Peptide based diagnostics: Are random-sequence peptides more useful than tiling proteome sequences?

Krupa Arun Navalkar, Stephen Johnston, Phillip Stafford

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.

Original languageEnglish (US)
Pages (from-to)10-21
Number of pages12
JournalJournal of Immunological Methods
Volume417
DOIs
StatePublished - Feb 1 2015

Fingerprint

Proteome
Peptides
Coccidioidomycosis
Coccidioides
Epitopes
Sensitivity and Specificity
Immunodominant Epitopes
Immunodiffusion
Amino Acid Substitution
Ligands

Keywords

  • Immunoassay
  • Immunodiagnostic
  • Immunosignature
  • Valley Fever

ASJC Scopus subject areas

  • Immunology
  • Immunology and Allergy
  • Medicine(all)

Cite this

Peptide based diagnostics : Are random-sequence peptides more useful than tiling proteome sequences? / Navalkar, Krupa Arun; Johnston, Stephen; Stafford, Phillip.

In: Journal of Immunological Methods, Vol. 417, 01.02.2015, p. 10-21.

Research output: Contribution to journalArticle

@article{21dcab1b3872417da4a88101029ce8f2,
title = "Peptide based diagnostics: Are random-sequence peptides more useful than tiling proteome sequences?",
abstract = "Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.",
keywords = "Immunoassay, Immunodiagnostic, Immunosignature, Valley Fever",
author = "Navalkar, {Krupa Arun} and Stephen Johnston and Phillip Stafford",
year = "2015",
month = "2",
day = "1",
doi = "10.1016/j.jim.2014.12.002",
language = "English (US)",
volume = "417",
pages = "10--21",
journal = "Journal of Immunological Methods",
issn = "0022-1759",
publisher = "Elsevier",

}

TY - JOUR

T1 - Peptide based diagnostics

T2 - Are random-sequence peptides more useful than tiling proteome sequences?

AU - Navalkar, Krupa Arun

AU - Johnston, Stephen

AU - Stafford, Phillip

PY - 2015/2/1

Y1 - 2015/2/1

N2 - Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.

AB - Diagnostics using peptide ligands have been available for decades. However, their adoption in diagnostics has been limited, not because of poor sensitivity but in many cases due to diminished specificity. Numerous reports suggest that protein-based rather than peptide-based disease detection is more specific. We examined two different approaches to peptide-based diagnostics using Coccidioides (aka Valley Fever) as the disease model. Although the pathogen was discovered more than a century ago, a highly sensitive diagnostic remains unavailable. We present a case study where two different approaches to diagnosing Valley Fever were used: first, overlapping Valley Fever epitopes representing immunodominant Coccidioides antigens were tiled using a microarray format of presynthesized peptides. Second, a set of random sequence peptides identified using a 10,000 peptide immunosignaturing microarray was compared for sensitivity and specificity. The scientific hypothesis tested was that actual epitope peptides from Coccidioides would provide sufficient sensitivity and specificity as a diagnostic. Results demonstrated that random sequence peptides exhibited higher accuracy when classifying different stages of Valley Fever infection vs. epitope peptides. The epitope peptide array did provide better performance than the existing immunodiffusion array, but when directly compared to the random sequence peptides, reported lower overall accuracy. This study suggests that there are competing aspects of antibody recognition that involve conservation of pathogen sequence and aspects of mimotope recognition and amino acid substitutions. These factors may prove critical when developing the next generation of high-performance immunodiagnostics.

KW - Immunoassay

KW - Immunodiagnostic

KW - Immunosignature

KW - Valley Fever

UR - http://www.scopus.com/inward/record.url?scp=84923030957&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84923030957&partnerID=8YFLogxK

U2 - 10.1016/j.jim.2014.12.002

DO - 10.1016/j.jim.2014.12.002

M3 - Article

C2 - 25497701

AN - SCOPUS:84923030957

VL - 417

SP - 10

EP - 21

JO - Journal of Immunological Methods

JF - Journal of Immunological Methods

SN - 0022-1759

ER -