# US 2023/0054899 A1 · High throughput genetic barcoding and analysis methods > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2023/0054899 A1 - Document ID: US20230054899A1 - Status: Published application - Kind: A1 - Application number: 17/758,828 - Filed: 2021-01-14 - Published: 2023-02-23 - Earliest claimed: 2020-01-14 - Assignees: William Marsh Rice University - Applicants: William Marsh Rice University - Inventors: David Yu ZHANG; Ping SONG; Omid VEISEH; Siavash PARKHIDEH; Sudip MUKHERJEE; Maria Isabel RUOCCO; Boram KIM; Yuxuan CHENG - Web page: https://patentgrep.com/patent/US20230054899A1 ## CPC - C12N 5/0012: {Cell encapsulation} - A61K 9/0024: {Solid, semi-solid or solidifying implants, which are implanted or injected in body tissue (compositions for intravenous administration, normal injectable solutions or dispersions for, e.g. subcutaneous administration A61K9/0019; brain implants A61K9/0085; (coated) prostheses, catheters or stents A61L)} - A61K 9/5036: {Polysaccharides, e.g. gums, alginate; Cyclodextrin} - A61K 35/39: Pancreas; Islets of Langerhans (Langerhans cells of epidermis A61K35/36) - A61K 49/0008: {Screening agents using (non-human) animal models or transgenic animal models or chimeric hosts, e.g. Alzheimer disease animal model, transgenic model for heart failure} - C12N 15/1065: {Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags} - C12N 2503/02: Drug screening - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) ## Abstract Provided herein are high-throughput methods for genetic barcoding and analysis, e.g., for tagging each biomaterial apsule with a barcode cell. These barcode cells are derived from patient samples, and thus embody natural human genetic variation. Also provided are SNP panels that can be used as genetic barcodes to identify the identity of a cell. ## Claims ### Claim 1 A method for identifying a cell encapsulation material following in vivo screening of cell encapsulation materials, the method comprising (a) preparing capsules containing barcode cells using various encapsulation materials, wherein the barcode cells comprise a plurality of SNPs that serve as a genetic barcode for each cell encapsulation material; (b) implanting the capsules into a test subject; (c) explanting the capsules after a set period of time; and (d) determining the sequence of the plurality of SNPs in the barcode cells of each explanted capsule, thereby identifying the cell encapsulation material of each capsule. ### Claim 2 (depends on 1) The method of claim 1, wherein all of the capsules made with the same encapsulation material comprise identical barcode cells. ### Claim 3 (depends on 1) The method of claim 1, wherein each type of barcode cell is used for only one encapsulation material. ### Claim 4 (depends on 1, 2, 3) The method of any one of claims 1-3, wherein the barcode cells are cells derived from a single subject. ### Claim 5 (depends on 1, 2, 3, 4) The method of any one of claims 1-4, wherein the barcode cells are HuVec cells isolated from a single subject. ### Claim 6 (depends on 1, 2, 3, 4, 5) The method of any one of claims 1-5, wherein the plurality of SNPs have variant allele frequencies of between 10% and 90%. ### Claim 7 (depends on 1, 2, 3, 4, 5, 6) The method of any one of claims 1-6, wherein the plurality of SNPs are broadly spaced across the 22 pairs of human autosomes. ### Claim 8 (depends on 7) The method of claim 7, wherein the plurality of SNPs are selected to minimize the likelihood of genetic linkage. ### Claim 9 (depends on 1, 2, 3, 4, 5, 6, 7, 8) The method of any one of claims 1-8, wherein the plurality of SNPs are present in non-coding regions of the genome. ### Claim 10 (depends on 9) The method of claim 9, wherein the non-coding regions of the genome are introns. ### Claim 11 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) The method of any one of claims 1-10, wherein the plurality of SNPs are not associated with any disease state. ### Claim 12 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11) The method of any one of claims 1-11, wherein the plurality of SNPs do not have an effect on human health. ### Claim 13 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12) The method of any one of claims 1-12, wherein the plurality of SNPs comprises at least 5 SNPs. ### Claim 14 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13) The method of any one of claims 1-13, wherein the plurality of SNPs comprises at least 30 SNPs. ### Claim 15 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14) The method of any one of claims 1-14, wherein the plurality of SNPs comprises 30 SNPs. ### Claim 16 (depends on 13, 14, 15) The method of any one of claims 13-15, wherein the SNPs are selected form the group consisting of