34 results about "Germline" patented technology

The embodiment of the invention provides an end-to-end B cell clone pedigree forest construction method and related equipment, and can be applied to the technical field of data processing. According to the method, a plurality of obtained receptor sequencing sequences are subjected to germline comparison identification to obtain a first test Fv sequence corresponding to each receptor sequencing sequence, and a germline Fv sequence corresponding to each receptor sequencing sequence is generated; performing integrity filtering on the first test Fv sequence, performing clone type division to obtain a plurality of first clone type sets, constructing corresponding first evolutionary trees to form a first pedigree forest on the basis of a second clone type set contract type conversion probability, and performing node optimization on all the first evolutionary trees to obtain a second pedigree forest; and after it is determined that the homotype category conversion probability after updating based on all the second evolutionary trees meets the preset requirement, visualization processing is performed on all the second evolutionary trees, so that the systematic cognition efficiency of related personnel on the adaptive immune response mechanism can be improved.

The invention relates to germline-targeting designs, stabilization designs, and / or combinations thereof, of proteins designed with modified surfaces helpful for immunization regimens, other protein modifications and / or development of nanoparticles, methods of making and using the same, and to (a) germline-targeting priming or boosting / shepherding immunogens to initiate or guide maturation of VRC01-class responses (b) PCT64 / PG9-germline-targeting designs (c) BG18-germline-targeting designs or boosting / shepherding immunogens to initiate or guide maturation of BG18-like responses, and / or (d) trimer stabilization and presentation in a membrane-bound format.

The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subject's genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.

Systems and methods for characterizing a mutation include obtaining reference sequence reads mapping to a genomic location of the mutation from a first sequencing reaction using a reference sample of a subject, and obtaining tumor sequence reads mapping to the genomic location of the mutation from a second sequencing reaction using a solid tumor sample of the subject. A reference base fraction of the mutation is determined using the reference sequence reads. A germline expectation of the mutation is determined using a tumor purity of the solid tumor sample, the major and the minor copy number at the genomic location of the mutation derived from tumor sequence reads. The reference base fraction and the germline expectation of the mutation are inputted into a model thereby obtaining, as output from the model, a determination of whether the mutation is a clonal hematopoiesis of indeterminate potential mutation or a germline mutation.

The application discloses a B cell immune repertoire antibody sequence feature analysis and specific screening method and related equipment, which can be applied to the technical field of data processing. According to the application, after the antibody sequencing sequence is subjected to germ line comparison and recognition to obtain corresponding first sequencing Fv sequence and germ line Fv sequence, the first sequencing Fv sequence is subjected to gene integrity filtering and structure integrity filtering, clonotype division and root node sequence reconstruction to obtain a second clonotype collection, and then a first lineage forest is constructed, and according to the second sequencing Fv sequence, the second clonotype collection or the first lineage forest, sequence feature analysis in multiple dimensions is carried out, so that the antibody sequence features can be analyzed from multiple dimensions such as sequence quality, sequence abundance, mutation degree, mutation preference and aggregation degree, the filtered BCR sequence has high affinity, and according to the sequence feature analysis results in multiple dimensions or the first lineage forest, a visualized graph is generated, so that relevant personnel can view the sequence features.

This invention provides low-viscosity antigen-binding proteins and methods for producing them. [Solution] The present invention relates to a method for reducing the viscosity of an antigen-binding protein by modifying the sequence in the framework region and / or Fc domain, which has been shown to be associated with high viscosity. The present invention provides antigen-binding proteins, particularly antibodies, that have been mutated to reduce viscosity. Preferred antigen-binding proteins according to the present invention include antibodies, as shown in Figure 1B, having one or more, preferably all, of the following: VH1|1-18 germline subfamily substitution; VH3|3-33 germline subfamily substitution; VK3|L16 germline subfamily substitution; VK3|L6 germline subfamily substitution; or Fc substitution.

A computer-implemented method for identifying a genomic variant is provided. The method includes obtaining one or more reference molecular sequences and sequencing data pertaining to a biological sample. One or more candidate variant positions are determined from the sequence reads for the biological sample. A classifier model is applied to each candidate variant position for selecting between a haplotype-aware or haplotype-agnostic variant analysis respectively. The classifier model is trained from haplotype structure and / or sequence reads identified with germline variants in a plurality of regions. Based on the application of the classifier model, respectively applying a haplotype-aware or haplotype-agnostic variant analysis to generate a variant identification for each candidate variant position.

Some embodiments of the methods and systems provided herein relate to variant calling from sequence data obtained from a single sample. In some embodiments, a somatic variant can be distinguished from a germline variant based on variant allele frequency in a sample and location in a genome.

