1
|
Corrie BD, Marthandan N, Zimonja B,
Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FM, Christley S, Scott
JK, et al: iReceptor: A platform for querying and analyzing
antibody/B-cell and T-cell receptor repertoire data across
federated repositories. Immunol Rev. 284:24–41. 2018.PubMed/NCBI View Article : Google Scholar
|
2
|
Chiffelle J, Genolet R, Perez MA, Coukos
G, Zoete V and Harari A: T-cell repertoire analysis and metrics of
diversity and clonality. Curr Opin Biotechnol. 65:284–295.
2020.PubMed/NCBI View Article : Google Scholar
|
3
|
Thorsson V, Gibbs DL, Brown SD, Wolf D,
Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy
JA, et al: The immune landscape of cancer. Immunity.
48:812–830.e14. 2018.PubMed/NCBI View Article : Google Scholar
|
4
|
Brown SD, Raeburn LA and Holt RA:
Profiling tissue-resident T cell repertoires by RNA sequencing.
Genome Med. 7(125)2015.PubMed/NCBI View Article : Google Scholar
|
5
|
Gill TR, Samy MD, Butler SN, Mauro JA,
Sexton WJ and Blanck G: Detection of productively rearranged TcR-α
V-J sequences in TCGA exome files: Implications for tumor
immunoscoring and recovery of antitumor T-cells. Cancer Inform.
15:23–28. 2016.PubMed/NCBI View Article : Google Scholar
|
6
|
Samy MD, Tong WL, Yavorski JM, Sexton WJ
and Blanck G: T cell receptor gene recombinations in human tumor
specimen exome files: Detection of T cell receptor-β VDJ
recombinations associates with a favorable oncologic outcome for
bladder cancer. Cancer Immunol Immunother. 66:403–410.
2017.PubMed/NCBI View Article : Google Scholar
|
7
|
Huda TI, Mihyu M, Gozlan EC, Arndt MF,
Diaz MJ, Zaman S, Chobrutskiy BI and Blanck G: Specific HLA
alleles, paired with TCR V- and J-gene segment usage, link to
distinct multiple myeloma survival rates. Leuk Lymphoma.
62:1711–1720. 2021.PubMed/NCBI View Article : Google Scholar
|
8
|
Gozlan EC, Chobrutskiy BI, Zaman S,
Yeagley M and Blanck G: Systemic adaptive immune parameters
associated with neuroblastoma outcomes: The significance of
gamma-delta T cells. J Mol Neurosci. 71:2393–2404. 2021.PubMed/NCBI View Article : Google Scholar
|
9
|
Hsiang M, Chobrutskiy BI, Diaz M, Huda TI,
Creadore S, Zaman S, Cios KJ, Gozlan EC and Blanck G: . Chemical
complementarity between immune receptors and cancer mutants,
independent of antigen presentation protein binding, is associated
with increased survival rates. Transl Oncol.
14(101069)2021.PubMed/NCBI View Article : Google Scholar
|
10
|
Chobrutskiy BI, Chobrutskiy A, Zaman S,
Yeagley M, Huda TI and Blanck G: High-throughput, sliding-window
algorithm for assessing chemical complementarity between immune
receptor CDR3 domains and cancer mutant peptides: TRG-PIK3CA
interactions and breast cancer. Mol Immunol. 135:247–253.
2021.PubMed/NCBI View Article : Google Scholar
|
11
|
Schmitz R, Wright GW, Huang DW, Johnson
CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer
AL, et al: Genetics and pathogenesis of diffuse large B-cell
lymphoma. N Engl J Med. 378:1396–1407. 2018.PubMed/NCBI View Article : Google Scholar
|
12
|
Chobrutskiy BI, Zaman S, Diviney A, Mihyu
MM and Blanck G: T-cell receptor-α CDR3 domain chemical features
correlate with survival rates in bladder cancer. J Cancer Res Clin
Oncol. 145:615–623. 2019.PubMed/NCBI View Article : Google Scholar
|
13
|
Yeagley M, Chobrutskiy BI, Gozlan EC,
Medikonda N, Patel DN, Falasiri S, Callahan BM, Huda T and Blanck
G: Electrostatic complementarity of T-cell receptor-alpha CDR3
domains and mutant amino acids is associated with better survival
rates for sarcomas. Pediatr Hematol Oncol. 38:251–264.
