National Genome Initiatives in Europe and the United Kingdom in the Era of Whole-Genome Sequencing: A Comprehensive Review

. 2022 Mar 21 ; 13 (3) : . [epub] 20220321

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid35328109

Identification of genomic variability in population plays an important role in the clinical diagnostics of human genetic diseases. Thanks to rapid technological development in the field of massive parallel sequencing technologies, also known as next-generation sequencing (NGS), complex genomic analyses are now easier and cheaper than ever before, which consequently leads to more effective utilization of these techniques in clinical practice. However, interpretation of data from NGS is still challenging due to several issues caused by natural variability of DNA sequences in human populations. Therefore, development and realization of projects focused on description of genetic variability of local population (often called "national or digital genome") with a NGS technique is one of the best approaches to address this problem. The next step of the process is to share such data via publicly available databases. Such databases are important for the interpretation of variants with unknown significance or (likely) pathogenic variants in rare diseases or cancer or generally for identification of pathological variants in a patient's genome. In this paper, we have compiled an overview of published results of local genome sequencing projects from United Kingdom and Europe together with future plans and perspectives for newly announced ones.

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Collins F.S. Contemplating the end of the beginning. Genome Res. 2001;11:641–643. doi: 10.1101/gr.1898. PubMed DOI

Levy S., Sutton G., Ng P.C., Feuk L., Halpern A.L., Walenz B.P., Axelrod N., Huang J., Kirkness E.F., Denisov G., et al. The diploid genome sequence of an individual human. PLoS Biol. 2007;5:e254. doi: 10.1371/journal.pbio.0050254. PubMed DOI PMC

Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., Makhijani V., Roth G.T., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008;452:872–876. doi: 10.1038/nature06884. PubMed DOI

The Genomes Project C., Auton A., Abecasis G.R., Altshuler D.M., Durbin R.M., Abecasis G.R., Bentley D.R., Chakravarti A., Clark A.G., Donnelly P., et al. A global reference for human genetic variation. [(accessed on 5 May 2021)];Nature. 2015 526:68. doi: 10.1038/nature15393. Available online: https://www.nature.com/articles/nature15393#supplementary-information. PubMed DOI PMC

Sudmant P.H., Rausch T., Gardner E.J., Handsaker R.E., Abyzov A., Huddleston J., Zhang Y., Ye K., Jun G., Hsi-Yang Fritz M., et al. An integrated map of structural variation in 2,504 human genomes. [(accessed on 5 May 2021)];Nature. 2015 526:75. doi: 10.1038/nature15394. Available online: https://www.nature.com/articles/nature15394#supplementary-information. PubMed DOI PMC

Nothnagel M., Lu T.T., Kayser M., Krawczak M. Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum. Mol. Genet. 2010;19:2927–2935. doi: 10.1093/hmg/ddq198. PubMed DOI

Nelis M., Esko T., Magi R., Zimprich F., Zimprich A., Toncheva D., Karachanak S., Piskackova T., Balascak I., Peltonen L., et al. Genetic structure of Europeans: A view from the North-East. PLoS ONE. 2009;4:e5472. doi: 10.1371/journal.pone.0005472. PubMed DOI PMC

Pan B., Kusko R., Xiao W., Zheng Y., Liu Z., Xiao C., Sakkiah S., Guo W., Gong P., Zhang C., et al. Similarities and differences between variants called with human reference genome HG19 or HG38. BMC Bioinform. 2019;20:101. doi: 10.1186/s12859-019-2620-0. PubMed DOI PMC

Tam V., Patel N., Turcotte M., Bossé Y., Paré G., Meyre D. Benefits and limitations of genome-wide association studies. Nat. Rev. Genet. 2019;20:467–484. doi: 10.1038/s41576-019-0127-1. PubMed DOI

Ng S.B., Turner E.H., Robertson P.D., Flygare S.D., Bigham A.W., Lee C., Shaffer T., Wong M., Bhattacharjee A., Eichler E.E., et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009;461:272–276. doi: 10.1038/nature08250. PubMed DOI PMC

Carss K.J., Arno G., Erwood M., Stephens J., Sanchis-Juan A., Hull S., Megy K., Grozeva D., Dewhurst E., Malka S., et al. Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease. Am. J. Hum. Genet. 2017;100:75–90. doi: 10.1016/j.ajhg.2016.12.003. PubMed DOI PMC

Wang J., Skoog T., Einarsdottir E., Kaartokallio T., Laivuori H., Grauers A., Gerdhem P., Hytonen M., Lohi H., Kere J., et al. Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples. Sci. Rep. 2016;6:33256. doi: 10.1038/srep33256. PubMed DOI PMC

