Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies
Abstract
:1. Introduction
2. Applications of Biobanking in Genomic Medicine and Research
3. World’s Largest Biobanks and Genomic Research
3.1. UK Biobank (UKB)
3.2. BioBank Japan (BBJ)
3.3. FinnGen Research Project
3.4. Estonian Biobank (EB)
3.5. China Kadoorie Biobank (CKB)
3.6. Tohoku Medical Megabank Project (TMM)
3.7. Taiwan Biobank (TWB)
3.8. LifeLines Cohort Study
3.9. Other Biobanks
4. Data Integration and Prospects of Trans-Biobank Research
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
GWAS | Genome-wide association study |
SNP | single-nucleotide polymorphism |
UKB | UK Biobank |
BBJ | BioBank Japan |
EB | Estonian biobank |
CKB | China Kadoorie Biobank |
TMM | Tohoku Medical Megabank Project |
WES | whole-exome sequencing |
WGS | whole-genome sequencing |
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Biobank | Location | Number of Participants a | Cohort | Biosamples | Sample Availability | Omics Data | Example Studies |
---|---|---|---|---|---|---|---|
UK Biobank | UK | 500,000 | closed, population aged 40–69 | blood, urine, saliva | yes | genotyping array, WGS, WES, metabolomics, telomere length | Bycroft et al., 2018 [37]; Wells et al., 2019 [38]; Watanabe et al., 2019 [26]; van Hout et al., 2020 [39]; Shikov et al., 2020 [27]; de Vincentis et al., 2022 [40]; Halldorsson et al., 2022 [15] |
BioBank Japan | Japan | 267,307 | closed, patient-based | serum, DNA, tumor tissues | yes | genotyping array, WGS, metabolome | Ishigaki et al., 2020 [41]; Matoba et al., 2020 [42] |
FinnGen | Finland | 538,600 | open, general population, 15 disease-specific cohorts | depends on sample collector b | depends on sample collector b | genotyping array | Desch et al., 2020 [43]; Kurki et al., 2022 [44]; Sun et al., 2022 [45] |
Estonian biobank | Estonia | 200,000 | open, adult population | whole blood and fractions, DNA, RNA | yes | WGS, WES, genotyping array, metabolomics (NMR), RNA seq., genome-wide methylation arrays, genome-wide gene expression array | Alver et al., 2019 [29]; Reisberg et al., 2019 [46] |
China Kadoorie Biobank | China | 512,891 | closed, residents of 5 urban and 5 rural provinces aged 30–79 | blood | no | genotyping array, WGS | Spracklen et al., 2020 [47]; Giannakopoulou et al., 2020 [48]; Zhu et al., 2021 [49]; Li et al., 2022 [50] |
Tohoku Medical Megabank Project | Japan | 157,000 | closed, adult residents of Miyagi and Iwate Prefecture, three-generation cohort | blood fractions, urine, saliva, breast milk, dental plaque, stimulated T-cells, and EBV-transformed B-cells | yes | WGS, genotyping array, metabolomics (NMR, LC-MS), genome-wide methylation arrays | Watanabe et al., 2018 [51]; Tadaka et al., 2019 [52]; Tadaka et al., 2021 [53]; Kawame et al., 2022 [28]; Ohneda et al., 2022 [54]; Park, 2022 [55] |
Taiwan Biobank | Taiwan | 181,635 | open, population aged 20–70, patient-based | blood, urine, saliva | yes | genotyping array, WGS, DNA methylation, HLA typing, metabolomics | Weiet al., 2021 [56]; Lee at al., 2022 [57]; Juang et al., 2021 [58] |
LifeLines Cohort Study | Netherlands | 167,000 | closed, residents of the northern part of country | blood, urine, saliva, scalp hair | yes | genotyping array, WGS, microbiome data | Bonder et al., 2016 [59]; Imhann et al., 2016 [60]; Zhernakova et al., 2018 [61] |
National Biobank of Korea | South Korea | 1,051,787 | population-based, patient-based | blood fractions, urine, saliva, DNA, tissue | yes | genotyping array | Namet al., 2022 [62]; Moon et al., 2019 [63] |
Karolinska Biobank | Sweden | 700,000 | collection-specific | whole blood and fractions, urine, saliva, DNA | depends on collection | genotyping array | Bonfiglio et al., 2018 [64] |
HUNT Biobank | Norway | 120,000 | open, adolescent and adult residents of Trøndelag | whole blood, plasma, serum, urine, saliva, feces, DNA | yes | genotyping array | Nielsen et al., 2018 [65]; Nielsen et al., 2020 [66]; Surakka et al., 2020 [67] |
Canadian Partnership for Tomorrow’s Health | Canada | 331,359 | open, residents of 9 provinces aged 30–74 | whole blood and fractions, urine, saliva, dry blood spots, nail fragments | yes | genotyping array | Lona-Durazo et al., 2021 [68]; Joseph et al., 2022 [69] |
All of Us Research Program | USA | 348,000 | open, adult minority population | whole blood, urine, saliva | no | WGS, genotyping array | n.a. |
BioVU | USA | 275,000 | open, pediatric and adult patient-based | DNA | yes | genotyping array | Zhenget al., 2021 [70]; Goldstein et al., 2020 [71]; Krebs et al., 2020 [72] |
Penn Medicine BioBank | USA | 52,853 | open, adult patient-based | blood, tissue | yes | genotyping array, WES | Parket al., 2021 [73]; Akbari et al., 2022 [74] |
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Lazareva, T.E.; Barbitoff, Y.A.; Changalidis, A.I.; Tkachenko, A.A.; Maksiutenko, E.M.; Nasykhova, Y.A.; Glotov, A.S. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J. Pers. Med. 2022, 12, 2040. https://doi.org/10.3390/jpm12122040
Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. Journal of Personalized Medicine. 2022; 12(12):2040. https://doi.org/10.3390/jpm12122040
Chicago/Turabian StyleLazareva, Tatyana E., Yury A. Barbitoff, Anton I. Changalidis, Alexander A. Tkachenko, Evgeniia M. Maksiutenko, Yulia A. Nasykhova, and Andrey S. Glotov. 2022. "Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies" Journal of Personalized Medicine 12, no. 12: 2040. https://doi.org/10.3390/jpm12122040