2021.PubMed/NCBI View Article : Google Scholar
|
14
|
Arturo JF, Chobrutskiy BI, Yeagley M,
Patel DN, Falasiri S, Patel JS and Blanck G: Electrostatic
complementarity of B-cell receptor CDR3s and TP53-mutant amino
acids in breast cancer is associated with increased disease-free
survival rates. Cell Mol Immunol. 17:776–778. 2020.PubMed/NCBI View Article : Google Scholar
|
15
|
Chobrutskiy BI, Yeagley M, Diviney A,
Zaman S, Gozlan EC, Tipping P, Koohestani DM, Roca AM and Blanck G:
A scoring system for the electrostatic complementarities of T-cell
receptors and cancer-mutant amino acids: Multi-cancer analyses of
associated survival rates. Immunology. 159:373–383. 2020.PubMed/NCBI View Article : Google Scholar
|
16
|
Chobrutskiy BI, Yeagley M, Tipping P,
Zaman S, Diviney A, Patel DN, Falasiri S, Uversky VN and Blanck G:
Chemical complementarity between immune receptor CDR3s and IDH1
mutants correlates with increased survival for lower grade glioma.
Oncogene. 39:1773–1783. 2020.PubMed/NCBI View Article : Google Scholar
|
17
|
Ostmeyer J, Lucas E, Christley S, Lea J,
Monson N, Tiro J and Cowell LG: Biophysicochemical motifs in T cell
receptor sequences as a potential biomarker for high-grade serous
ovarian carcinoma. PLoS One. 15(e0229569)2020.PubMed/NCBI View Article : Google Scholar
|
18
|
Chobrutskiy A, Chobrutskiy BI, Zaman S,
Hsiang M and Blanck G: Chemical features of blood-borne TRG CDR3s
associated with an increased overall survival in breast cancer.
Breast Cancer Res Treat. 185:591–600. 2021.PubMed/NCBI View Article : Google Scholar
|
19
|
Tong WL, Tu YN, Samy MD, Sexton WJ and
Blanck G: Identification of immunoglobulin V(D)J recombinations in
solid tumor specimen exome files: Evidence for high level B-cell
infiltrates in breast cancer. Hum Vaccin Immunother. 13:501–506.
2017.PubMed/NCBI View Article : Google Scholar
|
20
|
Chobrutskiy BI, Zaman S, Tong WL, Diviney
A and Blanck G: Recovery of T-cell receptor V(D)J recombination
reads from lower grade glioma exome files correlates with reduced
survival and advanced cancer grade. J Neurooncol. 140:697–704.
2018.PubMed/NCBI View Article : Google Scholar
|
21
|
Holehouse AS, Das RK, Ahad JN, Richardson
MO and Pappu RV: CIDER: Resources to analyze sequence-ensemble
relationships of intrinsically disordered proteins. Biophys J.
112:16–21. 2017.PubMed/NCBI View Article : Google Scholar
|
22
|
Tong WL, Callahan BM, Tu YN, Zaman S,
Chobrutskiy BI and Blanck G: Immune receptor recombinations from
breast cancer exome files, independently and in combination with
specific HLA alleles, correlate with better survival rates. Breast
Cancer Res Treat. 173:167–177. 2019.PubMed/NCBI View Article : Google Scholar
|
23
|
Diaz MJ, Chobrutskiy BI, Zaman S and
Blanck G: Immunogenomics of colorectal adenocarcinoma: Survival
distinctions represented by immune receptor, CDR3 chemical features
and high expression of BTN gene family members. Cancer Treat Res
Commun. 24(100196)2020.PubMed/NCBI View Article : Google Scholar
|
24
|
Gros A, Parkhurst MR, Tran E, Pasetto A,
Robbins PF, Ilyas S, Prickett TD, Gartner JJ, Crystal JS, Roberts
IM, et al: Prospective identification of neoantigen-specific
lymphocytes in the peripheral blood of melanoma patients. Nat Med.
