PhIP-Seq: PHAGE DISPLAY IMMUNOPRECIPITATION SEQUENCING
Overview of PhIP-Seq.
Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) is a powerful new method of multiplexed analysis that combines DNA high-throughput sequencing with next-generation proteomics. PhIP-Seq allows researchers to determine what antibodies were created by an individual’s unique history of immune exposures. PhIP-Seq is the highest-coverage antigen-specific assay yet developed, able to detect antibodies versus virtually any antigen via overlapping long peptides.
PhIP-Seq was developed at Harvard University in 2011. This work created a synthetic representation of the complete human proteome as a T7 bacteriophage display library. They built upon this work in 2015 by creating a synthetic representation of the complete human virome: the universe of known infectious viruses.
Since then, teams at UCSF and the Chan Zuckerberg Biohub have built upon and expanded the universe of antigen-specific profiling available via PhiP-Seq. PhIP-Seq has been used to perform revolutionary immune profiling on people suffering from multiple sclerosis, diabetes, rheumatoid arthritis, and more. CDI Labs was the first company to commercialize PhIP-Seq technology.
Technology overview.
PhIP-Seq: HuScan™ — Human proteome phage display.
The entire human proteome in a single antibody detection assay.
HuScan™ v2.0, an application of Bacteriophage-Display Immunoprecipitation Sequencing (PhIP-Seq), is composed of an entire normal human proteome as defined by the NCBI RefSeq database. The library contains proteins expressed as overlapping 49mer peptide tiles on the surface of bacteriophages. For an assay, an aliquot from this library is reacted with diluted patient serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide and whole-protein level.
PhIP-Seq: MouseScan™ — Murine proteome phage display.
The entire mouse proteome in a single antibody detection assay.
MouseScan™, an application of Bacteriophage-Display Immunoprecipitation Sequencing (PhIP-Seq), is composed of the entire normal mouse proteome (GRCm38.p5). The library contains all proteins expressed as overlapping 62mer peptide tiles on the surface of bacteriophages. For an assay, an aliquot from this library is reacted with diluted mouse serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide level.
Learn more about our ANTYGEN™ PhIP-Seq analysis services.
PhIP-Seq References: Projects by CDI Labs
[1]
A. Xagara, S. Fortis, M. Goulielmaki, F. Koinis, E. Chantzara, I. Samaras, V.N. Papadopoulos, V. Georgoulias, C.N. Baxevanis, A. Kotsakis, 21P Peripheral pre-existing T cell immunity as predictive biomarker in cancer immunotherapy for NSCLC patients, Immuno-Oncology and Technology. 16 (2022) 100126. https://doi.org/10.1016/j.iotech.2022.100126.
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C. Valencia-Sanchez, A.M. Knight, M.B. Hammami, Y. Guo, J.R. Mills, T.J. Kryzer, A.L. Piquet, A. Amin, M. Heinzelmann, C.F. Lucchinetti, V.A. Lennon, A. McKeon, S.J. Pittock, D. Dubey, Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome, J Neurol Neurosurg Psychiatry. 93 (2022) 196–200. https://doi.org/10.1136/jnnp-2021-326656.
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M. Naigeon, M. Roulleaux Dugage, F.-X. Danlos, C. De Oliveira, L. Boselli, J.-M. Jouniaux, F. Griscelli, A. Marabelle, L. Cassard, G. Roman, T. Hulett, B. Besse, N. Chaput-Gras, 20P Human virome epitope-level antiviral antibody profiling identified the cytomegalovirus (CMV) as the main driver of senescent immune phenotype (SIP) in patients with advanced non-small cell lung cancer (aNSCLC), Immuno-Oncology and Technology. 16 (2022) 100125. https://doi.org/10.1016/j.iotech.2022.100125.
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E.M. Gordon‐Lipkin, C.S. Marcum, S. Kruk, E. Thompson, S.E.M. Kelly, H. Kalish, L. Bellusci, S. Khurana, K. Sadtler, P.J. McGuire, Comprehensive profiling of the human viral exposome in households containing an at‐risk child with mitochondrial disease during the 2020–2021 COVID‐19 pandemic, Clinical & Translational Med. 12 (2022). https://doi.org/10.1002/ctm2.1100.
