Overcoming barriers to single-cell RNA sequencing adoption in low- and middle-income countries – European Journal of Human Genetics

  • Shendure J, Findlay GM, Snyder MW. Genomic medicine–progress, pitfalls, and promise. Cell. 2019;177:45–57.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gibbs RA. The human genome project changed everything. Nat Rev Genet. 2020;21:575–6.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Opinionome: Can DNA sequencing get any faster and cheaper? Broad Institute. 2016. https://www.broadinstitute.org/blog/opinionome-can-dna-sequencing-get-any-faster-and-cheaper.

  • The International HapMap Consortium. The International HapMap Project. Nature. 2003;426:789–96.

    Article 

    Google Scholar
     

  • Devuyst O. The 1000 genomes project: welcome to a new world. Perit Dial Int. 2015;35:676–7.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • The Cancer Genome Atlas Program (TCGA) – NCI. 2022. https://www.cancer.gov/ccg/research/genome-sequencing/tcga.

  • The Malaria Genomic Epidemiology Network. A global network for investigating the genomic epidemiology of malaria. Nature. 2008;456:732–7.

    Article 
    PubMed Central 

    Google Scholar
     

  • Wang T, Antonacci-Fulton L, Howe K, Lawson AH, Lucas KJ, Phillippy MA, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 2022;604:437–46.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Longo SK, Guo MG, Ji AL, Khavari PA. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat Rev Genet. 2021;22:627–44.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Elmentaite R, Domínguez Conde C, Yang L, Teichmann SA. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet. 2022;23:395–410.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Haque A, Engel J, Teichmann SA, Lönnberg T. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med. 2017;9:75.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bentley AR, Callier S, Rotimi CN. Diversity and inclusion in genomic research: why the uneven progress? J Community Genet. 2017;8:255–66.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Human Genome Reference Sequence. 2024. https://www.genome.gov/genetics-glossary/Human-Genome-Reference-Sequence.

  • Chen R, Butte AJ. The reference human genome demonstrates high risk of type 1 diabetes and other disorders. In: Biocomputing 2011. WORLD SCIENTIFIC, 2010, 231-42.

  • Ballouz S, Dobin A, Gillis JA. Is it time to change the reference genome? Genome Biol. 2019;20:159.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peterson RE, Kuchenbaecker K, Walters RK, Chen Y-C, Popejoy BA, Periyasamy S, et al. Genome-wide association studies in ancestrally diverse populations: opportunities, methods, pitfalls, and recommendations. Cell. 2019;179:589–603.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Popejoy AB, Fullerton SM. Genomics is failing on diversity. Nature. 2016;538:161–4.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017;27:849–64.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fatumo S, Chikowore T, Choudhury A, Ayub M, Martin AR, Kuchenbaecker K. A roadmap to increase diversity in genomic studies. Nat Med. 2022;28:243–50.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Manry J, Quintana-Murci L. A genome-wide perspective of human diversity and its implications in infectious disease. Cold Spring Harb Perspect Med. 2013;3:a012450.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bentley AR, Callier SL, Rotimi CN. Evaluating the promise of inclusion of African ancestry populations in genomics. npj Genom Med. 2020;5:1–9.

    Article 

    Google Scholar
     

  • McGuire AL, Gabriel S, Tishkoff SA, Wonkam A, Chakravarti A, Furlong MEE, et al. The road ahead in genetics and genomics. Nat Rev Genet. 2020;21:581–96.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gurdasani D, Carstensen T, Tekola-Ayele F, Pagani L, Tachmazidou I, Hatzikotoulas K, et al. The African genome variation project shapes medical genetics in Africa. Nature. 2015;517:327–32.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Scott EM, Halees A, Itan Y, Spencer GA, He Y, Azab AM, et al. Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nat Genet. 2016;48:1071–6.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Latin American Genomics Consortium | Research Organization. My Site.2024. https://www.latinamericangenomicsconsortium.org.

