-643-573-759-012 063-637-502-476-134 145-789-839-256-829 156-007-455-864-470 008-882-675-773-078 072-124-002-636-456 022-932-549-397-171 053-737-708-628-40X 097-027-295-647-986
CPC (with Group)	C12N15/10 C12N15/66 C40B70/00 C40B20/04 C12Q1/6806
Issuing Authority	United States Patent and Trademark Office (USPTO)
Kind	Patent Application Publication