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F.G. Dall’Olio, M. Lerousseau, G. Roman, F.-X. Danlos, M. Aldea, N. Chaput-Gras, D. Planchard, F. Barlesi, T. Hulett, A. Marabelle, B. Besse, 1070P Previous viral infections assessed by pan-virus phage immunoprecipitation sequencing (PhIP-Seq) predict response to immune checkpoint blockers (ICBs) in non-small cell lung cancer (NSCLC), Annals of Oncology. 33 (2022) S1043. https://doi.org/10.1016/j.annonc.2022.07.1196.
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L. Chouchane, J.-C. Grivel, E.A.B.A. Farag, I. Pavlovski, S. Maacha, A. Sathappan, H.E. Al-Romaihi, S.W.J. Abuaqel, M.M.A. Ata, A.I. Chouchane, S. Remadi, N. Halabi, A. Rafii, M.H. Al-Thani, N. Marr, M. Subramanian, J. Shan, Dromedary camels as a natural source of neutralizing nanobodies against SARS-CoV-2, JCI Insight. 6 (2021) e145785. https://doi.org/10.1172/jci.insight.145785.
All Publications
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E. Rackaityte, I. Proekt, H.S. Miller, A. Ramesh, J.F. Brooks, A.F. Kung, C. Mandel-Brehm, D. Yu, C. Zamecnik, R. Bair, S.E. Vazquez, S. Sunshine, C.L. Abram, C.A. Lowell, G. Rizzuto, M.R. Wilson, J. Zikherman, M.S. Anderson, J.L. DeRisi, Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities, (2023) 2023.04.07.535899. https://doi.org/10.1101/2023.04.07.535899.
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T. Kula, High-Throughput Approaches to Profiling Antibody and T Cell Targets, Ph.D., Harvard University, 2022. https://www.proquest.com/docview/2465806854/abstract/20D32AA7A91442E0PQ/1 (accessed May 23, 2022).
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T. Venkataraman, H. Swaminathan, C.A. Arze, S.M. Jacobo, A. Bhattacharyya, T. David, D.M. Nawandar, S. Delagrave, V. Mani, N.L. Yozwiak, H.B. Larman, Comprehensive profiling of antibody responses to the human anellome using programmable phage display, (2022) 2022.03.28.486145. https://doi.org/10.1101/2022.03.28.486145.
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S.E. Vazquez, S.A. Mann, A. Bodansky, A.F. Kung, Z. Quandt, E.M.N. Ferré, N. Landegren, D. Eriksson, P. Bastard, S.-Y. Zhang, J. Liu, A. Mitchell, C. Mandel-Brehm, B. Miao, G. Sowa, K. Zorn, A.Y. Chan, C. Shimizu, A. Tremoulet, K. Lynch, M.R. Wilson, O. Kampe, K. Dobbs, O.M. Delmonte, L.D. Notarangelo, J.C. Burns, J.-L. Casanova, M.S. Lionakis, T.R. Torgerson, M.S. Anderson, J.L. DeRisi, Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq, Immunology, 2022. https://doi.org/10.1101/2022.03.23.485509.
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P. Taeschler, C. Cervia, Y. Zurbuchen, S. Hasler, C. Pou, Z. Tan, S. Adamo, M.E. Raeber, E. Bächli, A. Rudiger, M. Stüssi-Helbling, L.C. Huber, P. Brodin, J. Nilsson, E. Probst-Müller, O. Boyman, Autoantibodies in COVID-19 correlate with anti-viral humoral responses and distinct immune signatures, (2022) 2022.01.08.22268901. https://doi.org/10.1101/2022.01.08.22268901.
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[8]
A. Chen, K. Kammers, H.B. Larman, R.B. Scharpf, I. Ruczinski, Detecting Antibody Reactivities in Phage ImmunoPrecipitation Sequencing Data, (2022) 2022.01.19.476926. https://doi.org/10.1101/2022.01.19.476926.