  • National Centre for Indigenous Genomics. Research Data Australia. 2024. https://researchdata.edu.au/national-centre-indigenous-genomics/619341.

  • Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Wagner J, et al. A complete reference genome improves analysis of human genetic variation. Science. 2022;376:eabl3533.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze A, Mikheenko A, et al. The complete sequence of a human genome. Science. 2022;376:44–53.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liao W-W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, et al. A draft human pangenome reference. Nature. 2023;617:312–24.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rood JE, Maartens A, Hupalowska A, Teichmann SA, Regev A. Impact of the Human Cell Atlas on medicine. Nat Med. 2022;28:2486–96.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Baldwin MJ, Cribbs AP, Guilak F, Snelling SJB. Mapping the musculoskeletal system one cell at a time. Nat Rev Rheumatol. 2021;17:247–8.

    Article 
    PubMed 

    Google Scholar
     

  • Rozenblatt-Rosen O, Stubbington MJT, Regev A, Teichmann SA. The Human Cell Atlas: from vision to reality. Nature. 2017;550:451–3.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • HuBMAP Consortium. et al. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;574:187–92.

    Article 
    CAS 

    Google Scholar
     

  • The Human Cell Atlas. White Paper. 2017. https://www.humancellatlas.org/wp-content/uploads/2019/11/HCA_WhitePaper_18Oct2017-copyright.pdf.

  • Global Burden 2019 Risk Factors Collaborators. Global burden of 87 risk factors in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2020;396:1223–49.

    Article 

    Google Scholar
     

  • Munung NS, Mayosi BM, de Vries J. Equity in international health research collaborations in Africa: Perceptions and expectations of African researchers. PLOS ONE. 2017;12:e0186237.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dara A, Dogga SK, Rop J, Ouologuem D, Tandina F, Talman MA, et al. Tackling malaria transmission at a single cell level in an endemic setting in sub-Saharan Africa. Nat Commun. 2022;13:2679.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Maher D, Aseffa A, Kay S, Bayona MT. External funding to strengthen capacity for research in low-income and middle-income countries: exigence, excellence and equity. BMJ Glob Health. 2020;5:e002212.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nguyen HCT, Baik B, Yoon S, Park T, Nam D. Benchmarking integration of single-cell differential expression. Nat Commun. 2023;14:1570.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xu C, Prete M, Webb S, Jardine L, Stewart JB, Hoo R, et al. Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell. 2023;186:5876–91.e20.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Banimfreg BH. A comprehensive review and conceptual framework for cloud computing adoption in bioinformatics. Healthc Anal. 2023;3:100190.

    Article 

    Google Scholar
     

  • Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, et al. Best practices for single-cell analysis across modalities. Nat Rev Genet. 2023;24:1–23.

    Article 

    Google Scholar
     

  • Baudrimont A, Jaquet V, Wallerich S, Voegeli S, Becskei A. Contribution of RNA degradation to intrinsic and extrinsic noise in gene expression. Cell Rep. 2019;26:3752–61.e5.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kharchenko PV. The triumphs and limitations of computational methods for scRNA-seq. Nat Methods. 2021;18:723–32.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu Y, Zhang K. Tools for the analysis of high-dimensional single-cell RNA sequencing data. Nat Rev Nephrol. 2020;16:408–21.

    Article 
    PubMed 

    Google Scholar
     

  • Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, et al. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biol. 2020;21:130.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Svensson V, Vento-Tormo R, Teichmann SA. Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. 2018;13:599–604.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods. 2014;11:163–6.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jia E, Shi H, Wang Y, Zhou Y, Liu Z, Pan M, et al. Optimization of library preparation based on SMART for ultralow RNA-seq in mice brain tissues. BMC Genomics. 2021;22:809.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol. 2023;24:695–713.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li H, Zhou J, Li Z, Chen S, Liao X, Zhang B, et al. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nat Commun. 2023;14:1548.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • The next generation of single-cell sequencing methods can be microfluidics-free. Nat Biotechnol. 2023;41:1524–5.