rs10230708, rs2043583, rs955456, rs966516, rs11247921, rs10510620, rs3789806, rs1884444, rs16754, rs28932178, rs10741037, rs10805227, rs10833604, rs10964389, rs11045749, rs12213948, rs12259813, rs1516755, rs1937037, rs2616187, rs2710998, rs2874755, rs4665582, rs4712476, rs611628, rs7893462, rs7902135, rs9466930, rs2862909, and rs1338945. ### Claim 17 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16) The method of any one of claims 1-16, wherein the plurality of SNPs is sufficient to unambiguously determine the identity of the barcode cell. ### Claim 18 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17) The method of any one of claims 1-17, wherein determining the sequence of the plurality of SNPs in the barcode cells of each explanted capsule comprises (i) isolating each explanted capsule by distributing each capsule individually into a well of a multi-well plate; and (ii) amplifying each of the SNPs in the barcode cells of each isolated capsule using locus-specific forward and reverse primers. ### Claim 19 (depends on 18) The method of claim 18, wherein the locus-specific forward and reverse primers comprise universal sequences. ### Claim 20 (depends on 18, 19) The method of claim 18 or 19, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iii) appending location-specific information to each of the amplified SNPs by adding one of eight unique location-specific forward primers and one of twelve unique location-specific reverse primers to each well, where the combination of location-specific forward and location-specific reverse primers is unique to a single well of the plate. ### Claim 21 (depends on 18, 19, 20) The method of any one of claims 18-20, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iii) appending location-specific information to each of the amplified SNPs by adding the same location-specific forward primer to the wells of each row on the plate and the same location-specific reverse primer to the wells of each column on the plate. ### Claim 22 (depends on 18, 19, 20, 21) The method of any one of claims 18-21, wherein the location-specific forward and location-specific reverse primers comprise unique Hamming barcodes. ### Claim 23 (depends on 22) The method of claim 22, wherein each Hamming barcode is seven nucleotides long. ### Claim 24 (depends on 22, 23) The method of claim 22 or 23, wherein each of the Hamming barcodes lack sequence identity at at least 2 nucleotide positions as compared to any of the other Hamming barcodes. ### Claim 25 (depends on 22, 23, 24) The method of any one of claims 22-24, wherein each of the Hamming barcodes has a Hamming distance of at least two relative to every other Hamming barcode. ### Claim 26 (depends on 18, 19, 20, 21, 22, 23, 24, 25) The method of any one of claims 18-25, wherein amplification comprises performing PCR. ### Claim 27 (depends on 18, 19, 20, 21, 22, 23, 24, 25) The method of any one of claims 18-25, wherein amplification is performed using Taq polymerase or a high-fidelity polymerase. ### Claim 28 (depends on 27) The method of claim 27, wherein the high-fidelity polymerase is Q5, Phusion, or KAPA. ### Claim 29 (depends on 20, 21, 22, 23, 24, 25, 26, 27, 28) The method of any one of claims 20-28, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iv) combining the amplification products from each well of the plate, preparing a sequencing library, and sequencing the library. ### Claim 30 (depends on 29) The method of claim 29, wherein different wells determined to have barcode cells comprising the same genotype for the plurality of SNPs are identified as containing the capsules made using the same cell encapsulation material. ### Claim 31 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30) The method of any one of claims 1-30, wherein the cell encapsulation material is an alginate encapsulation material. ### Claim 32 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31) The method of any one of claims 1-31, wherein each capsule further comprises therapeutic cells. ### Claim 33 (depends on 32) The method of claim 32, wherein the therapeutic cells are insulin-secreting cells. ### Claim 34 (depends on 33) The method of claim 33, wherein the therapeutic cells are islet cells. ### Claim 35 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34) The method of any one of claims 1-34, wherein each capsule comprises about 10,000 cells. ### Claim 36 (depends on 32, 33, 34, 35) The method of any one of claims 32-35, wherein the cells in each capsule are 80% therapeutic cells and 20% barcode cells. ### Claim 37 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36) The method of any one of claims 1-36, wherein the test subject is a mouse. ### Claim 38 (depends on 37) The method of claim 37, wherein the mouse is a C57BL/6 mouse. ### Claim 39 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38) The method of any one of claims 1-38, wherein more than one capsule is implanted at a single implantation site. ### Claim 40 (depends on 39) The method of claim 39, wherein the capsules comprise