This application provides an end-to-end method and related equipment for constructing a B-cell clonal lineage forest, applicable to the field of data processing technology. This application identifies the first test Fv sequence corresponding to each receptor sequencing sequence by performing germline alignment on multiple acquired receptor sequencing sequences, and generates a germline Fv sequence corresponding to each receptor sequencing sequence. Then, the first test Fv sequences are filtered for integrity and further classified into several first clonal type sets. Based on these second clonal type sets and the same-type class conversion probability, corresponding first phylogenetic trees are constructed to form a first lineage forest. Node optimization is performed on all first phylogenetic trees. After confirming that the same-type class conversion probability meets preset requirements after updating all second phylogenetic trees, all second phylogenetic trees are visualized, thereby improving the efficiency of relevant personnel's systematic understanding of adaptive immune response mechanisms.

The invention provides a method for measuring the mutation rate of a sexual reproduction animal whole genome level nucleotide germline. The method comprises the following steps: (1) performing genome sequencing on a to-be-detected species to obtain sequences of all coding proteins of the to-be-detected species; (2) constructing a phylogenetic tree of a to-be-tested species; (3) obtaining the divergence time Tdivergence between the species to be detected and the sibling species; (4) optimizing the phylogenetic tree of the species to be tested; and (5) obtaining the annual germline mutation rate [mu] year of the species to be detected. The principle of the method is as follows: neutral regions or neutral sites are widely distributed in a genome, and mutations generated at the positions are generally not influenced by natural selection; the mutation rate of the germline can be calculated by analyzing the change of the variation frequency of the sites along with time. The method provided by the invention not only is widely applicable to sexual reproduction animal species with obtained genome or transcriptome data, but also is accurate and efficient, fills up the blank of the prior art, and has great significance in theoretical research and practical application of biomedical engineering.

The present invention provides genetically modified animals (e.g., mice), humanized heavy chain antibodies, humanized nanobodies, and methods for producing and using them. [Solution] Provided are genetically modified non-human animals (e.g., genetically modified mice) that can be designed to produce heavy chain antibodies that can be used to generate single-domain antibodies or nanobodies. In one embodiment, a genetically modified mouse is provided comprising a germline modification comprising deletion of nucleic acid sequences comprising one or more heavy chain C region genes; the genetically modified mouse expresses an IgG heavy chain antibody and secretes an IgG heavy chain antibody in its serum.

Context-specific tumor-only mutation classification is described. A mutation classification module may classify a mutation identified in sequencing data from a tumor sample as germline or somatic based on a likelihood ratio relative to a threshold, the likelihood ratio comparing a germline model likelihood of a germline model of the mutation to a somatic model likelihood of a somatic model of the mutation and the threshold calculated based on a context of the mutation. The mutation classification module may output the classification of the mutation.

The invention disclosed herein generally relates to methods of assessing and monitoring tumor load through analysis of tumor DNA in cancer patients. Quantitative measures derived from cell-free DNA and germline DNA are used to assess and monitor tumor load. By assessing and monitoring tumor load, cancer may be detected in a subject. The tumor load of a subject may be assessed at a number of different time points to monitor a progression, regression, or recurrence of cancer in a subject.

Provided is a method of selecting a camelid nanobody from a library of camelid nanobody sequences collected from B cells from a camelid immunized with an antigen. The method comprises: (a) identifying a camelid nanobody that has at least one of the following features (i) a phenylalanine (F) at position 42 (IMGT numbering); (ii) a short hinge; (iii) two or more cysteines in the nanobody sequence; (iv) a glutamine (Q) at position 123 (IMGT numbering); (v) low immunogenicity metric; (vi) non-classic VHH derived from germline IGHV3 or a valine (V) at position 42 (IMGT numbering); (vii) non-classic VHH derived from germline IGHV4 or an isoleucine (I) at position 42 (IMGT numbering); (viii) a histidine (H), aspartic acid (D) or glutamic acid (E) in the CDR region; (ix) a histidine (H), aspartic acid (D) or glutamic acid (E) in the first three amino acid residues, the FR2 region, or the first sixteen amino acid residues of the FR3 region of the nanobody sequence; (x) a tyrosine (Y) at position 42 (IMGT numbering), and the nanobody having a loop, concave paratope structure configuration; or (xi) a phenylalanine (F) at position 42 (IMGT numbering), and the nanobody having a convex paratope structure configuration; and (b) measuring one or more biological activities of the nanobody identified in step (a).