  • Department of Health, Education, and Welfare, National Commission for the Protection of Human Subjects of Biomedical and Behavioral Research. The Belmont Report. Ethical principles and guidelines for the protection of human subjects of research. J Am Coll Dent. 2014;81:4–13.


    Google Scholar
     

  • World Medical Association. World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects. JAMA. 2013;310:2191–4.

    Article 

    Google Scholar
     

  • Makolo AU, Smile O, Ezekiel KB, Destefano AM, McCall JL, Isokpehi RD. Leveraging H3Africa scholarly publications for technology-enhanced personalized bioinformatics education. Educ Sci. 2022;12:859.

    Article 

    Google Scholar
     

  • Fullwiley D, Gibbon S. Genomics in emerging and developing economies. In: Gibbon S, Prainsack B, Hilgartner S, Lamoreaux J (eds). Handbook of Genomics, Health and Society. Routledge: London (UK), 2018. http://www.ncbi.nlm.nih.gov/books/NBK554738/ (accessed 12 Jan2024).

  • de Vries J, Bull SJ, Doumbo O, Ibrahim M, Mercereau-Puijalon O, Kwiatkowski D, et al. Ethical issues in human genomics research in developing countries. BMC Med Ethics. 2011;12:5.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yeager KA, Bauer-Wu S. Cultural humility: essential foundation for clinical researchers. Appl Nurs Res. 2013;26:251–6.

    Article 
    PubMed 

    Google Scholar
     

  • Tindana P, de Vries J. Broad consent for genomic research and biobanking: perspectives from low- and middle-income countries. Annu Rev Genomics Hum Genet. 2016;17:375–93.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tekola F, Bull SJ, Farsides B, Newport JM, Adeyemo A, Rotimi NC, et al. Tailoring consent to context: designing an appropriate consent process for a biomedical study in a low income setting. PLOS Negl Trop Dis. 2009;3:e482.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Han H-R, Xu A, Mendez KJW, Okoye S, Cudjoe J, Bahouth M, et al. Exploring community engaged research experiences and preferences: a multi-level qualitative investigation. Res Involv Engagem. 2021;7:19.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • World Health Organization. Community engagement: a health promotion guide for universal health coverage in the hands of the people. World Health Organization. https://iris.who.int/bitstream/handle/10665/334379/9789240010529-eng.pdf?sequence=1&isAllowed=y License: CC BY-NC-SA 3.0 IGO. 2020.

  • Nuyens Y. No Development Without Research: A challenge for capacity strengthening. 2005. https://www.files.ethz.ch/isn/128224/2005-ResearchReport-NoDevelopment.pdf.

  • Haelewaters D, Hofmann TA, Romero-Olivares AL. Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South. PLOS Comput Biol. 2021;17:e1009277.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kerasidou A. The role of trust in global health research collaborations. Bioethics. 2019;33:495–501.

    Article 
    PubMed 

    Google Scholar
     

  • Faure MC, Munung NS, Ntusi NAB, Pratt B, de Vries J. Considering equity in global health collaborations: a qualitative study on experiences of equity. PLOS ONE. 2021;16:e0258286.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Race, Ethnicity, and Genetics Working Group. The use of racial, ethnic, and ancestral categories in human genetics research. Am J Human Genet. 2005;77:519–32.

  • Lee SS-J, Fullerton SM, McMahon CE, Bentz M, Saperstein A, Jeske M, et al. Targeting representation: interpreting calls for diversity in precision medicine research. Yale J Biol Med. 2022;95:317–26.

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Landry LG, Ali N, Williams DR, Rehm HL, Bonham VL. Lack of diversity in genomic databases is a barrier to translating precision medicine research into practice. Health Aff. 2018;37:780–5.

    Article 

    Google Scholar
     

  • Addie S, Alper J, Beachy SH (eds.). Understanding Disparities in Access to Genomic Medicine: Proceedings of a Workshop. National Academies Press: Washington, D.C., 2018. https://doi.org/10.17226/25277.