The largest database of trusted experimental protocols

Genotype

Genotype refers to the genetic makeup of an individual, including the alleles present at specific gene loci.
It provides information about an organism's inhereted traits and potential for expression.
Genotype research aims to identify and understand the genetic factors that influence phenotypic characteristics, disease susceptibility, and response to therapies.
Accurate and reproducible genotype analysis is crucial for advancing personalized medicine and drug development.
PubCompare.ai's AI-powered platform can enhance your genotype research by helping you easily locate relevant protocols, make informed comparisons, and optimize your experimental design.
Experience the power of AI-driven genotype optimization today.

Most cited protocols related to «Genotype»

In order to understand the modeling choices underlying our new imputation algorithm, it is crucial to consider the statistical issues that arise in imputation datasets. For simplicity, we will discuss these issues in the context of Scenario A, although we will also extend them to Scenario B in the Results section. Fundamentally, imputation is very similar to phasing, so it is no surprise that most imputation algorithms are based on population genetic models that were originally used in phasing methods. The most important distinction between phasing and imputation datasets is that the latter include large proportions of systematically missing genotypes.
Large amounts of missing data greatly increase the space of possible outcomes, and most phasing algorithms are not able to explore this space efficiently enough to be useful for inference in large studies. A standard way to overcome this problem with HMMs [6] (link),[11] (link) is to make the approximation that, conditional on the reference panel, each study individual's multilocus genotype is independent of the genotypes for the rest of the study sample. This transforms the inference problem into a separate imputation step for each study individual, with each step involving only a small proportion of missing data since the reference panel is assumed to be missing few, if any, genotypes.
In motivating our new imputation methodology, we pointed out that modeling the study individuals independently, rather than jointly, sacrifices phasing accuracy at typed SNPs; this led us to propose a hybrid approach that models the study haplotypes jointly at typed SNPs but independently at untyped SNPs. We made the latter choice partly to improve efficiency – it is fast to impute untyped alleles independently for different haplotypes, which allows us to use all of the information in large reference panels – but also because of the intuition that there is little to be gained from jointly modeling the study sample at untyped SNPs.
By contrast, the recently published BEAGLE [13] (link) imputation approach fits a full joint model to all individuals at all SNPs. To overcome the difficulties caused by the large space of possible genotype configurations, BEAGLE initializes its model using a few ad-hoc burn-in iterations in which genotype imputation is driven primarily by the reference panel. The intuition is that this burn-in period will help the model reach a plausible part of parameter space, which can be used as a starting point for fitting a full joint model.
This alternative modeling strategy raises the question of whether, and to what extent, it is advantageous to model the study sample jointly at untyped SNPs. One argument [20] (link) holds that there is no point in jointly modeling such SNPs because all of the linkage disequilibrium information needed to impute them is contained in the reference panel. A counterargument is that, as with any statistical missing data problem, the “correct” inference approach is to create a joint model of all observed and missing data. We have found that a full joint model may indeed improve accuracy on small, contrived imputation datasets (data not shown), and this leads us to believe that joint modeling could theoretically increase accuracy in more realistic datasets.
However, a more salient question is whether there is any useful information to be gained from jointly modeling untyped SNPs, and whether this information can be obtained with a reasonable amount of computational effort. Most imputation methods, including our new algorithm, implicitly assume that such information is not worth pursuing, whereas BEAGLE assumes that it is. We explore this question further in the sections that follow.
Publication 2009
Alleles Genotype Haplotypes Hybrids Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Intuition Joints Seizures Single Nucleotide Polymorphism
Because allele sequences may only be partially available (e.g., exons
only), HISAT-genotype first identifies two alleles based on the sequences
commonly available for all alleles, e.g. exons. For example, the IMGT/HLA
database includes many sequences for some key exons of HLA genes, but it
contains far fewer complete sequences comprising all exons, introns, and UTRs of
the genes. So far 3,644 alleles have been classified for HLA-A. Although all
alleles of HLA-A have known sequences for exons 2 and 3, only 383 alleles have
full-length sequences available. The sequences for the remaining 3,261 alleles
include either all 8 exons or a subset of them. HLA-B has 4,454 alleles, of
which 416 have full sequences available. HLA-C has 3,290 alleles, with only 590
fully sequenced, HLA-DQA1 has 76 alleles with 53 fully sequenced, HLA-DQB1 has
978 alleles with 69 fully sequenced, and HLA-DRB1 has 1,972 alleles, with only
43 fully sequenced. During this step, HISAT-genotype first chooses
representative alleles from groups of alleles that have the same exon sequences.
Next it identifies alleles in the representative alleles that are highly likely
to be present in a sequenced sample. Then the other alleles from the groups with
the same exons as the representatives are selected for assessment during the
next step. Second, HISAT-genotype further identifies candidate alleles based on
both exons and introns. HISAT-genotype applies the following statistical model
in each of the two steps to find maximum likelihood estimates of abundance
through an Expectation-Maximization (EM) algorithm39 . We previously implemented an EM
solution in our Centrifuge system40 , and we used a similar algorithm in HISAT-genotype, with
modifications to the variable definitions as follows.
Publication 2019
Alleles Exons Genes Genotype HLA-B Antigens HLA-C Antigens HLA-DQA1 HLA-DQB1 antigen HLA-DRB1 Antigen Introns Untranslated Regions
, where αj is the updated estimate of allele
j’s abundance. α′ is
then used in the next iteration.
HISAT-genotype finds the abundances α that best
reflect the given read alignments, that is, the abundances that maximize the
likelihood function L(α
C) above by repeating the EM procedure no more than 1000
times or until the difference between the previous and current estimates of
abundances, j=1Aαjαj , is less than 0.0001.
Publication 2019
Genotype
A detailed description of materials and methods is given in Methods. The work-flow and organization of the project are given in Supplementary Fig. 16. Case series came from previously established collections with nationally representative recruitment: 2,000 samples were genotyped for each. The control samples came from two sources: half from the 1958 Birth Cohort and the remainder from a new UK Blood Service sample. The latter collection was established specifically for this study and is a UK national repository of anonymized DNA samples from 3,622 consenting blood donors. The vast majority of subjects were self-reported as of European Caucasian ancestry. All DNA samples were requantified and tested for degradation and PCR amplification. Genotyping was performed using GeneChip 500K arrays at the Affymetrix Services Lab (California): arrays not passing the 93% call rate threshold at P=0.33 with the Dynamic Model algorithm were repeated. CEL (cell intensity) files were transferred to WTCCC for quantile normalization, and genotypes called using a new genotyping algorithm, CHIAMO, developed for this project. QC/QA measures included sample call rate, overall heterozygosity and evidence of non-European ancestry (809 samples excluded; 16,179 retained for analysis). SNPs were excluded from analysis because of missing data rates, departures from Hardy-Weinberg equilibrium and other metrics (31,011 excluded; 469,557 retained). Standard 1-d.f. and 2-d.f. tests of case-control association were supplemented with bayesian approaches, multilocus methods (data imputation) and analyses with combined data sets, either as additional cases (to detect variants influencing multiple phenotypes) or as an expanded reference group (to increase power). Results for each SNP for all analyses reported will be available from http://www.wtccc.org.uk, as will details allowing other researchers to apply for access to WTCCC genotype data. Software packages developed within the WTCCC are available on request (see Methods for details).
Publication 2007
Birth Cohort BLOOD Caucasoid Races Cells DNA, A-Form Donor, Blood Europeans Gene Chips Genotype Heterozygote Phenotype
A VCF file (Fig. 1a) consists of a header section and a data section. The header contains an arbitrary number of meta-information lines, each starting with characters ‘##’, and a TAB delimited field definition line, starting with a single ‘#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.

