XenScan: PhIP-Seq Antibody Profiling

Based on Immune Epitope Database (IEDB) xenoantigens; epitope-level antibody profiling service via T7 phage display and immunoprecipitation sequencing

XenScan: PhIP-Seq Antibody Profiling

Based on Immune Epitope Database (IEDB) xenoantigens; epitope-level antibody profiling service via T7 phage display and immunoprecipitation sequencing

High-throughput xenoantibody discovery service.

Immune exposures to non-human proteins (“xenoantigens”), are a major component of an individual’s unique antibody fingerprint. Xenoantigens originate from plants, animals, foods, fungi, insects, the microbiome, pathogenic bacteria, parasites, and most anything else a person might encounter across their lifetime.

ANTYGENXenScan™ service provides an unparalleled way to assay a patient’s xenoantigen exposure history by comprehensively analyzing xenoantibodies to a phage library displaying peptides from 604 unique xenoantigens representing 213 unique species curated by the Immune Epitope Database (IEDB) this library contains every full-length UniProt protein with an IEDB-reported antigen that does not originate from humans, viruses, or malaria (plasmodium). This product is available as a service to both academic and industry customers.

Download an overview of our XenScan™ service.

CDI Antygen™ XenScan™ is provided as a complete analysis service (readout similar to HuScan).

Understanding Your HuScan and VirScan Results

XenScan™ Content.

CDI Antygen™ XenScan™ contains 604 xenoantigens from IEDB.

Download XenScan™ IEDB PhIP-Seq Content List

213 species are profiled by XenScan™ antibody testing.