Chapman M.A., Lawrence M.S., Keats J.J., Cibulskis K., Sougnez C., Schinzel A.C., Harview C.L., Brunet J.P., Ahmann G.J., Adli M., et al. Initial genome sequencing and analysis of multiple myeloma. Nature. 2011;471:467–472. doi: 10.1038/nature09837. PubMed DOI PMC

Alioto T., Buchhalter I., Derdak S., Hutter B., Eldridge M.D., Hovig E., Heisler L.E., Beck T.A., Simpson J.T., Tonon L., et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat. Commun. 2015;6:10001. doi: 10.1038/ncomms10001. PubMed DOI PMC

Bach J.E., Oldenburg J., Muller C.R., Rost S. Mutational spectrum and deep intronic variants in the factor VIII gene of haemophilia A patients. Identification by next generation sequencing. Hamostaseologie. 2016;36:S25–S28. PubMed

Bucossi S., Polimanti R., Ventriglia M., Mariani S., Siotto M., Ursini F., Trotta L., Scrascia F., Callea A., Vernieri F., et al. Intronic rs2147363 variant in ATP7B transcription factor-binding site associated with Alzheimer’s disease. J. Alzheimer’s Dis. JAD. 2013;37:453–459. doi: 10.3233/JAD-130431. PubMed DOI

Gelfman S., Wang Q., McSweeney K.M., Ren Z., La Carpia F., Halvorsen M., Schoch K., Ratzon F., Heinzen E.L., Boland M.J., et al. Annotating pathogenic non-coding variants in genic regions. Nat. Commun. 2017;8:236. doi: 10.1038/s41467-017-00141-2. PubMed DOI PMC

Tremblay J., Hamet P. Role of genomics on the path to personalized medicine. Metab. Clin. Exp. 2013;62((Suppl. 1)):S2–S5. doi: 10.1016/j.metabol.2012.08.023. PubMed DOI

Riggs E.R., Andersen E.F., Cherry A.M., Kantarci S., Kearney H., Patel A., Raca G., Ritter D.I., South S.T., Thorland E.C., et al. Technical standards for the interpretation and reporting of constitutional copy-number variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) Genet. Med. Off. J. Am. Coll. Med. Genet. 2020;22:245–257. doi: 10.1038/s41436-019-0686-8. PubMed DOI PMC

Gudmundsson S., Singer-Berk M., Watts N.A., Phu W., Goodrich J.K., Solomonson M., Rehm H.L., MacArthur D.G., O’Donnell-Luria A. Variant interpretation using population databases: Lessons from gnomAD. Hum. Mutat. 2021 doi: 10.1002/humu.24309. Early View . PubMed DOI PMC

MacDonald J.R., Ziman R., Yuen R.K., Feuk L., Scherer S.W. The Database of Genomic Variants: A curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42:D986–D992. doi: 10.1093/nar/gkt958. PubMed DOI PMC

Rehm H.L., Berg J.S., Brooks L.D., Bustamante C.D., Evans J.P., Landrum M.J., Ledbetter D.H., Maglott D.R., Martin C.L., Nussbaum R.L., et al. ClinGen--the Clinical Genome Resource. N. Engl. J. Med. 2015;372:2235–2242. doi: 10.1056/NEJMsr1406261. PubMed DOI PMC

Stenson P.D., Mort M., Ball E.V., Chapman M., Evans K., Azevedo L., Hayden M., Heywood S., Millar D.S., Phillips A.D., et al. The Human Gene Mutation Database (HGMD(®)): Optimizing its use in a clinical diagnostic or research setting. Hum. Genet. 2020;139:1197–1207. doi: 10.1007/s00439-020-02199-3. PubMed DOI PMC

Fokkema I.F., den Dunnen J.T., Taschner P.E. LOVD: Easy creation of a locus-specific sequence variation database using an “LSDB-in-a-box” approach. Hum. Mutat. 2005;26:63–68. doi: 10.1002/humu.20201. PubMed DOI

Hehir-Kwa J.Y., Marschall T., Kloosterman W.P., Francioli L.C., Baaijens J.A., Dijkstra L.J., Abdellaoui A., Koval V., Thung D.T., Wardenaar R., et al. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nat. Commun. 2016;7:12989. doi: 10.1038/ncomms12989. PubMed DOI PMC

Levy-Sakin M., Pastor S., Mostovoy Y., Li L., Leung A.K.Y., McCaffrey J., Young E., Lam E.T., Hastie A.R., Wong K.H.Y., et al. Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat. Commun. 2019;10:1025. doi: 10.1038/s41467-019-08992-7. PubMed DOI PMC