different cell encapsulation materials. ### Claim 41 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39) The method of any one of claims 1-39, wherein capsules comprising different cell encapsulation materials are implanted at a single implantation site. ### Claim 42 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39) The method of any one of claims 1-39, wherein more than one cell encapsulation material is implanted at a single implantation site. ### Claim 43 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42) The method of any one of claims 1-42, wherein up to 200 capsules are implanted at each implantation site. ### Claim 44 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42) The method of any one of claims 1-42, wherein at least 200 capsules are implanted at each implantation site. ### Claim 45 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43) The method of any one of claims 1-43, wherein up to 3000 capsules are implanted at each implantation site. ### Claim 46 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45) The method of any one of claims 1-45, wherein the capsules are explanted about one month after implantation. ### Claim 47 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46) The method of any one of claims 1-46, wherein the method is a method for in vivo screening of cell encapsulation materials that maximize encapsulated cell viability. ### Claim 48 (depends on 47) The method of claims 47, wherein cell viability is measured using Live/Dead cell staining. ### Claim 49 (depends on 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48) The method of any one of claims 1-48, wherein the method is a method for in vivo screening of cell encapsulation materials that minimize fibrosis at the implantation site. ### Claim 50 (depends on 49) The method of claim 49, wherein the implantation site is examined for fibrosis. ### Claim 51 A genetic barcode comprising a plurality of SNPs that unambiguously determine the identity of a cell or an organism comprising the cell. ### Claim 52 (depends on 51) The genetic barcode of claim 51, wherein the plurality of SNPs have variant allele frequencies of between 10% and 90%. ### Claim 53 (depends on 51, 52) The genetic barcode of claim 51 or 52, wherein the plurality of SNPs are broadly spaced across the 22 pairs of human autosomes. ### Claim 54 (depends on 53) The genetic barcode of claim 53, wherein the plurality of SNPs are selected to minimize the likelihood of genetic linkage. ### Claim 55 (depends on 51, 52, 53, 54) The genetic barcode of any one of claims 51-54, wherein the plurality of SNPs are present in non-coding regions of the genome. ### Claim 56 (depends on 55) The genetic barcode of claim 55, wherein the non-coding regions of the genome are introns. ### Claim 57 (depends on 51, 52, 53, 54, 55, 56) The genetic barcode of any one of claims 51-56, wherein the plurality of SNPs are not associated with any disease state. ### Claim 58 (depends on 51, 52, 53, 54, 55, 56, 57) The genetic barcode of any one of claims 51-57, wherein the plurality of SNPs do not have an effect on human health. ### Claim 59 (depends on 51, 52, 53, 54, 55, 56, 57, 58) The genetic barcode of any one of claims 51-58, wherein the plurality of SNPs comprises at least 5 SNPs. ### Claim 60 (depends on 51, 52, 53, 54, 55, 56, 57, 58, 59) The genetic barcode of any one of claims 51-59, wherein the plurality of SNPs comprises at least 30 SNPs. ### Claim 61 (depends on 51, 52, 53, 54, 55, 56, 57, 58, 59, 60) The genetic barcode of any one of claims 51-60, wherein the plurality of SNPs comprises 30 SNPs. ### Claim 62 (depends on 59, 60, 61) The genetic barcode of any one of claims 59-61, wherein the SNPs are selected from the group consisting of rs10230708, rs2043583, rs955456, rs966516, rs11247921, rs10510620, rs3789806, rs1884444, rs16754, rs28932178, rs10741037, rs10805227, rs10833604, rs10964389, rs11045749, rs12213948, rs12259813, rs1516755, rs1937037, rs2616187, rs2710998, rs2874755, rs4665582, rs4712476, rs611628, rs7893462, rs7902135, rs9466930, rs2862909, and rs1338945. ### Claim 63 (depends on 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62) A method of identifying a cell as having come from a specific individual, the method comprising determining the sequence of the plurality of SNPs of any one of claims 51-62 for both the cell and the specific individual, wherein if the sequence of the plurality of SNPs is the same for both the cell and the specific individual, then the cell is identifying as having come from the specific individual. ### Claim 64 A method for identifying a cell encapsulation material following in vivo screening of cell encapsulation materials, the method comprising (a) preparing a plurality of barcode cells derived from one or more subjects, wherein each composition of barcode cells comprises a unique profile of a plurality of SNPs that serve as