48 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 present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.

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 present invention provides systems and methods for predicting an allergic response in a subject by measuring the amounts of RNA species from B cells that encode at least a part of the Immunoglobulin E (IgE) constant region (Cε), such as nonproductive epsilon germline transcripts (εGLTs).

This article reports a method for determining the epitope of an antibody that specifically binds to a therapeutic antibody, the method comprising the steps of: a) culturing a sample comprising serum and the antibody that specifically binds to the therapeutic antibody separately with: i) at least one Fab fragment of the therapeutic antibody, and ii) at least one Fab fragment of the therapeutic antibody, wherein the HVRs that form the complementary site have been replaced by germline sequences, and detecting the binding or non-binding of the antibody that specifically binds to the therapeutic antibody to at least one Fab fragment in either i) or ii), and b) determining that the epitope of the antibody that specifically binds to the therapeutic antibody is in at least one HVR that has been replaced in ii), provided that binding is detected in i) and non-binding is detected in ii).

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.

Compositions containing chimeric RNA molecules which comprise meristem targeting sequences that are fused to RNA cargo sequences that include gene editing molecules are provided. Methods of using the compositions to efficiently edit plant genomes without intervening tissue culture steps are also provided. The solutions described here relate to engineered RNA molecules useful in producing plants with altered genomes. As such, it relates to substantially purified compositions, vectors, systems, as well as genomes of plants.

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.

Provided are germline mutational signatures that can improve somatic calling and detection of somatic mutational signatures.

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 herein are methods and transgenic systems termed Ifegenia (Inherited Female Elimination by Genetically Encoded Nucleases to Interrupt Alleles) comprising transgenic animal strains encoding Cas9 and / or gRNA that targets a female essential gene which are capable of passing down these genes as well as mutant female essential genes in wild populations in order to suppress the population of the animals, as well as methods and systems for making such animals. In some instances, the methods and systems provided herein result in both somatic and heritable germline mutations of the female essential gene resulting in daughter killing, and female essential gene mutant males reproductively viable to pass along the female essential gene mutation and related transgenes into subsequent generations. The methods and systems are adaptable to population control of insects, in particular mosquitoes such as Anopheles gambiae.

Described herein are methods of preparing an enriched library of nucleic acids, comprising: (a) identifying a panel of patient-specific somatic variants present in a tumor sample from a patient, wherein the somatic variants comprise one or more of (i) tumor somatic variants, (ii) non-tumor somatic variants, and (iii) germline sites incorrectly identified as somatic; (b) preparing a sample of cell- free DNA fragments from the patient for sequencing; (c) selectively enriching the cell-free DNA for the fragments comprising one or more of the somatic variants to generate an enriched library; and (d) analyzing the enriched library by generating sequencing reads for each somatic variant position, wherein analyzing comprises applying a classification model to the somatic variants to classify each somatic variant as either tumor, non-tumor, or germline variants.

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.

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.

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 systems and methods to detect somatic or germline variants from cell-free DNA (cfDNA). Generally, the systems and methods comprise receiving sequencing information from cfDNA from said subject, determining whether measures are above or below a threshold; and classifying each as being of somatic origin or classifying each locus as being of germline origin.

An analysis method of analyzing a nucleic acid sequence derived from a patient sample with a computer, may include: obtaining analysis data relating to a mutation determined based on nucleic acid sequence data derived from the patient sample; and generating a first report providing information relating to the determined mutation in a first form which is different from a second form of a second report, wherein the second report provides information relating to a germline mutation among the determined mutation in the second form.

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.