(a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (bf) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.

Publication 2011
Alleles Character Chromosomes Colon Deletion Mutation Genetic Diversity Genome Genotype Haplotypes Human Body

Most recents protocols related to «Genotype»

Not available on PMC !

Example 3

STING protein expression was measured in different breast cancer cell subtypes by western blot analysis on protein extracts from the breast cancer cell lines. Western results are shown in FIGS. 22A and 22C. STING protein levels are shown relative to β-actin control protein levels. Genotypes of the cell lines (ER+/−, PR+/−, and HER2+/−) are shown in FIG. 22B. The data presented herein demonstrates that STING levels are generally increased in TNBC (Triple Negative Breast Cancer) and luminal B cancer cell subtypes.

TNBC cell lines were also assayed for their responsiveness to the STING agonist AduroS100. Cells were treated with AduroS100 or a control and CXCL10 levels secreted into the supernatant were measured. As is shown in FIG. 22D, all TNBC cell lines showed elevated levels of the CXCL10 chemokine when treated with AduroS100 relative to a control, indicating that TNBC cells are responsive to treatment with a STING agonist, regardless of STING levels.

Patent 2024
Actins Breast Cancer 3 Cell Lines Cells Chemokine CXCL10 ERBB2 protein, human Genotype Malignant Neoplasm of Breast Malignant Neoplasms MCF-7 Cells Phenobarbital Proteins Triple Negative Breast Neoplasms Western Blot

Example 25

To confirm the function of BCAR in TCR T targeting NY-ESO-1, tumor cell line J82-NY ESO1 with HLA genotype A: 0201 was used as target cells to measure the killing effect of BCAR-TCR T cells.