22:433–438. 2016.PubMed/NCBI View
Article : Google Scholar
|
25
|
Patel DN, Yeagley M, Arturo JF, Falasiri
S, Chobrutskiy BI, Gozlan EC and Blanck G: A comparison of immune
receptor recombination databases sourced from tumour exome or
RNAseq files: Verifications of immunological distinctions between
primary and metastatic melanoma. Int J Immunogenet. 48:409–418.
2021.PubMed/NCBI View Article : Google Scholar
|
26
|
Thorsélius M, Kröber A, Murray F, Thunberg
U, Tobin G, Bühler A, Kienle D, Albesiano E, Maffei R, Dao-Ung LP,
et al: Strikingly homologous immunoglobulin gene rearrangements and
poor outcome in VH3-21-using chronic lymphocytic leukemia patients
independent of geographic origin and mutational status. Blood.
107:2889–2894. 2006.PubMed/NCBI View Article : Google Scholar
|
27
|
Stamatopoulos K, Belessi C, Moreno C,
Boudjograh M, Guida G, Smilevska T, Belhoul L, Stella S,
Stavroyianni N, Crespo M, et al: Over 20% of patients with chronic
lymphocytic leukemia carry stereotyped receptors: Pathogenetic
implications and clinical correlations. Blood. 109:259–270.
2007.PubMed/NCBI View Article : Google Scholar
|
28
|
Wong MK, Liu JT, Budylowksi P, Yue FY, Li
Z, Rini JM, Carlyle JR, Zia A, Ostrowski M and Martin A: Convergent
CDR3 homology amongst Spike-specific antibody responses in
convalescent COVID-19 subjects receiving the BNT162b2 vaccine. Clin
Immunol. 237(108963)2022.PubMed/NCBI View Article : Google Scholar
|
29
|
Babel N, Brestrich G, Gondek LP, Sattler
A, Wlodarski MW, Poliak N, Bethke N, Thiel A, Hammer MH, Reinke P
and Maciejewski JP: Clonotype analysis of cytomegalovirus-specific
cytotoxic T lymphocytes. J Am Soc Nephrol. 20:344–352.
2009.PubMed/NCBI View Article : Google Scholar
|
30
|
Smith NP, Ruiter B, Virkud YV, Tu AA,
Monian B, Moon JJ, Love JC and Shreffler WG: Identification of
antigen-specific TCR sequences based on biological and statistical
enrichment in unselected individuals. JCI Insight.
6(e140028)2021.PubMed/NCBI View Article : Google Scholar
|
31
|
Joshi C, Sivaprakasam K, Christley S,
Ireland S, Rivas J, Zhang W, Sader D, Logan R, Lambracht-Washington
D, Rosenberg R, et al: CSF-derived CD4(+) T-cell diversity is
reduced in patients with Alzheimer clinical syndrome. Neurol
Neuroimmunol Neuroinflamm. 9(e1106)2021.PubMed/NCBI View Article : Google Scholar
|
32
|
Gate D, Saligrama N, Leventhal O, Yang AC,
Unger MS, Middeldorp J, Chen K, Lehallier B, Channappa D, De Los
Santos MB, et al: Clonally expanded CD8 T cells patrol the
cerebrospinal fluid in Alzheimer's disease. Nature. 577:399–404.
2020.PubMed/NCBI View Article : Google Scholar
|