Absidia glauca (Pin mould) • Acidocella sp. MX-AZ02 • Alternaria alternata (Alternaria rot fungus) (Torula alternata) • Amaranthus caudatus (Love-lies-bleeding) (Inca-wheat) • Ambrosia artemisiifolia (Short ragweed) • Ambrosia artemisiifolia var. elatior (Short ragweed) (Ambrosia elatior) • Anacardium occidentale (Cashew) • Anisakis simplex (Herring worm) • Apis mellifera (Honeybee) • Apium graveolens (Celery) • Apophysomyces trapeziformis • Arabidopsis thaliana (Mouse-ear cress) • Arachis hypogaea (Peanut) • Armoracia rusticana (Horseradish) (Armoracia laphatifolia) • Artemisia vulgaris (Mugwort) • Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) • Aspergillus restrictus • Babesia microti (strain RI) • Bacillus anthracis • Bacillus subtilis (strain 168) • Bertholletia excelsa (Brazil nut) • Betula pendula (European white birch) (Betula verrucosa) • Blattella germanica (German cockroach) (Blatta germanica) • Blomia tropicalis (Mite) • Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) • Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) • Borreliella bavariensis (strain ATCC BAA-2496 / DSM 23469 / PBi) (Borrelia bavariensis) • Borreliella burgdorferi (Lyme disease spirochete) (Borrelia burgdorferi) • Bos taurus (Bovine) • Brassica napus (Rape) • Brugia malayi (Filarial nematode worm) • Burkholderia multivorans CF2 • Burkholderia pseudomallei (strain K96243) • Caenorhabditis briggsae • Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast) • Candidatus Neoehrlichia mikurensis • Carya illinoinensis (Pecan) • Centruroides noxius (Mexican scorpion) • Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) • Chamaecyparis obtusa (Hinoki false-cypress) • Chironomus thummi thummi (Midge) • Chlamydia pneumoniae (Chlamydophila pneumoniae) • Chlamydia trachomatis (strain D/UW-3/Cx) • Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A) • Clostridium botulinum (strain Okra / Type B1) • [Clostridium] papyrosolvens DSM 2782 • [Clostridium] termitidis CT1112 • Clostridium tetani (strain Massachusetts / E88) • Cochliobolus lunatus (Filamentous fungus) (Curvularia lunata) • Corylus avellana (European hazel) (Corylus maxima) • Corynebacterium diphtheriae (strain ATCC 27012 / C7 (beta)) • Corynebacterium genitalium ATCC 33030 • Cryptococcus arboriformis • Cryptomeria japonica (Japanese cedar) (Cupressus japonica) • Cryptosporidium parvum (strain Iowa II) • Cucumis melo (Muskmelon) • Cynodon dactylon (Bermuda grass) (Panicum dactylon) • Danio rerio (Zebrafish) (Brachydanio rerio) • Dermatophagoides farinae (American house dust mite) • Dermatophagoides pteronyssinus (European house dust mite) • Dickeya chrysanthemi (Pectobacterium chrysanthemi) (Erwinia chrysanthemi) • Drawida gracilis • Drosophila melanogaster (Fruit fly) • Drosophila persimilis (Fruit fly) • Drosophila pseudoobscura pseudoobscura (Fruit fly) • Dyella japonica A8 • Echinococcus granulosus (Hydatid tapeworm) • Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas) • Entamoeba histolytica • Enterobacteria phage P1 (Bacteriophage P1) • Escherichia coli • Escherichia coli (strain K12) • Escherichia coli O157:H7 • Escherichia coli O78:H11 (strain H10407 / ETEC) • Fagopyrum esculentum (Common buckwheat) (Polygonum fagopyrum) • Farfantepenaeus aztecus (Brown shrimp) (Penaeus aztecus) • Fasciola gigantica (Giant liver fluke) • Felis catus (Cat) (Felis silvestris catus) • Frateuria aurantia (strain ATCC 33424 / DSM 6220 / NBRC 3245 / NCIMB 13370) (Acetobacter aurantius) • Gadus morhua (Atlantic cod) • Gallus gallus (Chicken) • Giardia intestinalis (strain ATCC 50803 / WB clone C6) (Giardia lamblia) • Glycine max (Soybean) (Glycine hispida) • Haemophilus influenzae (strain 10810) • Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) • Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) • Helicobacter pylori XZ274 • Heligmosomoides polygyrus (Parasitic roundworm) • Helix pomatia (Roman snail) (Edible snail) • Hesperocyparis arizonica (Arizona cypress) (Cupressus arizonica) • Hevea brasiliensis (Para rubber tree) (Siphonia brasiliensis) • Holcus lanatus (Yorkshire-fog) (Nothoholcus lanatus) • Ixodes scapularis (Black-legged tick) (Deer tick) • Juglans nigra (Black walnut) (Wallia nigra) • Juglans regia (English walnut) • Juniperus ashei (Ozark white cedar) • Juniperus virginiana (Eastern redcedar) (Sabina virginiana) • Lactobacillus delbrueckii subsp. bulgaricus (strain 2038) • Leishmania braziliensis • Leishmania chagasi • Leishmania donovani (strain BPK282A1) • Leishmania infantum • Leishmania major • Leishmania panamensis • Lens culinaris (Lentil) (Cicer lens) • Lentinula edodes (Shiitake mushroom) (Lentinus edodes) • Lepidoglyphus destructor (Storage mite) (Glycyphagus destructor) • Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601) • Lipomyces anomalus • Lipomyces starkeyi (Oleaginous yeast) • Lipomyces tetrasporus • Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) • Litopenaeus vannamei (Whiteleg shrimp) (Penaeus vannamei) • Lolium perenne (Perennial ryegrass) • Malassezia furfur (Pityriasis versicolor infection agent) (Pityrosporum furfur) • Malassezia sympodialis (strain ATCC 42132) (Atopic eczema-associated yeast) • Malus domestica (Apple) (Pyrus malus) • Mangifera indica (Mango) • Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) • Mus musculus (Mouse) • Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) • Mycobacterium gordonae • Mycobacterium leprae (strain Br4923) • Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10) • Mycoplasma penetrans (strain HF-2) • Mycoplasma pneumoniae (strain ATCC 29342 / M129) • Myrmecia pilosula (Jack jumper ant) (Australian jumper ant) • Myxozyma sp. KAL • Naegleria gruberi (Amoeba) • Neisseria meningitidis serogroup B (strain MC58) • Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (Aspergillus fumigatus) • Olea europaea (Common olive) • Onchocerca volvulus • Ophiocordyceps robertsii • Orientia tsutsugamushi str. Karp • Oryctolagus cuniculus (Rabbit) • Oryza sativa subsp. japonica (Rice) • Paenibacillus sp. (strain JDR-2) • Pan troglodytes (Chimpanzee) • Paralichthys olivaceus (Bastard halibut) (Hippoglossus olivaceus) • Parietaria judaica (Pellitory-of-the-wall) (Parietaria diffusa) • Paspalum notatum (Bahia grass) • Penaeus monodon (Giant tiger prawn) • Penicillium chrysogenum (Penicillium notatum) • Periplaneta americana (American cockroach) (Blatta americana) • Phleum pratense (Common timothy) • Poa pratensis (Kentucky bluegrass) (Phalaris japonica) • Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) • Prochlorococcus marinus (strain MIT 9312) • Prunus armeniaca (Apricot) (Armeniaca vulgaris) • Prunus avium (Cherry) (Cerasus avium) • Prunus domestica (Garden plum) • Prunus dulcis (Almond) (Amygdalus dulcis) • Prunus persica (Peach) (Amygdalus persica) • Pseudomonas aeruginosa • Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) • Pseudomonas chloritidismutans AW-1 • Pseudomonas psychrophila • Pseudomonas sp. (strain RS-16) • Pseudomonas stutzeri CCUG 29243 • Psychrobacter sp. G • Rhodococcus sp. AW25M09 • Rhynchogastrema glucofermentans • Ricinus communis (Castor bean) • Rickettsia bellii str. RML Mogi • Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker’s yeast) • Salmo salar (Atlantic salmon) • Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) • Schistosoma mansoni (Blood fluke) • Scylla paramamosain (Mud crab) • Sesamum indicum (Oriental sesame) (Sesamum orientale) • Shigella flexneri • Sinapis alba (White mustard) (Brassica hirta) • Solanum lycopersicum (Tomato) (Lycopersicon esculentum) • Solanum tuberosum (Potato) • Spirosoma linguale (strain ATCC 33905 / DSM 74 / LMG 10896) • Staphylococcus aureus (strain NCTC 8325) • Streptococcus agalactiae MRI Z1-217 • Streptococcus downei F0415 • Streptococcus dysgalactiae subsp. equisimilis AC-2713 • Streptococcus oralis (strain Uo5) • Streptococcus pneumoniae • Streptococcus pneumoniae (strain ATCC BAA-255 / R6) • Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) • Streptococcus pyogenes serotype M5 (strain Manfredo) • Streptococcus sp. group G • Streptomyces levis • Styela plicata (Wrinkled sea squirt) (Ascidia plicata) • Sus scrofa (Pig) • Taenia crassiceps • Taenia saginata (Beef tapeworm) (Cysticercus bovis) • Taenia solium (Pork tapeworm) • Tetronarce californica (Pacific electric ray) (Torpedo californica) • Thermobifida fusca (strain YX) • Toxoplasma gondii • Toxoplasma gondii (strain ATCC 50861 / VEG) • Trichomonas vaginalis • Trichophyton rubrum CBS 289.86 • Triticum aestivum (Wheat) • Tropheryma whipplei (strain TW08/27) (Whipple’s bacillus) • Trypanosoma brucei brucei (strain 927/4 GUTat10.1) • Trypanosoma cruzi • Tupaia chinensis (Chinese tree shrew) • Turbo cornutus (Horned turban) (Battilus cornutus) • Uncultured phage WW-nAnB • Vespula vidua (Ground hornet) • Vespula vulgaris (Yellow jacket) (Wasp) • Vibrio anguillarum (Listonella anguillarum) • Wolbachia sp. subsp. Brugia malayi (strain TRS) • Wuchereria bancrofti • Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) • Yersinia pestis • Zea mays (Maize) • Ziziphus mauritiana