1×105 J82-NY ESO1 tumor cells were seeded on the RTCA (Real Time Cell Analysis) electrode plate, and cultured overnight to allow adhesion. The cells were divided into three groups—A, B and C. In group A, 1×105, 1×104, 1×103, 1×102 BCAR-TCR T were co-cultured with J82-NY-ESO-1 cells, respectively. In group B, 1×105, 1×104, 1×103, 1×102 BCAR-TCR T together with 1×105 B cells were co-cultured with J82-NY-ESO-1 cells. Group C was blank control. RTCA system was used to record “Cell Index” every ten minutes for 24 hours.

As shown in FIG. 20, in group A where B cell was absent, only the highest dose of 1×105 BCAR-TCR T showed significant killing effect on J82-NY ESO1 tumor cells, while in group B, in the presence of B cells, even the lowest dose of 1×102 BCAR-TCR T showed a significant killing effect on J82-NY ESO1 tumor cells that is comparable to that of 1×105 BCAR-TCR T dose in group A, indicating an increase of efficacy of about 1000 times.

Patent 2024
B-Lymphocytes Cell Line, Tumor Cells Cultured Cells Genotype Neoplasms Ribavirin T-Lymphocyte
Not available on PMC !

Example 2

We correlated the degree of Paneth cell defect (percentage of Paneth cells with normal morphology) with numbers of ATG16L1 T300A or NOD2 risk alleles. As shown in FIG. 8A and FIG. 8B, neither the numbers of risk alleles of ATG16L1 T300A nor NOD2 correlated with Paneth cell phenotype. Likewise, neither the sum total of ATG16L1 T300A nor NOD2 risk alleles correlated with Paneth cell phenotype (FIG. 8C). This suggests that in this population of pediatric CD patients, environmental factor(s) may play a more significant role in modulating Paneth cell function.

Patent 2024
Alleles Genotype Paneth Cells Patients Phenotype Physiology, Cell
Not available on PMC !

Example 1

We demonstrated the expression of STAT1 was higher in AD cases than the aged matched control cases (FIGS. 1A and 1B). In FIG. 1A, no staining of Phosphorylated STAT1 (pSTAT1) was seen in the control cells. In contrast, as shown in the same FIG. 1A and the enlarged snapshot of the photo of Case-1 in FIG. 1B, much more staining of pSTAT1 was seen in each of the three cases.

To understand whether the activation of STAT1 pathway was causal for the pathogenesis of AD, or was an consequence of neuro-inflammation in late stage of AD, we crossed STAT1−/− mice with APP/PS1 mice to generate AD mice with STAT1−/− background. APP/PS1/STAT1−/− mice, and their littermate controls of APP/PS1 genotype were kept to 3-4 months and sacrificed for histological examination of Aβ deposition. Surprisingly, we found consistent reduction in Aβ number as well as areas occupied by Aβ in Stat1−/− mice (FIGS. 2A and 2B), Similar results were observed when we measure Aβ42 in TBS or formic acid extraction (FIGS. 2C and 2D). Furthermore, the reduction in Aβ was not due to change in APP expression level, or the secretase cleavages APP (FIGS. 16A and 16B).

Patent 2024
Cells Cytokinesis Figs formic acid Genotype Inflammation Mice, House Mice, Knockout Mice, Laboratory pathogenesis Secretase STAT1 protein, human Vision
The samples were received in ethylenediaminetetraacetate (EDTA) tubes. According to the manufacturer’s instructions, DNA was extracted using the GeneJET Whole Blood Genomic DNA Purification Mini Kit (Thermofisher, Paisley, United Kingdom). The purified DNA was assessed for quality and quantity using NanoDrop 200 spectrophotometer (Thermofisher, Paisley, United Kingdom). Using standard polymerase chain reaction (PCR) techniques, a primer was used to capture the single nucleotide variant corresponding to the UCP2−866 G/A polymorphism (rs659366). In brief, 50 ng of DNA template was mixed with 0.5 µM of each of forward (5’ CAC GCT GCT TCT GCC AGG AC 3’) and reverse (5’ AGG CGT CAG GAG ATG GAC CG 3’) primers in a volume of 12.5 µL of sterile water. To make a total volume of 25 L, the mixture was mixed with an equal volume (12.5 µL) of the 2X PCR master mix (Phusion Green Host Start II High-Fidelity PCR Master Mix) (Thermo Fisher Scientific, Paisley, UK). The following thermal profile was used for the PCR amplification: Initial denaturation at 95°C for 4 minutes, then 35 cycles of denaturation at 94°C for 30 seconds, annealing at 58°C for 30 seconds, and elongation at 72°C for 30 seconds, followed by a 10-minute final extension step at 72°C. PCR products were digested by Mlu I restriction enzyme (NEB, Ipswich, MA, USA) and separated on 2% agarose gel electrophoresis. Due to the lack of a Mlu I site, the (−866)A/A genotype was identified by a single 363 bp fragment, whereas the wild-type (−866)G/G genotype was digested into 295 bp and 68 bp fragments.12 (link),14 (link)
Publication 2023
BLOOD DNA Restriction Enzymes Electrophoresis, Agar Gel Genetic Polymorphism Genome Genotype Neoplasm Metastasis Nucleotides Oligonucleotide Primers Polymerase Chain Reaction Sterility, Reproductive