Walter K., Min J.L., Huang J., Crooks L., Memari Y., McCarthy S., Perry J.R., Xu C., Futema M., Lawson D., et al. The UK10K project identifies rare variants in health and disease. Nature. 2015;526:82–90. doi: 10.1038/nature14962. PubMed DOI PMC

Marx V. The DNA of a nation. Nature. 2015;524:503. doi: 10.1038/524503a. PubMed DOI

Mark C., Jim D., Martin D., Leila E., Tom F., Sue H., Tim H., Luke J., Nick M., Jeanna M.-P., et al. The 100,000 Genomes Project Protocol. [(accessed on 24 October 2021)]. Available online: https://figshare.com/articles/journal_contribution/GenomicEnglandProtocol_pdf/4530893/4.

Turnbull C., Scott R.H., Thomas E., Jones L., Murugaesu N., Pretty F.B., Halai D., Baple E., Craig C., Hamblin A., et al. The 100 000 Genomes Project: Bringing whole genome sequencing to the NHS. BMJ. 2018;361:k1687. doi: 10.1136/bmj.k1687. PubMed DOI

Klintman J., Barmpouti K., Knight S.J.L., Robbe P., Dreau H., Clifford R., Ridout K., Burns A., Timbs A., Bruce D., et al. Clinical-grade validation of whole genome sequencing reveals robust detection of low-frequency variants and copy number alterations in CLL. Br. J. Haematol. 2018;182:412–417. doi: 10.1111/bjh.15406. PubMed DOI

Radziwon A., Arno G., Wheaton D., McDonagh E.M., Baple E.L., Webb-Jones K., Webster A.R., MacDonald I.M. Single-base substitutions in the CHM promoter as a cause of choroideremia. Hum. Mutat. 2017;38:704–715. doi: 10.1002/humu.23212. PubMed DOI

Gräf S., Haimel M., Bleda M., Hadinnapola C., Southgate L., Li W., Hodgson J., Liu B., Salmon R.M., Southwood M., et al. Identification of rare sequence variation underlying heritable pulmonary arterial hypertension. Nat. Commun. 2018;9:1416. doi: 10.1038/s41467-018-03672-4. PubMed DOI PMC

Lopez J., Coll J., Haimel M., Kandasamy S., Tarraga J., Furio-Tari P., Bari W., Bleda M., Rueda A., Gräf S., et al. HGVA: The Human Genome Variation Archive. Nucleic Acids Res. 2017;45:W189–W194. doi: 10.1093/nar/gkx445. PubMed DOI PMC

Jonsson H., Sulem P., Kehr B., Kristmundsdottir S., Zink F., Hjartarson E., Hardarson M.T., Hjorleifsson K.E., Eggertsson H.P., Gudjonsson S.A., et al. Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature. 2017;549:519–522. doi: 10.1038/nature24018. PubMed DOI

Gudbjartsson D.F., Helgason H., Gudjonsson S.A., Zink F., Oddson A., Gylfason A., Besenbacher S., Magnusson G., Halldorsson B.V., Hjartarson E., et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 2015;47:435–444. doi: 10.1038/ng.3247. PubMed DOI

Humphreys K., Grankvist A., Leu M., Hall P., Liu J., Ripatti S., Rehnstrom K., Groop L., Klareskog L., Ding B., et al. The genetic structure of the Swedish population. PLoS ONE. 2011;6:e22547. doi: 10.1371/journal.pone.0022547. PubMed DOI PMC

Ameur A., Dahlberg J., Olason P., Vezzi F., Karlsson R., Martin M., Viklund J., Kahari A.K., Lundin P., Che H., et al. SweGen: A whole-genome data resource of genetic variability in a cross-section of the Swedish population. Eur. J. Hum. Genet. EJHG. 2017;25:1253–1260. doi: 10.1038/ejhg.2017.130. PubMed DOI PMC

Borodulin K., Tolonen H., Jousilahti P., Jula A., Juolevi A., Koskinen S., Kuulasmaa K., Laatikainen T., Mannisto S., Peltonen M., et al. Cohort Profile: The National FINRISK Study. Int. J. Epidemiol. 2017;47:696–696i. doi: 10.1093/ije/dyx239. PubMed DOI

Lim E.T., Wurtz P., Havulinna A.S., Palta P., Tukiainen T., Rehnstrom K., Esko T., Magi R., Inouye M., Lappalainen T., et al. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet. 2014;10:e1004494. doi: 10.1371/journal.pgen.1004494. PubMed DOI PMC

FinnGen. [(accessed on 15 December 2021)]. Available online: https://www.finngen.fi/en/about.