The invention provides an HIV-1 Env-derived immunogen that simultaneously engages more than one lineage of germline bNAbs specific for different neutralization target sites of the native HIV-1 Env trimer. In certain embodiments, the inventive immunogen comprises a chimeric Env, with binding sites drawn from more than one native Env proteins. These can be used both in the form of full-length / minimally truncated membrane-bound trimers (e.g., expressed from cDNA, mRNA or viral vectors, which also are provided by the present invention, as are cells comprising the immunogen) or, alternatively, in the form of soluble truncated trimers (e.g., SOSIP or IP trimers). Also provided are a pharmaceutical composition comprising the inventive immunogen, nucleic acids encoding the same, and / or cells comprising them, and a method of vaccinating a human patient against HIV using the inventive immunogen and composition.

The invention concerns a method for producing a shoot of a plant comprising germline progenitor cells of a recalcitrant plant. The germline progenitor cells may be modified to comprise a mutation in a sequence of interest. The invention further pertains to plants obtainable by the method of the invention, wherein the plant preferably comprises at least the L2-meristem layer of the recalcitrant plant.

Genetically modified non-human animals are provided that express an immunoglobulin variable domain that comprises at least one histidine, wherein the at least one histidine is encoded by a substitution of a non-histidine codon in the germline of the animal with a histidine codon, or the insertion of a histidine codon in a germline immunoglobulin nucleic acid sequence. Immunoglobulin genes comprising histidines in one or more CDRs, in an N-terminal region, and / or in a loop 4 region are also provided. Immunoglobulin variable domains comprising one or more histidines (e.g., histidine clusters) substituted for non-antigen-binding non-histidine residues. Non-human animals that are progeny of animals comprising modified heavy chain variable loci (V, D, J segments), modified light chain variable loci (V, J segments), and rearranged germline light chain genes (VJ sequences) are also provided. Non-human animals that make immunoglobulin domains that bind antigens in a pH-sensitive manner are provided.

Providing a new method for determining gene mutations in JMML. [Solution] A method for determining gene mutations in juvenile myelomonocytic leukemia (JMML), comprising the step of determining that the subject has gene mutations in the CBL group or NF1 group if the distribution of monocyte morphology in a blood sample taken from the subject is as follows: (1) if there is a lot of A and a little D, the subject is in the PTPN11_somatic group; (2) if there is a lot of B, the subject is in the PTPN11_germline group; (3) if there is a lot of C, the subject is in the KRAS group; (4) if there is little A and C and a lot of B and D, the subject is in the NRAS group; or (5) if the subject does not fall into any of the above categories (1) to (4), the subject is in the CBL group or NF1 group. A is a monocyte that has cytoplasmic vacuoles and a club-shaped nucleus; B is a monocyte that does not form a cytoplasmic vacuole and has a club-shaped nucleus; C is a monocyte that has cytoplasmic vacuoles and a round nucleus; D represents a monocyte that does not form a cytoplasmic vacuole and has a round nucleus.

The invention relates to PGT121-germline-targeting designs, trimer stabilization designs, combinations of those two, trimers designed with modified surfaces helpful for immunization regimens, other trimer modifications and on development of trimer nanoparticles and methods of making and using the same.

This invention discloses a method for constructing and applying an anti-obesity animal model based on ISCA1 / 2 gene regulation, belonging to the field of biomedical technology. The method utilizes CRISPR-Cas9 gene editing technology to design specific single-stranded guide RNAs targeting the ISCA1 and ISCA2 genes in mice. Cas9 mRNA and sgRNA are introduced into fertilized eggs of C57BL / 6J strain mice via microinjection. The injected embryos are then transferred into pseudopregnant mice to obtain F0 generation chimeric mice. By mating F0 generation mice with wild-type C57BL / 6J mice, F1 generation heterozygous mice carrying the target mutation in the germline are selected, thus obtaining the anti-obesity animal model. This model is not only a phenotypic model but also a mechanistic research model, suitable for drug target validation, energy metabolism pathway exploration, and personalized treatment strategy evaluation.

The invention relates to PGT121-germline-targeting designs, trimer stabilization designs, combinations of those two, trimers designed with modified surfaces helpful for immunization regimens, other trimer modifications and on development of trimer nanoparticles and methods of making and using the same.

The present disclosure provides a method for selecting hypogammaglobulinemia patients in need of immunoglobulin replacement therapy (IgG-RT) by analyzing the patient's B cell repertoire. The method can be used before treating the patient with IgG-RT. The method can also include treating the patient. Also provided herein is a diagnostic product in a computer-readable medium that provides information for patient selection. The B cell repertoire can be measured by the number or abundance of individual antibody clones, by calculating a diversity index value for antibody clones, by calculating the total frequency of the 10 to 30 most frequent antibody clones, by determining the frequency of variable region gene (V region) usage in antibody clones, by measuring the percent germline identity of V or J regions in the BCR repertoire by comparing them with corresponding germline sequences, and / or by determining the somatic mutation frequency in different regions along the V region.