Top products related to «Genotype»

Sourced in United States, United Kingdom, Canada, China, Germany, Japan, Belgium, Israel, Lao People's Democratic Republic, Italy, France, Austria, Sweden, Switzerland, Ireland, Finland
Prism 6 is a data analysis and graphing software developed by GraphPad. It provides tools for curve fitting, statistical analysis, and data visualization.
Sourced in United States, Austria, Canada, Belgium, United Kingdom, Germany, China, Japan, Poland, Israel, Switzerland, New Zealand, Australia, Spain, Sweden
Prism 8 is a data analysis and graphing software developed by GraphPad. It is designed for researchers to visualize, analyze, and present scientific data.
Sourced in United States, Austria, Japan, Belgium, United Kingdom, Cameroon, China, Denmark, Canada, Israel, New Caledonia, Germany, Poland, India, France, Ireland, Australia
SAS 9.4 is an integrated software suite for advanced analytics, data management, and business intelligence. It provides a comprehensive platform for data analysis, modeling, and reporting. SAS 9.4 offers a wide range of capabilities, including data manipulation, statistical analysis, predictive modeling, and visual data exploration.
Sourced in United States, Japan, United Kingdom, Austria, Canada, Germany, Poland, Belgium, Lao People's Democratic Republic, China, Switzerland, Sweden, Finland, Spain, France
GraphPad Prism 7 is a data analysis and graphing software. It provides tools for data organization, curve fitting, statistical analysis, and visualization. Prism 7 supports a variety of data types and file formats, enabling users to create high-quality scientific graphs and publications.
Sourced in United States, Germany, United Kingdom, Israel, Canada, Austria, Belgium, Poland, Lao People's Democratic Republic, Japan, China, France, Brazil, New Zealand, Switzerland, Sweden, Australia
GraphPad Prism 5 is a data analysis and graphing software. It provides tools for data organization, statistical analysis, and visual representation of results.
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
Sourced in United States, Germany, China, Japan, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Belgium, Denmark, Netherlands, India, Ireland, Lithuania, Singapore, Sweden, Norway, Austria, Brazil, Argentina, Hungary, Sao Tome and Principe, New Zealand, Hong Kong, Cameroon, Philippines
TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
Sourced in United States, Austria, Germany, Poland, United Kingdom, Canada, Japan, Belgium, China, Lao People's Democratic Republic, France
Prism 9 is a powerful data analysis and graphing software developed by GraphPad. It provides a suite of tools for organizing, analyzing, and visualizing scientific data. Prism 9 offers a range of analysis methods, including curve fitting, statistical tests, and data transformation, to help researchers and scientists interpret their data effectively.
Sourced in United States, China, Germany, United Kingdom, Hong Kong, Canada, Switzerland, Australia, France, Japan, Italy, Sweden, Denmark, Cameroon, Spain, India, Netherlands, Belgium, Norway, Singapore, Brazil
The HiSeq 2000 is a high-throughput DNA sequencing system designed by Illumina. It utilizes sequencing-by-synthesis technology to generate large volumes of sequence data. The HiSeq 2000 is capable of producing up to 600 gigabases of sequence data per run.

More about "Genotype"

Genotype refers to the genetic makeup of an individual, encompassing the alleles present at specific gene loci.
This genetic information provides insights into an organism's inherited traits, disease susceptibility, and potential for expression.
Genotype research, powered by advanced technologies like the HiSeq 2000 sequencing system, aims to identify and understand the genetic factors that influence phenotypic characteristics, including those related to personalized medicine and drug development.
Accurate and reproducible genotype analysis is crucial for advancing these fields.
PubCompare.ai's AI-driven platform can enhance your genotype research by helping you easily locate relevant protocols from literature, preprints, and patents, and make informed comparisons to identify the best approaches for your needs.
Our intelligent comparisons, powered by statistical analysis tools like GraphPad Prism 5, 7, and 9, as well as SAS 9.4, can help you optimize your experimental design and improve the reliability of your results.
When it comes to genotype analysis, the use of effective reagents like TRIzol and TRIzol reagent is also essential for efficient RNA extraction and purification.
By combining the power of AI-driven protocol optimization with the right experimental tools, you can drive your genotype research forward with confidence and contribute to the advancement of personalized medicine and drug development.
Experience the transformative power of AI-powered genotype optimization today and take your research to new heights.
Discover how PubCompare.ai can help you navigate the complex landscape of genotype research and make informed decisions that lead to more accurate and reproducible results.