Log In Sign up
The largest database of trusted experimental protocols

Immunoseq analyzer software

Manufactured by Adaptive Biotechnologies
Visit Supplier
Sourced in United States

The ImmunoSEQ Analyzer software is a powerful tool designed to analyze and visualize immune repertoire data. This software provides a comprehensive suite of analysis tools to explore and interpret the diversity and composition of T-cell and B-cell receptor sequences. The ImmunoSEQ Analyzer software offers a user-friendly interface and advanced analytical capabilities to researchers and scientists working in the field of immunology and immune-related research.

Automatically generated - may contain errors

Lab products found in correlation

Dneasy blood tissue kit, by Qiagen (3 mentions) Dneasy blood and tissue kit, by Qiagen (2 mentions) Nextseq 500, by Illumina (2 mentions) Immunoseq, by Adaptive Biotechnologies (1 mentions) Nsolver analysis software v4, by NanoString (1 mentions) Rneasy mini kit, by Qiagen (1 mentions) Ncounter pancancer immune profiling panel, by NanoString (1 mentions) Immunoseq hstcrb kit, by Adaptive Biotechnologies (1 mentions) Immunoseq assay, by Adaptive Biotechnologies (1 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions) Viia 7 system, by Thermo Fisher Scientific (1 mentions) Quantifast sybr green pcr kit, by Qiagen (1 mentions)

9 protocols using immunoseq analyzer software

1

Longitudinal Analysis of T Cell Receptor Repertoires

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
All the rearranged T cell receptor β chain gene (TRB) repertoires analysed in this study have been generated by Adaptive Biotechnologies (Seattle, WA, USA) by high throughput sequencing following multiplex amplification of all possible V(D)J combinations. After sequencing, immunoSEQ Analyzer software (Adaptive Biotechnologies) was used to automatically annotate rearranged TRB genes and their complementary determining regions 3 (CDR3). A cross-sectional dataset of rearranged TRB gene repertoires generated from 587 donors aged from 1 to 74 years was downloaded in June 2017 from the Adaptive Biotechnologies website1 (31 (link)). A second longitudinal dataset was obtained from 6 donors with informed consent, sampled 3 times each, around 10 years apart as described (25 (link)). The characteristics of both sets are provided in Table 1.
Mika J., Yoshida K., Kusunoki Y., Candéias S.M, & Polanska J. (2023). Sex- and age-specific aspects of human peripheral T-cell dynamics. Frontiers in Immunology, 14, 1224304.
+ Open protocol
+ Expand
2

Profiling B and T Cell Receptor Repertoires

Check if the same lab product or an alternative is used in the 5 most similar protocols
DNA was extracted from FACS-sorted bone marrow B220+IgM− cells and thymic CD4+CD8+CD3εlo cells using the Qiagen DNeasy Blood & Tissue Kit (Qiagen; 69506). High-throughput DNA sequencing of rearranged Igh and Tcrb genes was performed using ImmunoSEQ and was performed by Adaptive Biotechnologies. Gene segment usage was analyzed by ImmunoSEQ Analyzer software (Adaptive Biotechnologies) and R.
Beilinson H.A., Glynn R.A., Yadavalli A.D., Xiao J., Corbett E., Saribasak H., Arya R., Miot C., Bhattacharyya A., Jones J.M., Pongubala J.M., Bassing C.H, & Schatz D.G. (2021). The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination. The Journal of Experimental Medicine, 218(10), e20210250.
+ Open protocol
+ Expand
3

TCR Sequencing and Immune Profiling of Tumor Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genomic DNA was extracted from tumors using the DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD). TCRβ sequencing was performed by Adaptive Biotechnologies (Seattle, WA), and analyzed using the immunoSEQ analyzer software by Adaptive Biotechnologies (Adaptive Biotechnologies).
Total RNA was extracted from the indicated tumors on day 28 post tumor transplant using the RNeasy Mini kit (Qiagen, Germantown, MD). nCounter PanCancer Immune Profiling Panel (NanoString Technologies; Seattle, WA) analysis, run by the Genomics Laboratory, Frederick National Laboratory for Cancer Research (Frederick, MD), was performed on the RNA. Data files were analyzed using the nSolver analysis software v.4.0.70 (NanoString; Seattle, WA) with the mRNA counts normalized to housekeeping genes and with the untreated sample as the categorical reference value. Nanostring data are available in the GEO database under accession number GSE162799. Common genes associated with immune activation, suppression, and exhaustion were depicted.
Fabian K.P., Malamas A.S., Padget M.R., Solocinski K., Wolfson B., Fujii R., Sater H.A., Schlom J, & Hodge J.W. (2020). Therapy of Established Tumors with Rationally Designed Multiple Agents Targeting Diverse Immune-Tumor Interactions: Engage, Expand, Enable. Cancer immunology research, 9(2), 239-252.
+ Open protocol
+ Expand
4