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H. Yue, Y. Li, M. Yang, C. Mao, T7 Phage as an Emerging Nanobiomaterial with Genetically Tunable Target Specificity, Advanced Science. 9 (2022) 2103645. https://doi.org/10.1002/advs.202103645.
[10]
T. Venkataraman, C. Valencia, M. Mangino, W. Morgenlander, S.J. Clipman, T. Liechti, A. Valencia, P. Christofidou, T. Spector, M. Roederer, P. Duggal, H.B. Larman, Analysis of antibody binding specificities in twin and SNP-genotyped cohorts reveals that antiviral antibody epitope selection is a heritable trait, Immunity. 55 (2022) 174-184.e5. https://doi.org/10.1016/j.immuni.2021.12.004.
[11]
C. Valencia-Sanchez, A.M. Knight, M.B. Hammami, Y. Guo, J.R. Mills, T.J. Kryzer, A.L. Piquet, A. Amin, M. Heinzelmann, C.F. Lucchinetti, V.A. Lennon, A. McKeon, S.J. Pittock, D. Dubey, Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome, J Neurol Neurosurg Psychiatry. 93 (2022) 196–200. https://doi.org/10.1136/jnnp-2021-326656.
[12]
C.K. Tiu, F. Zhu, L.-F. Wang, R. de Alwis, Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology, Pathogens. 11 (2022) 568. https://doi.org/10.3390/pathogens11050568.
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[14]
L. Ma, H. Ouyang, A. Su, Y. Zhang, D. Pang, T. Zhang, R. Sun, W. Wang, Z. Xie, D. Lv, AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level, ACS Synth. Biol. 11 (2022) 1856–1864. https://doi.org/10.1021/acssynbio.2c00018.
[15]
J. Liu, K.A. Knopp, E. Rackaityte, C.Y. Wang, M.T. Laurie, S. Sunshine, A.S. Puschnik, J.L. DeRisi, Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus, MBio. (2022) e00205-22. https://doi.org/10.1128/mbio.00205-22.
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T.V. Lanz, R.C. Brewer, P.P. Ho, J.-S. Moon, K.M. Jude, D. Fernandez, R.A. Fernandes, A.M. Gomez, G.-S. Nadj, C.M. Bartley, R.D. Schubert, I.A. Hawes, S.E. Vazquez, M. Iyer, J.B. Zuchero, B. Teegen, J.E. Dunn, C.B. Lock, L.B. Kipp, V.C. Cotham, B.M. Ueberheide, B.T. Aftab, M.S. Anderson, J.L. DeRisi, M.R. Wilson, R.J.M. Bashford-Rogers, M. Platten, K.C. Garcia, L. Steinman, W.H. Robinson, Clonally Expanded B Cells in Multiple Sclerosis Bind EBV EBNA1 and GlialCAM, Nature. (2022) 1–12. https://doi.org/10.1038/s41586-022-04432-7.
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M.E. Garrett, J.G. Galloway, C. Wolf, J.K. Logue, N. Franko, H.Y. Chu, F.A. Matsen IV, J.M. Overbaugh, Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection, ELife. 11 (2022) e73490. https://doi.org/10.7554/eLife.73490.
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[20]
X. Castro Dopico, G.B. Karlsson Hedestam, A family matter: Anti-viral antibody responses, Immunity. 55 (2022) 8–10. https://doi.org/10.1016/j.immuni.2021.12.008.
[21]
A.R. Bourgonje, S. Andreu-Sánchez, T. Vogl, S. Hu, A. Vich Vila, S. Leviatan, A. Kurilshikov, S. Klompus, I.N. Kalka, H.M. van Dullemen, A. Weinberger, M.C. Visschedijk, E.A.M. Festen, K.N. Faber, C. Wijmenga, G. Dijkstra, E. Segal, J. Fu, A. Zhernakova, R.K. Weersma, DOP53 In-depth characterisation of the serum antibody epitope repertoire in Inflammatory Bowel Disease by high-throughput phage-displayed immunoprecipitation sequencing, Journal of Crohn’s and Colitis. 16 (2022) i100–i102. https://doi.org/10.1093/ecco-jcc/jjab232.092.
