Comparison of Proteomic Assessment Methods in Multiple Cohort Studies.

TitleComparison of Proteomic Assessment Methods in Multiple Cohort Studies.
Publication TypePublication
Year2020
AuthorsRaffield LM, Dang H, Pratte KA, Jacobson S, Gillenwater LA, Ampleford E, Barjaktarevic I, Basta P, Clish CB, Comellas AP, Cornell E, Curtis JL, Doerschuk C, Durda P, Emson C, Freeman CM, Guo X, Hastie AT, Hawkins GA, Herrera J, W Johnson C, Labaki WW, Liu Y, Masters B, Miller M, Ortega VE, Papanicolaou G, Peters S, Taylor KD, Rich SS, Rotter JI, Auer P, Reiner AP, Tracy RP, Ngo D, Gerszten RE, O'Neal WK, Bowler RP
Corporate AuthorsNHLBI Trans-Omics for Precision Medicine(TOPMed) Consortium
JournalProteomics
Volume20
Issue12
Paginatione1900278
Date Published2020 Jun
ISSN1615-9861
KeywordsAdult, Aged, Aged, 80 and over, Cohort Studies, Female, Humans, Immunoassay, Male, Middle Aged, Myocardial Infarction, Proteome, Proteomics, Pulmonary Disease, Chronic Obstructive, Smokers
Abstract

Novel proteomics platforms, such as the aptamer-based SOMAscan platform, can quantify large numbers of proteins efficiently and cost-effectively and are rapidly growing in popularity. However, comparisons to conventional immunoassays remain underexplored, leaving investigators unsure when cross-assay comparisons are appropriate. The correlation of results from immunoassays with relative protein quantification is explored by SOMAscan. For 63 proteins assessed in two chronic obstructive pulmonary disease (COPD) cohorts, subpopulations and intermediate outcome measures in COPD Study (SPIROMICS), and COPDGene, using myriad rules based medicine multiplex immunoassays and SOMAscan, Spearman correlation coefficients range from -0.13 to 0.97, with a median correlation coefficient of ≈0.5 and consistent results across cohorts. A similar range is observed for immunoassays in the population-based Multi-Ethnic Study of Atherosclerosis and for other assays in COPDGene and SPIROMICS. Comparisons of relative quantification from the antibody-based Olink platform and SOMAscan in a small cohort of myocardial infarction patients also show a wide correlation range. Finally, cis pQTL data, mass spectrometry aptamer confirmation, and other publicly available data are integrated to assess relationships with observed correlations. Correlation between proteomics assays shows a wide range and should be carefully considered when comparing and meta-analyzing proteomics data across assays and studies.