The invention provides a method for reconstructing functional gametes of fish cryopreserved germline stem cells based on zebra fish nanos2- / -mutant receptors, which specifically comprises the following steps: S1, collecting embryos of selfing progenies of zebra fish nanos2- / -and nanos + / -mutants, culturing and screening out nanos2- / -mutants to obtain receptor fish; s2, after gonads of the cryopreserved fishes are recovered, donor fish germline stem cells are obtained; s3, transplanting the germline stem cells of the body fish in the step S2 into the receptor fish in the step S1, culturing to obtain positive individuals, and continuously culturing to obtain the functional gametes of the zebra fish. Based on a selection strategy taking a nanos2 <- / -> mutant receptor as an excellent receptor, verification is carried out in experimental animal zebra fish cryopreserved germline stem cells: colonization and differentiation of germline stem cells from a donor source can be effectively supported, so that functional ova and sperms are generated, and the limitation that donor ova are difficult to obtain in an existing belly borrowing reproduction technology is broken through; and a new way is provided for long-term preservation and recovery of fish germplasm resources.

The application relates to a breast cancer risk assessment method and related equipment. The method comprises the following steps: obtaining germline genome sequencing data of a target object; the target object is a patient to be evaluated who is positive for breast nodules according to an ultrasonic examination result; inputting the germline genome sequencing data into a breast cancer germline genome evaluation model to obtain a breast cancer germline etiology score result of the target object; determining an immune exhaustion state evaluation result according to immune cell detection data of the target object and immune exhaustion reference information; the immune exhaustion reference information is obtained based on immune exhaustion analysis data of a non-breast cancer population; combining the breast cancer germline etiology score result and the immune exhaustion state evaluation result to obtain a breast cancer risk assessment result of the target object; the immune exhaustion state evaluation result is used for verifying the breast cancer germline etiology score result from the function level of immune cells. The method can effectively improve the accuracy of breast cancer risk assessment.

Genetically modified non-human animals are provided that express an immunoglobulin variable domain that comprises at least one histidine, wherein the at least one histidine is encoded by a substitution of a non-histidine codon in the germline of the animal with a histidine codon, or the insertion of a histidine codon in a germline immunoglobulin nucleic acid sequence. Immunoglobulin genes comprising histidines in one or more CDRs, in an N-terminal region, and / or in a loop 4 region are also provided. Immunoglobulin variable domains comprising one or more histidines (e.g., histidine clusters) substituted for non-antigen-binding non-histidine residues. Non-human animals that are progeny of animals comprising modified heavy chain variable loci (V, D, J segments), modified light chain variable loci (V, J segments), and rearranged germline light chain genes (VJ sequences) are also provided. Non-human animals that make immunoglobulin domains that bind antigens in a pH-sensitive manner are provided.

The present invention relates to placental alkaline phosphatase (ALPP) and / or germline alkaline phosphatase (ALPPL2)-specific antigen-binding molecules, related fusion proteins, conjugates, and methods for producing the same. In a further aspect, the present invention relates to conjugated single domain antibodies (VHH domains).

Sequential immunization strategies to guide the maturation of antibodies against the human immunodeficiency virus (HIV) are described. The sequential immunization strategies utilize an HIV envelope protein (Env) that binds germline (gl) B cells as a first (prime) immunization and an Env with a functional glycosylated N276 as a second (boost) immunization. The sequential immunization strategies successfully elicit neutralizing antibodies against HIV.

Methods are provided for detecting SVs from sequencing data from a tumor sample and classifying those SVs as somatic or germline without the use of matched normal sequences. Methods use a database of SVs and SNP profiles from previous samples. Methods include comparing a subject SNP profile to sample SNP profiles in the database and excluding from further analysis database entries with matching SNP profiles (as presumably originating from the same subject). Where SVs from the tumor sample match SVs found in samples from other people, the tumor SVs are called as being germline. When the tumor SVs do not have any matches among data from other people, those SVs are called as somatic.

Immunization strategies to naturally guide the maturation of antibodies against the human immunodeficiency virus (HIV) in HIV-infected subjects are described. The strategies include immunization utilizing an HIV envelope protein (Env) that binds germline (gl) B cells combined with taking HIV-infected subjects off of anti-viral medications, allowing natural virus to guide the maturation of gl B cells activated by the immunization. When B cells effectively mature against the HIV virus. HIV-infected subjects may remain off of anti-viral medications.

The present invention relates to a method for producing a shoot of a plant comprising a germline progenitor cell of a difficult-to-regenerate plant. The germline progenitor cell may be modified to contain a mutation in a sequence of interest. The present invention further relates to a plant obtainable by the method of the invention, wherein the plant preferably comprises at least the L2 meristem layer of the difficult-to-regenerate plant.