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H. Abolhassani, N. Landegren, P. Bastard, M. Materna, M. Modaresi, L. Du, M. Aranda-Guillén, F. Sardh, F. Zuo, P. Zhang, H. Marcotte, N. Marr, T. Khan, M. Ata, F. Al-Ali, R. Pescarmona, A. Belot, V. Béziat, Q. Zhang, J.-L. Casanova, O. Kämpe, S.-Y. Zhang, L. Hammarström, Q. Pan-Hammarström, Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome, J Clin Immunol. 42 (2022) 471–483. https://doi.org/10.1007/s10875-022-01215-7.
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N. Ghosh, this link will open in a new window Link to external site, Autoantibodies as Biomarkers of Immune-Related Adverse Events from Immune Checkpoint Inhibition, Ph.D., Weill Medical College of Cornell University, 2021. https://www.proquest.com/docview/2572580109/abstract/EBBB4710575A4CC7PQ/1 (accessed May 23, 2022).
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T. Venkataraman, C. Valencia, M. Mangino, W. Morgenlander, S.J. Clipman, T. Liechti, A. Valencia, P. Christofidou, T. Spector, M. Roederer, P. Duggal, H.B. Larman, Antiviral Antibody Epitope Selection is a Heritable Trait, 2021. https://doi.org/10.1101/2021.03.25.436790.
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C. Mandel-Brehm, S.E. Vazquez, C. Liverman, M. Cheng, Z. Quandt, A.F. Kung, B. Miao, E. Disse, C. Cugnet-Anceau, S. Dalle, E. Orlova, E. Frolova, B.E. Oftedal, M.S. Lionakis, E.S. Husebye, J.L. DeRisi, M.S. Anderson, Perilipin-1 autoantibodies linked to idiopathic lipodystrophy in the setting of two distinct breaks in immune tolerance, Allergy and Immunology, 2021. https://doi.org/10.1101/2021.09.24.21263657.
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T. Khan, M. Rahman, I. Ahmed, F.A. Ali, P. Jithesh, N. Marr, Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens, Genetics, 2021. https://doi.org/10.1101/2021.01.11.426296.
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J.W. Angkeow, D.R. Monaco, A. Chen, T. Venkataraman, S. Jayaraman, C. Valencia, B.M. Sie, T. Liechti, P.N. Farhadi, G. Funez-dePagnier, C.A. Sherman-Baust, M.Q. Wong, C.L. Sears, P.J. Simner, J.L. Round, P. Duggal, U. Laserson, T.S. Steiner, R. Sen, T.E. Lloyd, M. Roederer, A.L. Mammen, R.S. Longman, L.G. Rider, H.B. Larman, Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors, (2021) 2021.10.01.462481. https://doi.org/10.1101/2021.10.01.462481.
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T.L. Voyer, S. Sakata, M. Tsumura, T. Khan, A. Esteve-Sole, B.K. Al-Saud, H.E. Gungor, P. Taur, V. Jeanne-Julien, M. Christiansen, L.-M. Köhler, G.E. ElGhazali, J. Rosain, S. Nishimura, F. Sakura, M. Bouaziz, C. Oleaga-Quintas, A. Nieto-Patlán, À. Deyà-Martinez, Y.A. Torun, A.-L. Neehus, M. Roynard, S.E. Bozdemir, N.A. Kaabi, M.A. Hassani, I. Mersiyanova, F. Rozenberg, C. Speckmann, I. Hainmann, F. Hauck, M.H. Alzahrani, S.H. Alhajjar, S. Al-Muhsen, T. Cole, R. Fuleihan, P.D. Arkwright, R. Badolato, L. Alsina, L. Abel, M. Desai, H. Al-Mousa, A. Shcherbina, N. Marr, S. Boisson-Dupuis, J.-L. Casanova, S. Okada, J. Bustamante, Genetic, Immunological, and Clinical Features of 32 Patients with Autosomal Recessive STAT1 Deficiency, The Journal of Immunology. 207 (2021) 133–152. https://doi.org/10.4049/jimmunol.2001451.
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