T-cell Receptor Repertoire Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
T-cell receptor repertoire analysis was performed using Adaptive Biotechnologies immunoSEQ v3 assay, which employs bias-controlled multiplex PCR amplification and high-throughput sequencing to target rearranged T-cell receptor genes. The manufacturer’s protocol was followed in order to utilize the immunoSEQ hsTCRB kit to amplify the complementarity determining region 3 (CDR3) locus from genomic DNA extracted from sorted T-cells or tissue. Following the confirmation of amplification and a successful final library preparation, sequencing was performed on the Illumina NextSeq 500 to a depth of 2 million pairs of sequencing reads per sample for survey-level analysis, or 5–6 million pairs per sample for deep-level analysis. The data were then analyzed using the Adaptive Biotechnologies immunoSEQ Analyzer software, which identifies and counts the V, D, and J genes, filters non-productive sequences, and reports and tracks T cell clonality.
Creelan B.C., Wang C., Teer J.K., Toloza E.M., Yao J., Kim S., Landin A.M., Mullinax J.E., Saller J.J., Saltos A.N., Noyes D.R., Montoya L.B., Curry W., Pilon-Thomas S.A., Chiappori A.A., Tanvetyanon T., Kaye F.J., Thompson Z.J., Yoder S.J., Fang B., Koomen J.M., Sarnaik A.A., Chen D.T., Conejo-Garcia J.R., Haura E.B, & Antonia S.J. (2021). Tumor-infiltrating lymphocyte treatment for anti-PD-1 resistant metastatic lung cancer: a phase I trial. Nature medicine, 27(8), 1410-1418.
+ Open protocol
+ Expand
5

Analyzing T Cell Diversity Metrics

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Diversity and richness were calculated using the Adaptive Biotechnologies ImmunoSEQ Analyzer Software. Heterogeneity, defined here as T cell richness in our sample, was estimated by the iChao1 method (30 (link)). iChao1 is a nonparametric estimator of the lower bound, or minimum number of unique templates predicted within a subject’s repertoire at 95% confidence. Diversity scores were used to analyze highly abundant TCR clones in each sample (31 (link)). Clonality is based on Pielous evenness (J) and Shannon diversity (H) (32 ), which calculates a number between 0 and 1, with the higher value indicating lower diversity, or increased expansion of a single clone, in the sample. Formulae are given below, where pi is the proportion of clonotype i, b is the base of the logarithm, and S is the number of clonotypes.
Enninga E.A., Raber P., Quinton R.A., Ruano R., Ikumi N., Gray C.M., Johnson E.L., Chakraborty R, & Kerr S.E. (2020). Maternal T cells in the Human Placental Villi support an Allograft Response during Non-Infectious Villitis. Journal of immunology (Baltimore, Md. : 1950), 204(11), 2931-2939.
+ Open protocol
+ Expand
6

Comprehensive TCR Repertoire Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genomic DNA of biopsy tissue or PBMCs was isolated using DNeasy Blood & Tissue Kit (Qiagen Cat No. 69506) according to manufacturer recommendations. TCR repertoire analysis was performed using the Adaptive Biotechnologies ImmunoSEQ assay v3. The CDR3 locus of sorted T cells were amplified by ImmunoSEQ hsTCRB kit (ImmunoSEQ hsTCRB kit v3 – Adaptive Biotechnologies Cat No. ISK10101) and sequenced on the Illumina NextSeq 500 to a targeted depth of 2 million sequencing reads per sample. The data were analyzed using the Adaptive Biotechnologies ImmunoSEQ Analyzer software, to identify the V, D, and J genes, filter non-productive sequences, and report and track T-cell clones. Productive clones and their frequencies were exported for further analysis. Shared clones between any tumors and any blood samples at both pre-treatment and on-treatment time points were visualized by R package eulerr. The proportional frequencies of top 10 most abundant clonotypes in tumors were tracked across all samples at all time points and visualized by trackClonetypes function in R package immunarch (56 (link)), where T cells with identical CDR3 amino acid sequence and V gene were considered as the same clonotype.
Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Müller K.M., Pande N., Shang Z., Yu N, & Gutell R.R. (2002). The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 2.
+ Open protocol
+ Expand
7