Besenbacher S., Liu S., Izarzugaza J.M.G., Grove J., Belling K., Bork-Jensen J., Huang S., Als T.D., Li S., Yadav R., et al. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. [(accessed on 19 September 2021)];Nat. Commun. 2015 6:5969. doi: 10.1038/ncomms6969. Available online: https://www.nature.com/articles/ncomms6969#supplementary-information. PubMed DOI PMC

Maretty L., Jensen J.M., Petersen B., Sibbesen J.A., Liu S., Villesen P., Skov L., Belling K., Theil Have C., Izarzugaza J.M.G., et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. [(accessed on 19 September 2021)];Nature. 2017 548:87. doi: 10.1038/nature23264. Available online: https://www.nature.com/articles/nature23264#supplementary-information. PubMed DOI

NCGC Conditions for use of the 1000 Genomes. [(accessed on 27 November 2021)]. Available online: https://kreftgenomikk.no/en/vilkar-for-bruk-av-1000genomes-no/

Leitsalu L., Haller T., Esko T., Tammesoo M.L., Alavere H., Snieder H., Perola M., Ng P.C., Magi R., Milani L., et al. Cohort Profile: Estonian Biobank of the Estonian Genome Center, University of Tartu. Int. J. Epidemiol. 2015;44:1137–1147. doi: 10.1093/ije/dyt268. PubMed DOI

Rovite V., Wolff-Sagi Y., Zaharenko L., Nikitina-Zake L., Grens E., Klovins J. Genome Database of the Latvian Population (LGDB): Design, Goals, and Primary Results. J. Epidemiol. 2018;28:353–360. doi: 10.2188/jea.JE20170079. PubMed DOI PMC

Urnikyte A., Domarkiene I., Stoma S., Ambrozaityte L., Uktveryte I., Meskiene R., Kasiulevicius V., Burokiene N., Kucinskas V. CNV analysis in the Lithuanian population. BMC Genet. 2016;17:64. doi: 10.1186/s12863-016-0373-6. PubMed DOI PMC

Rancelis T., Arasimavicius J., Ambrozaityte L., Kavaliauskiene I., Domarkiene I., Karciauskaite D., Kucinskiene Z.A., Kucinskas V. Analysis of pathogenic variants from the ClinVar database in healthy people using next-generation sequencing. Genet. Res. 2017;99:e6. doi: 10.1017/S0016672317000040. PubMed DOI PMC

Dopazo J., Amadoz A., Bleda M., Garcia-Alonso L., Alemán A., García-García F., Rodriguez J.A., Daub J.T., Muntané G., Rueda A., et al. 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation. Mol. Biol. Evol. 2016;33:1205–1218. doi: 10.1093/molbev/msw005. PubMed DOI PMC

NAGEN: Proyecto Genoma 1000 Navarra (NAGEN 1000) [(accessed on 13 November 2021)]. Available online: https://www.nagen1000navarra.es/en.

Peña-Chilet M., Roldán G., Perez-Florido J., Ortuño F.M., Carmona R., Aquino V., Lopez-Lopez D., Loucera C., Fernandez-Rueda J.L., Gallego A., et al. CSVS, a crowdsourcing database of the Spanish population genetic variability. Nucleic Acids Res. 2021;49:D1130–D1137. doi: 10.1093/nar/gkaa794. PubMed DOI PMC

Lévy Y. Genomic medicine 2025: France in the race for precision medicine. Lancet. 2016;388:2872. doi: 10.1016/S0140-6736(16)32467-9. PubMed DOI

Boomsma D.I., Wijmenga C., Slagboom E.P., Swertz M.A., Karssen L.C., Abdellaoui A., Ye K., Guryev V., Vermaat M., van Dijk F., et al. The Genome of the Netherlands: Design, and project goals. Eur. J. Hum. Genet. EJHG. 2014;22:221–227. doi: 10.1038/ejhg.2013.118. PubMed DOI PMC

Francioli L.C., Menelaou A., Pulit S.L., van Dijk F., Palamara P.F., Elbers C.C., Neerincx P.B.T., Ye K., Guryev V., Kloosterman W.P., et al. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 2014;46:818–825. doi: 10.1038/ng.3021. PubMed DOI

Di Gaetano C., Fiorito G., Ortu M.F., Rosa F., Guarrera S., Pardini B., Cusi D., Frau F., Barlassina C., Troffa C., et al. Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection. PLoS ONE. 2014;9:e91237. doi: 10.1371/journal.pone.0091237. PubMed DOI PMC