DOI10.1002/pmic.201900278
Alternate JournalProteomics
PubMed ID32386347
PubMed Central IDPMC7425176
Grant ListN01HC95163 / HL / NHLBI NIH HHS / United States
75N93020D00002 / AI / NIAID NIH HHS / United States
N01HC95169 / HL / NHLBI NIH HHS / United States
N01 HC095162 / HC / NHLBI NIH HHS / United States
N01HC95164 / HL / NHLBI NIH HHS / United States
R01 HL132320 / HL / NHLBI NIH HHS / United States
75N98020D00007 / OD / NIH HHS / United States
N01 HC095164 / HC / NHLBI NIH HHS / United States
75N95020D00004 / DA / NIDA NIH HHS / United States
N01 HC095163 / HC / NHLBI NIH HHS / United States
75N95020D00003 / DA / NIDA NIH HHS / United States
T32 HL007749 / HL / NHLBI NIH HHS / United States
HHSN268201500003C / HL / NHLBI NIH HHS / United States
HHSN268200900019C / HL / NHLBI NIH HHS / United States
75N90020D00002 / CL / CLC NIH HHS / United States
R01 HL132947 / HL / NHLBI NIH HHS / United States
P30 DK040561 / DK / NIDDK NIH HHS / United States
N01HC95160 / HL / NHLBI NIH HHS / United States
R01 HL120393 / HL / NHLBI NIH HHS / United States
U54 HG003067 / HG / NHGRI NIH HHS / United States
N01 HC095168 / HC / NHLBI NIH HHS / United States
UL1 TR001079 / TR / NCATS NIH HHS / United States
75N96020D00002 / ES / NIEHS NIH HHS / United States
P30 ES005605 / ES / NIEHS NIH HHS / United States
75N95020D00002 / DA / NIDA NIH HHS / United States
75N99020D00003 / OF / ORFDO NIH HHS / United States
U01 HL089897 / HL / NHLBI NIH HHS / United States
N01 HC095165 / HC / NHLBI NIH HHS / United States
N01HC95162 / HL / NHLBI NIH HHS / United States
N01HC95168 / HL / NHLBI NIH HHS / United States
U01 HL089856 / HL / NHLBI NIH HHS / United States
75N90020D00003 / CL / CLC NIH HHS / United States
75N96020D00003 / ES / NIEHS NIH HHS / United States
HHSN268200900015C / HL / NHLBI NIH HHS / United States
T32 HL129982 / HL / NHLBI NIH HHS / United States
HHSN268200900016C / HL / NHLBI NIH HHS / United States
N01 HC095169 / HC / NHLBI NIH HHS / United States
P30 DK063491 / DK / NIDDK NIH HHS / United States
75N99020D00002 / OF / ORFDO NIH HHS / United States
I01 CX000911 / CX / CSRD VA / United States
HHSN268201800001C / HL / NHLBI NIH HHS / United States
75N99020D00006 / OF / ORFDO NIH HHS / United States
N01 HC095159 / HC / NHLBI NIH HHS / United States
N01HC95165 / HL / NHLBI NIH HHS / United States
U01 HL137880 / HL / NHLBI NIH HHS / United States
N01HC95159 / HL / NHLBI NIH HHS / United States
N01 HC095161 / HC / NHLBI NIH HHS / United States
75N95020D00007 / DA / NIDA NIH HHS / United States
N01HC95161 / HL / NHLBI NIH HHS / United States
UL1 TR001420 / TR / NCATS NIH HHS / United States
75N95020D00005 / DA / NIDA NIH HHS / United States
R01 HL133870 / HL / NHLBI NIH HHS / United States
HHSN268201500003I / HL / NHLBI NIH HHS / United States
75N92021D00006 / HL / NHLBI NIH HHS / United States
HHSN268200900018C / HL / NHLBI NIH HHS / United States
75N99020D00005 / OF / ORFDO NIH HHS / United States
N01 HC095166 / HC / NHLBI NIH HHS / United States
N01HC95167 / HL / NHLBI NIH HHS / United States
75N99020D00007 / OF / ORFDO NIH HHS / United States
HHSN268200900017C / HL / NHLBI NIH HHS / United States
HHSN268200900020C / HL / NHLBI NIH HHS / United States
HHSN268200900013C / HL / NHLBI NIH HHS / United States
UL1 TR000040 / TR / NCATS NIH HHS / United States
R01 HL117626 / HL / NHLBI NIH HHS / United States
N01HC95166 / HL / NHLBI NIH HHS / United States
Merit Review I01 CX000911 / VA / VA / United States
HHSN268200900014C / HL / NHLBI NIH HHS / United States
N01 HC095167 / HC / NHLBI NIH HHS / United States
75N99020D00004 / OF / ORFDO NIH HHS / United States
N01 HC095160 / HC / NHLBI NIH HHS / United States
MS#: 
MS150
Manuscript Full Title: 
Comparison of Proteomic Assessment Methods in Multiple Cohort Studies.
Manuscript Lead/Corresponding Author Affiliation: 
Genomics and Informatics Center (University of North Carolina at Chapel Hill)
ECI: 
Manuscript Status: 
Published and Public