a genetic barcode for each cell encapsulation material; (b) fabricating capsules using various encapsulation materials and barcode cells; (c) implanting the capsules into a test subject; (d) explanting the capsules after a set period of time; and (d) determining the sequence of the plurality of SNPs in the barcode cells of each explanted capsule, thereby identifying the cell encapsulation material of each capsule. ### Claim 65 (depends on 64) The method of claim 64, wherein all of capsules made with the same encapsulation material have an identical composition of barcode cells. ### Claim 66 (depends on 64) The method of claim 64, wherein each composition of barcode cells is used to encode only one encapsulation material. ### Claim 67 (depends on 64, 65, 66) The method of any one of claims 64-66, wherein each capsule comprises barcode cells from one or two subjects. ### Claim 68 (depends on 64, 65, 66, 67) The method of any one of claims 64-67, wherein the barcode cells are HuVec cells isolated from one or two subjects. ### Claim 69 (depends on 64, 65, 66, 67, 68) The method of any one of claims 64-68, wherein the plurality of SNPs have variant allele frequencies between 10% and 90%. ### Claim 70 (depends on 64, 65, 66, 67, 68, 69) The method of any one of claims 64-69, wherein the plurality of SNPs are broadly spaced across the 22 pairs of human autosomes. ### Claim 71 (depends on 70) The method of claim 70, wherein the plurality of SNPs are selected to minimize the likelihood of genetic linkage. ### Claim 72 (depends on 64, 65, 66, 67, 68, 69, 70, 71) The method of any one of claims 64-71, wherein the plurality of SNPs are present in non-coding regions of the genome. ### Claim 73 (depends on 72) The method of claim 72, wherein the non-coding regions of the genome are introns. ### Claim 74 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73) The method of any one of claims 64-73, wherein the plurality of SNPs are not associated with any disease state. ### Claim 75 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74) The method of any one of claims 64-74, wherein the plurality of SNPs do not have an effect on human health. ### Claim 76 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75) The method of any one of claims 64-75, wherein the plurality of SNPs comprises at least 5 SNPs. ### Claim 77 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76) The method of any one of claims 64-76, wherein the plurality of SNPs comprises 30 SNPs. ### Claim 78 The method of 72 or 73, wherein the SNPs are selected from the group consisting of rs10230708, rs2043583, rs955456, rs966516, rs11247921, rs10510620, rs3789806, rs1884444, rs16754, rs28932178, rs10741037, rs10805227, rs10833604, rs10964389, rs11045749, rs12213948, rs12259813, rs1516755, rs1937037, rs2616187, rs2710998, rs2874755, rs4665582, rs4712476, rs611628, rs7893462, rs7902135, rs9466930, rs2862909, and rs1338945. ### Claim 79 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78) The method of any one of claims 64-78, wherein the plurality of SNPs is sufficient to unambiguously determine the composition of barcode cells. ### Claim 80 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79) The method of any one of claims 64-79, wherein determining the sequence of the plurality of SNPs in the barcode cells of each explanted capsule comprises (i) isolating each explanted capsule by distributing each capsule individually into a well of a multi-well plate; and (ii) amplifying each of the SNPs in the barcode cells of each isolated capsule using locus-specific forward and reverse primers. ### Claim 81 (depends on 80) The method of claim 80, wherein the locus-specific forward and reverse primers comprise universal sequences. ### Claim 82 (depends on 80, 81) The method of claim 80 or 81, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iii) appending location-specific information to each of the amplified SNPs by adding one of eight unique location-specific forward primers and one of twelve unique location-specific reverse primers to each well, where the combination of location-specific forward and location-specific reverse primers is unique to a single well of the plate. ### Claim 83 (depends on 80, 81, 82) The method of any one of claims 80-82, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iii) appending location-specific information to each of the amplified SNPs by adding the same location-specific forward primer to the wells of each row on the plate and the same location-specific reverse primer to the wells of each column on the plate. ### Claim 84 (depends on 80, 81, 82, 83) The method of any one of claims 80-83, wherein the location-specific forward and location-specific reverse primers comprise unique Hamming barcodes. ### Claim 85 (depends on 84) The method of claim 84, wherein each Hamming barcode is seven nucleotides long. ### Claim 86 (depends on 84, 