Vai S., Ghirotto S., Pilli E., Tassi F., Lari M., Rizzi E., Matas-Lalueza L., Ramirez O., Lalueza-Fox C., Achilli A., et al. Genealogical relationships between early medieval and modern inhabitants of Piedmont. PLoS ONE. 2015;10:e0116801. doi: 10.1371/journal.pone.0116801. PubMed DOI PMC

Cocca M., Barbieri C., Concas M.P., Robino A., Brumat M., Gandin I., Trudu M., Sala C.F., Vuckovic D., Girotto G., et al. A bird’s-eye view of Italian genomic variation through whole-genome sequencing. Eur. J. Hum. Genet. 2020;28:435–444. doi: 10.1038/s41431-019-0551-x. PubMed DOI PMC

Lemm S. Germany’s Largest Research Programme for Genome Sequencing Launched. [(accessed on 25 September 2021)]. Available online: https://idw-online.de/de/news725422.

Analysis of Czech Genomes for Theranostics (ACGT) [(accessed on 19 November 2021)]. Available online: https://www.acgt.cz/en/

Genomic Map of Poland. [(accessed on 12 October 2021)]. Available online: http://ecbig.pl/page/genomic-map-of-poland/

Kaja E., Lejman A., Sielski D., Sypniewski M., Gambin T., Suchocki T., Dawidziuk M., Golik P., Wojtaszewska M., Stępień M., et al. ‘The Thousand Polish Genomes Project’—A national database of Polish variant allele frequencies. bioRxiv. 2021:451425. doi: 10.1101/2021.07.07.451425. PubMed DOI PMC

SGP Slovenski Genomski Projekt. [(accessed on 19 November 2021)]. Available online: http://genom.si/en/index.html.

Patrinos G.P., Pasparakis E., Koiliari E., Pereira A.C., Hünemeier T., Pereira L.V., Mitropoulou C. Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries. Am. J. Hum. Genet. 2020;107:589–595. doi: 10.1016/j.ajhg.2020.08.005. PubMed DOI PMC

Mitropoulos K., Merkouri Papadima E., Xiromerisiou G., Balasopoulou A., Charalampidou K., Galani V., Zafeiri K.V., Dardiotis E., Ralli S., Deretzi G., et al. Genomic variants in the FTO gene are associated with sporadic amyotrophic lateral sclerosis in Greek patients. Hum Genom. 2017;11:30. doi: 10.1186/s40246-017-0126-2. PubMed DOI PMC

Balasopoulou A., Stanković B., Panagiotara A., Nikčevic G., Peters B.A., John A., Mendrinou E., Stratopoulos A., Legaki A.I., Stathakopoulou V., et al. Novel genetic risk variants for pediatric celiac disease. Hum Genom. 2016;10:34. doi: 10.1186/s40246-016-0091-1. PubMed DOI PMC

CY-BIOBANK Center of Excellence—Biobanking and the Cyprus Human Genome Project. [(accessed on 1 September 2021)]. Available online: https://www.ucy.ac.cy/mmrc/en/cybiobank.

Borg J. Malta Human Genome Project. [(accessed on 24 October 2021)]. Available online: https://www.researchgate.net/publication/327954831_Malta_Human_Genome_Project?channel=doi&linkId=5baf348592851ca9ed2e8197&showFulltext=true.

Oleksyk T.K., Brukhin V., O’Brien S.J. The Genome Russia project: Closing the largest remaining omission on the world Genome map. Gigascience. 2015;4:53. doi: 10.1186/s13742-015-0095-0. PubMed DOI PMC

Zhernakova D.V., Kliver S., Cherkasov N., Tamazian G., Rotkevich M., Krasheninnikova K., Evsyukov I., Sidorov S., Dobrynin P., Yurchenko A.A., et al. Analytical “bake-off” of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis. PLoS ONE. 2018;13:e0200423. doi: 10.1371/journal.pone.0200423. PubMed DOI PMC

The Beyond 1 Million Genomes (B1MG) [(accessed on 2 October 2021)]. Available online: https://b1mg-project.eu/

Saunders G., Baudis M., Becker R., Beltran S., Béroud C., Birney E., Brooksbank C., Brunak S., Van den Bulcke M., Drysdale R., et al. Leveraging European infrastructures to access 1 million human genomes by 2022. Nat. Rev. Genet. 2019;20:693–701. doi: 10.1038/s41576-019-0156-9. PubMed DOI PMC

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