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The correctness of large scale analysis of genomic data Cover

The correctness of large scale analysis of genomic data

Open Access
|Dec 2021

References

  1. [1] Bai H., Guo X., Zhang D., et al. The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. Genome Biology and Evolution, 6(12):3122–3136, 2014.10.1093/gbe/evu242454008325377941
  2. [2] Brittain H., Scott R., and Thomas E. The rise of the genome and personalised medicine. Clinical Medicine, 17(6):545–551, 2017.10.7861/clinmedicine.17-6-545629769529196356
  3. [3] Caulfield M., Davies J., Dennys M., et al. National genomic research library, 2020.
  4. [4] Chan T., Golub G., and Leveque R. Algorithms for computing the sample variance: Analysis and recommendations. The American Statistician, 37(3):242–247, 1983.
  5. [5] Chen S., Zhou Y., Chen Y., et al. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17):i884–i890, 2018.
  6. [6] Cho Y., Kim H., Kim H., et al. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nature Communications, 7:13637, 2016.10.1038/ncomms13637512304627882922
  7. [7] Cibulskis K., McKenna A., Fennell T., et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics, 27(18):2601–2602, 2011.
  8. [8] Consortium T.. G. P. A global reference for human genetic variation. Nature, 526(7571):68–74, 2015.
  9. [9] Danecek P., Bonfield J., Liddle J., et al. Twelve years of SAMtools and BCFtools. GigaScience, 10(2), 2021.10.1093/gigascience/giab008793181933590861
  10. [10] Durbin R., Altshuler D., Abecasis G., et al. A map of human genome variation from population-scale sequencing. Nature, 467(7319):1061–1073, 2010.10.1038/nature09534304260120981092
  11. [11] Fiévet A., Bernard V., Tenreiro H., et al. ART-DeCo: easy tool for detection and characterization of cross-contamination of DNA samples in diagnostic next-generation sequencing analysis. European Journal of Human Genetics, 27(5), 2019.10.1038/s41431-018-0317-x646187230683922
  12. [12] Fiorito G., Di Gaetano C., Guarrera S., et al. The Italian genome reflects the history of Europe and the Mediterranean basin. European Journal of Human Genetics, 24(7):1056–1062, 2016.10.1038/ejhg.2015.233507088726554880
  13. [13] Guo J., Wu Y., Zhu Z., et al. Global genetic differentiation of complex traits shaped by natural selection in humans. Nature Communications, 9(1):1865, 2018.10.1038/s41467-018-04191-y595181129760457
  14. [14] Hehir-Kwa J., Marschall T., Kloosterman W., et al. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants. Nature Communications, 7:12989, 2016.10.1038/ncomms12989505969527708267
  15. [15] Kehr B., Helgadottir A., and Melsted P. Diversity in non-repetitive human sequences not found in the reference genome. Nature Genetics, 49(4):588–593, 2017.10.1038/ng.380128250455
  16. [16] Li Q., Tian S., Yan B., et al. Building a Chinese pan-genome of 486 individuals. Communications Biology, 4(1):1016, 2021.10.1038/s42003-021-02556-6840563534462542
  17. [17] McDermott U. Next-generation sequencing and empowering personalised cancer medicine. Drug Discovery Today, 20(12):1470–1475, 2015.10.1016/j.drudis.2015.10.00826494142
  18. [18] Nagasaki M., Yasuda J., Katsuoka F., et al. Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nature Communications, 6(1):8018, 2015.10.1038/ncomms9018456075126292667
  19. [19] Takayama J., Tadaka S., Yano K., et al. Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference. Nature Communications, 12(1):226, 2021.10.1038/s41467-020-20146-8780165833431880
  20. [20] Tishkoff S. and Kidd K. Implications of biogeography of human populations for ’race’ and medicine. Nature Genetics, 36(11):S21–S27, 2004.10.1038/ng143815507999
  21. [21] Van der Auwera G. and O’Connor B. Genomics in the cloud : using Docker, GATK, and WDL in Terra. O’Reilly Media, Sebastopol, CA, first edition. edition, 2020.
  22. [22] Welford B. Note on a method for calculating corrected sums of squares and products. Technometrics, 4(3):419–420, 1962.10.1080/00401706.1962.10490022
  23. [23] Zhao S., Agafonov O., Azab A., et al. Accuracy and efficiency of germline variant calling pipelines for human genome data. Scientific Reports, 10(1):20222, 2020.10.1038/s41598-020-77218-4767882333214604
  24. [24] Zimani A., Peterlin B., and Kovanda A. Increasing genomic literacy through national genomic projects. Frontiers in Genetics, 12:693253, 2021.10.3389/fgene.2021.693253838771334456970
DOI: https://doi.org/10.2478/fcds-2021-0024 | Journal eISSN: 2300-3405 | Journal ISSN: 0867-6356
Language: English
Page range: 423 - 436
Submitted on: Oct 2, 2021
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Accepted on: Nov 27, 2021
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Published on: Dec 17, 2021
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year

© 2021 Pawel Wojciechowski, Karol Krause, Piotr Lukasiak, Jacek Blazewicz, published by Poznan University of Technology
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.