PMID- 34140649
OWN - NLM
STAT- MEDLINE
DCOM- 20220322
LR  - 20220322
IS  - 1476-5438 (Electronic)
IS  - 1018-4813 (Print)
IS  - 1018-4813 (Linking)
VI  - 29
IP  - 11
DP  - 2021 Nov
TI  - A comparison of genotyping arrays.
PG  - 1611-1624
LID - 10.1038/s41431-021-00917-7 [doi]
AB  - Array technology to genotype single-nucleotide variants (SNVs) is widely used in 
      genome-wide association studies (GWAS), clinical diagnostics, and linkage 
      studies. Arrays have undergone a tremendous growth in both number and content 
      over recent years making a comprehensive comparison all the more important. We 
      have compared 28 genotyping arrays on their overall content, genome-wide 
      coverage, imputation quality, presence of known GWAS loci, mtDNA variants and 
      clinically relevant genes (i.e., American College of Medical Genetics (ACMG) 
      actionable genes, pharmacogenetic genes, human leukocyte antigen (HLA) genes and 
      SNV density). Our comparison shows that genome-wide coverage is highly correlated 
      with the number of SNVs on the array but does not correlate with imputation 
      quality, which is the main determinant of GWAS usability. Average imputation 
      quality for all tested arrays was similar for European and African populations, 
      indicating that this is not a good criterion for choosing a genotyping array. 
      Rather, the additional content on the array, such as pharmacogenetics or HLA 
      variants, should be the deciding factor. As the research question of a study will 
      in large part determine which class of genes are of interest, there is not just 
      one perfect array for all different research questions. This study can thus help 
      as a guideline to determine which array best suits a study's requirements.
CI  - (c) 2021. The Author(s).
FAU - Verlouw, Joost A M
AU  - Verlouw JAM
AUID- ORCID: 0000-0003-2373-0981
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - Clemens, Eva
AU  - Clemens E
AD  - Department of Pediatric Oncology, Erasmus MC, Rotterdam, The Netherlands.
AD  - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
FAU - de Vries, Jard H
AU  - de Vries JH
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - Zolk, Oliver
AU  - Zolk O
AUID- ORCID: 0000-0002-8220-3834
AD  - Institute of Clinical Pharmacology, Brandenburg Medical School, Immanuel Klinik 
      Rudersdorf, Rudersdorf, Germany.
FAU - Verkerk, Annemieke J M H
AU  - Verkerk AJMH
AUID- ORCID: 0000-0002-7523-3656
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - Am Zehnhoff-Dinnesen, Antoinette
AU  - Am Zehnhoff-Dinnesen A
AD  - Clinic of Phoniatrics and Pedaudiology, University Hospital Munster, Munster, 
      Germany.
FAU - Medina-Gomez, Carolina
AU  - Medina-Gomez C
AUID- ORCID: 0000-0001-7999-5538
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - Lanvers-Kaminsky, Claudia
AU  - Lanvers-Kaminsky C
AD  - Department of Pediatric Hematology and Oncology, University Children's Hospital, 
      Muenster, Germany.
FAU - Rivadeneira, Fernando
AU  - Rivadeneira F
AUID- ORCID: 0000-0001-9435-9441
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - Langer, Thorsten
AU  - Langer T
AD  - Department of Pediatric Oncology and Hematology, University Hospital for Children 
      and Adolescents Lubeck, Lubeck, Germany.
FAU - van Meurs, Joyce B J
AU  - van Meurs JBJ
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
FAU - van den Heuvel-Eibrink, Marry M
AU  - van den Heuvel-Eibrink MM
AUID- ORCID: 0000-0002-7760-879X
AD  - Department of Pediatric Oncology, Erasmus MC, Rotterdam, The Netherlands.
AD  - Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
FAU - Uitterlinden, Andre G
AU  - Uitterlinden AG
AUID- ORCID: 0000-0002-7276-3387
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.
AD  - Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands.
FAU - Broer, Linda
AU  - Broer L
AUID- ORCID: 0000-0003-0011-123X
AD  - Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands. 
      l.broer@erasmusmc.nl.
LA  - eng
SI  - NTR/NTR6831
PT  - Comparative Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210618
PL  - England
TA  - Eur J Hum Genet
JT  - European journal of human genetics : EJHG
JID - 9302235
RN  - 0 (Reagent Kits, Diagnostic)
SB  - IM
MH  - Genetic Testing/methods/*standards
MH  - Genome-Wide Association Study/methods/standards
MH  - Genotyping Techniques/methods/*standards
MH  - Humans
MH  - Oligonucleotide Array Sequence Analysis/methods/*standards
MH  - Reagent Kits, Diagnostic/standards
MH  - Sensitivity and Specificity
PMC - PMC8560858
COIS- The authors declare no competing interests.
EDAT- 2021/06/19 06:00
MHDA- 2022/03/23 06:00
PMCR- 2021/06/18
CRDT- 2021/06/18 06:35
PHST- 2021/03/05 00:00 [received]
PHST- 2021/05/25 00:00 [accepted]
PHST- 2021/05/12 00:00 [revised]
PHST- 2021/06/19 06:00 [pubmed]
PHST- 2022/03/23 06:00 [medline]
PHST- 2021/06/18 06:35 [entrez]
PHST- 2021/06/18 00:00 [pmc-release]
AID - 10.1038/s41431-021-00917-7 [pii]
AID - 917 [pii]
AID - 10.1038/s41431-021-00917-7 [doi]
PST - ppublish
SO  - Eur J Hum Genet. 2021 Nov;29(11):1611-1624. doi: 10.1038/s41431-021-00917-7. Epub 
      2021 Jun 18.