85) The method of claim 84 or 85, wherein each of the Hamming barcodes lack sequence identity at at least 2 nucleotide positions as compared to any of the other Hamming barcodes. ### Claim 87 (depends on 84, 85, 86) The method of any one of claims 84-86, wherein each of the Hamming barcodes has a Hamming distance of at least two relative to every other Hamming barcode. ### Claim 88 (depends on 80, 81, 82, 83, 84, 85, 86, 87) The method of any one of claims 80-87, wherein amplification comprises performing PCR. ### Claim 89 (depends on 80, 81, 82, 83, 84, 85, 86, 87) The method of any one of claims 80-87, wherein amplification is performed using Taq polymerase or a high-fidelity polymerase. ### Claim 90 (depends on 89) The method of claim 89, wherein the high-fidelity polymerase is Q5, Phusion, or KAPA. ### Claim 91 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90) The method of any one of claims 64-90, wherein determining the sequence of the plurality of SNPs in the barcode cells further comprises (iv) combining the amplification products from each well of the plate, preparing a sequencing library, and sequencing the library. ### Claim 92 (depends on 91) The method of claim 91, wherein different wells determined to have barcode cells comprising the same genotype for the plurality of SNPs are identified as containing the capsules made using the same cell encapsulation material. ### Claim 93 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92) The method of any one of claims 64-92, wherein the cell encapsulation material is an alginate encapsulation material. ### Claim 94 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93) The method of any one of claims 64-93, wherein each capsule further comprises therapeutic cells. ### Claim 95 (depends on 94) The method of claim 94, wherein the therapeutic cells are insulin-secreting cells. ### Claim 96 (depends on 95) The method of claim 95, wherein the therapeutic cells are islet cells. ### Claim 97 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96) The method of any one of claims 64-96, wherein each capsule comprises about 10,000 cells. ### Claim 98 (depends on 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97) The method of any one of claims 32-97, wherein the cells in each capsule are 80% therapeutic cells and 20% barcode cells. ### Claim 99 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98) The method of any one of claims 64-98, wherein the subject for in vivo test is a mouse. ### Claim 100 (depends on 99) The method of claim 99, wherein the mouse is a C57BL/6 mouse. ### Claim 101 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98) The method of any one of claims 64-98, wherein the subject for in vivo test is a non-human primate. ### Claim 102 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101) The method of any claims 64-101, wherein more than one capsule is implanted at a single implantation site. ### Claim 103 (depends on 102) The method of claim 102, wherein the capsules comprise different cell encapsulation materials. ### Claim 104 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102) The method of any of claims 64-102, wherein capsules comprising different cell encapsulation materials are implanted at a single implantation site. ### Claim 105 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102) The method of any of claims 64-102, wherein more than one cell encapsulation material is implanted at a single implantation site. ### Claim 106 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105) The method of any of claims 64-105, wherein up to 200 capsules are implanted at each site in a mouse. ### Claim 107 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105) The method of any of claims 64-105, wherein at least 200 capsules are implanted at each site in a mouse. ### Claim 108 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106) The method of any of claims 64-106, wherein up to 3000 capsules are implanted at each site in a non-human primate. ### Claim 109 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108) The method of any of claims 64-108, wherein the capsules are explanted about one month after implantation. ### Claim 110 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109) The method of any of claims 64-109, wherein the method is a method for in vivo screening of cell encapsulation materials that maximize encapsulated cell viability. ### Claim 111 (depends on 110) The method of claim 110, wherein cell viability is measured using live/dead cell staining. ### Claim 112 (depends on 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111) The method of any of claims 64-111, wherein the method is a method for in vivo screening of cell encapsulation materials that minimize fibrosis at the implantation site. ### Claim 113 (depends on 112) The method of claim 112, wherein the implantation site is examined for fibrosis.