XenScan™ technical details.

XenScan builds upon the original VirScan (Xu, et al, 2015) and HuScan PhIP-Seq libraries (Larman, et al, 2011). This xenoantigen library based on the Immune Epitope Database (IEDB) was first reported alongside an updated VirScan library (Mina, et al, 2019).  This oligonucleotide library was PCR-amplified with adaptors for cloning and inserted into a T7 phage display vector that was expanded in E. Coli. The expanded T7 phage library quality is confirmed by sequencing to have >90% of the library within one log of overall average clonal frequency. An aliquot from this library is then 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. A more detailed description of this process is available (Mohan, et al, 2018).

XenScan™ service details & data deliverables.

A typical XenScan™ service involves case and control serum or plasma samples. These are heat deactivated and undergo a protein A/G pulldown assay, PCR amplification, and next-generation sequencing. Raw sequence data are run through a normalization and quantitation pipeline as previously described (Mohan et al., 2018).  Raw pipeline outputs are then provided to customers as normalized read counts data tables for both whole proteins and individual 56mer peptides.

XenScan™ service sample requirements.

Human serum or plasma: Send two 10μL aliquots per sample.

Human (CSF) cerebrospinal fluid: Send two 100μL aliquots per sample.

Ten sample minimum.

Note: HuScan™, VirScan™, & XenScan™ can be run together in a single-well assay at reduced cost.

Cohort balancing (studies  >88 samples):  Individual PhIP-Seq studies are prepared in x96 well plates using aliquots of our phage library; each study requires x8 protein A/G beads-only internal control samples per sequencer run (provided free-of-charge).  Data are most reproducible within a single sequencer run. Sequencer runs are currently limited to x3 96-well plates (288 experimental samples + x8 protein A/G beads per run).   While data from multiple days is easily pooled by our informatics pipeline, customers running larger studies may wish to consider balancing case/control or replicate samples within and across processing days.

Sample shipping & sample return.

We will include shipping details in your quote – you must cover the cost of shipping samples to CDI. Typically, after you receive your report, CDI keeps the remaining samples for two months and then disposes of them. When shipping to us, please let us know if you want the remaining samples returned after the study is complete. We will charge for return shipping.

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