PMID- 34967113
OWN - NLM
STAT- MEDLINE
DCOM- 20220405
LR  - 20220520
IS  - 1552-4930 (Electronic)
IS  - 1552-4922 (Linking)
VI  - 101
IP  - 4
DP  - 2022 Apr
TI  - A simple strategy for sample annotation error detection in cytometry datasets.
PG  - 351-360
LID - 10.1002/cyto.a.24525 [doi]
AB  - Mislabeling samples or data with the wrong participant information can affect 
      study integrity and lead investigators to draw inaccurate conclusions. Quality 
      control to prevent these types of errors is commonly embedded into the analysis 
      of genomic datasets, but a similar identification strategy is not standard for 
      cytometric data. Here, we present a method for detecting sample identification 
      errors in cytometric data using expression of human leukocyte antigen (HLA) class 
      I alleles. We measured HLA-A*02 and HLA-B*07 expression in three longitudinal 
      samples from 41 participants using a 33-marker CyTOF panel designed to identify 
      major immune cell types. 3/123 samples (2.4%) showed HLA allele expression that 
      did not match their longitudinal pairs. Furthermore, these same three samples' 
      cytometric signature did not match qPCR HLA class I allele data, suggesting that 
      they were accurately identified as mismatches. We conclude that this technique is 
      useful for detecting sample-labeling errors in cytometric analyses of 
      longitudinal data. This technique could also be used in conjunction with another 
      method, like GWAS or PCR, to detect errors in cross-sectional data. We suggest 
      widespread adoption of this or similar techniques will improve the quality of 
      clinical studies that utilize cytometry.
CI  - (c) 2021 International Society for Advancement of Cytometry.
FAU - Smithmyer, Megan E
AU  - Smithmyer ME
AUID- ORCID: 0000-0002-1005-0621
AD  - Center for Interventional Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Wiedeman, Alice E
AU  - Wiedeman AE
AUID- ORCID: 0000-0001-7329-7288
AD  - Center for Translational Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Skibinski, David A G
AU  - Skibinski DAG
AUID- ORCID: 0000-0001-8528-2278
AD  - Center for Interventional Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
AD  - Nexelis, 645 Elliot Avenue West, Suite 300, Seattle, Washington, USA.
FAU - Savage, Adam K
AU  - Savage AK
AUID- ORCID: 0000-0003-1913-5485
AD  - Allen Institute for Immunology, Seattle, Washington, USA.
FAU - Acosta-Vega, Carolina
AU  - Acosta-Vega C
AUID- ORCID: 0000-0002-0993-5465
AD  - Center for Translational Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Scheiding, Sheila
AU  - Scheiding S
AUID- ORCID: 0000-0001-5466-9568
AD  - Center for Translational Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Gersuk, Vivian H
AU  - Gersuk VH
AUID- ORCID: 0000-0003-4123-9926
AD  - Center for Systems Immunology, Benaroya Research Institute, Seattle, Washington, 
      USA.
FAU - O'Rourke, Colin
AU  - O'Rourke C
AD  - Center for Interventional Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Long, S Alice
AU  - Long SA
AUID- ORCID: 0000-0002-0281-1240
AD  - Center for Translational Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Buckner, Jane H
AU  - Buckner JH
AUID- ORCID: 0000-0002-9005-1885
AD  - Center for Translational Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
FAU - Speake, Cate
AU  - Speake C
AUID- ORCID: 0000-0003-1480-4272
AD  - Center for Interventional Immunology, Benaroya Research Institute, Seattle, 
      Washington, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20211229
PL  - United States
TA  - Cytometry A
JT  - Cytometry. Part A : the journal of the International Society for Analytical 
      Cytology
JID - 101235694
SB  - IM
MH  - Alleles
MH  - *Cross-Sectional Studies
MH  - Humans
MH  - Real-Time Polymerase Chain Reaction
OTO - NOTNLM
OT  - cytometry
OT  - human leukocyte antigen
OT  - quality control
OT  - reproducible research
OT  - sample mix-up
OT  - sample swap
EDAT- 2021/12/31 06:00
MHDA- 2022/04/06 06:00
CRDT- 2021/12/30 05:57
PHST- 2021/11/19 00:00 [revised]
PHST- 2021/09/02 00:00 [received]
PHST- 2021/12/15 00:00 [accepted]
PHST- 2021/12/31 06:00 [pubmed]
PHST- 2022/04/06 06:00 [medline]
PHST- 2021/12/30 05:57 [entrez]
AID - 10.1002/cyto.a.24525 [doi]
PST - ppublish
SO  - Cytometry A. 2022 Apr;101(4):351-360. doi: 10.1002/cyto.a.24525. Epub 2021 Dec 
      29.