Profiling T-cell Receptor Diversity

Check if the same lab product or an alternative is used in the 5 most similar protocols
To study T-cell receptor rearrangement and clonality, we selected 14 representative patients (7 with HPV+ disease and 7 with HPV− disease) for further analysis. Genomic DNA (gDNA) was isolated from PBMCs at baseline and during treatment (week 6) and compared with gDNA isolated from initial tumor biopsies for each cancer patient using a DNeasy Blood & Tissue kit (Qiagen, Hilden, Germany). Further analysis was performed using a prequalified multiplex polymerase chain reaction (PCR) assay, composed of forward and reverse primers that directly target the family of variable (V) genes (forward primers) and joining (J) genes (reverse primers). Each V and J gene primers act as priming pairs to amplify somatically recombined TCRs, and each primer contained a specific universal DNA sequence. Following the initial PCR amplification, each amplicon was amplified a second time with forward and reverse primers containing the universal sequence and adaptor sequence needed for DNA sequencing (immunoSEQ RUO Kit Adaptive Biotech). Immunosequencing data were analyzed using immunoSEQ Analyzer software (Adaptive Biotechnologies, Seattle, WA, USA).
Callejas-Valera J.L., Vermeer D.W., Lucido C.T., Williamson C., Killian M., Vermeer P.D., Spanos W.C, & Powell S.F. (2022). Characterization of the Immune Response to PD-1 Blockade during Chemoradiotherapy for Head and Neck Squamous Cell Carcinoma. Cancers, 14(10), 2499.
+ Open protocol
+ Expand
8

High-Throughput TCR Sequencing from FFPE Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols
A high-throughput TCR sequence survey from paraffin-embedded tissue was performed according to protocol described elsewhere (56 (link)). Briefly, sections from paraffin blocks of the prostate were collected for DNA extraction using the QIAamp DNA FFPE Tissue Kit (QIAGEN Inc.), per the manufacturer’s instructions. The TCRβ CD3 (CDR3β) region was amplified, sequenced, and quantified from a standardized 1200 ng of DNA using the immunoSEQ assay as previously described (Adaptive Biotechnologies) (56 (link), 72 (link)). TCR sequence and clonality were determined by the Shannon diversity index using immunoSEQ Analyzer software (Adaptive Biotechnologies) (56 (link)).
Zhang J., Liu D., Li G., Staveley-O’Carroll K.F., Graff J.N., Li Z, & Wu J.D. (2017). Antibody-mediated neutralization of soluble MIC significantly enhances CTLA4 blockade therapy. Science Advances, 3(5), e1602133.
+ Open protocol
+ Expand
9

Quantifying T-cell receptor rearrangements

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Genomic DNA was extracted from DN3 or DP cells using the DNeasy Blood and Tissue kit (Qiagen). To measure Tcrb rearrangements in DN3 cells, a Taqman PCR assay was used to quantify Vβ-to-DJβ1.1 and Vβ-to-DJβ2.1 rearrangement levels with a primer specific for each Vβ paired and a probe, FAM or HEX, specific for Jβ1.1 or Jβ2.1, respectively. Taqman PCR was performed with conditions according to the manufacturer’s instructions (IDT DNA) on the ViiA 7 system (Applied Biosystems). PCR of CD19 was used for normalization. Primers, probes, and reaction conditions are as described (20 (link)). To assay Tcrb repertoire, DNA from DN3 thymocytes were sent to Adaptive Biotechnologies, who used multiplex PCR to amplify and deep sequence Vβ-Dβ-Jβ rearrangements. Gene segment usage was analyzed by ImmunoSEQ Analyzer software (Adaptive Biotechnologies). To assess Tcra rearrangements in DP cells, representative Vα-Jα rearrangements were quantified using a QuantiFast SYBR Green PCR kit (Qiagen) on the ViiA 7 system (Applied Biosystems) as described (21 (link), 22 (link)). PCR of β2M was used for normalization. We quantified Vα14-Jα18 rearrangments as described (23 (link)).
Burn T.N., Miot C., Gordon S.M., Culberson E.J., Diamond T., Kreiger P.A., Hayer K.E., Bhattacharyya A., Jones J.M., Bassing C.H, & Behrens E.M. (2022). The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCR β and α Genes and Influences Development of αβ T Cell Lineages. Journal of immunology (Baltimore, Md. : 1950).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!