ORIGINAL RESEARCH

Breast cancer: analysis of driver somatic mutations detected by next-generation sequencing

About authors

1 Genotek Inc., Moscow

2 Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Russia

3 Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia

4 Blokhin National Medical Research Center of Oncology, Moscow, Russia

5 Institute of Biomedical Chemistry (IBMC), Moscow, Russia

Correspondence should be addressed: Valery Ilyinsky
Nastavnichesky per., d. 17, str. 1, pod. 14, 15, Moscow, 105120; ur.ketoneg@ofni

About paper

Funding: this work was supported by the Ministry of Education and Science of the Russian Federation (Project ID RFMEFI60716X0152).

All authors' contribution to this work is equal: selection and analysis of literature, research planning, data collection, analysis, and interpretation, drafting of a manuscript, editing.

Received: 2017-12-12 Accepted: 2017-12-22 Published online: 2018-01-24
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  1. DeSantis CE, Ma J, Goding Sauer A, Newman LA, Jemal A. Breast Cancer Statistics, 2017, Racial Disparity in Mortality by State. CA Cancer J Clin. 2017 Nov; 67 (6): 439–48. DOI: 10.3322/caac.21412.
  2. Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med. 2017 Nov; 141 (11): 1544–57. DOI: 10.5858/arpa.2016-0501-RA.
  3. Melchor L, Benítez J. The complex genetic landscape of familial breast cancer. Hum Geneti. 2013 Aug; 132 (8): 845–63. DOI: 10.1007/s00439-013-1299-y.
  4. Giuliano AE, Connolly JL, Edge SB, Mittendorf EA, Rugo HS, Solin LJ et al. Breast Cancer-Major changes in the American Joint Committee on Cancer eighth edition cancer staging manual. CA Cancer J Clin. 2017 Jul 8; 67 (4): 290–303. DOI: 10.3322/caac.21393.
  5. Tsukanov KYu, Krasnenko AYu, Plakhina DA, Korostin DO, Churov AV, Druzhilovskaya OS et al. A bioinformatic pipeline for NGS data analysis and mutation calling in human solid tumors. Biomed Khim. 2017; 63 (5): 413–7.
  6. Martin M. Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads. EMBnet.journal. 2011; 17: 10–2.
  7. Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009 Jul 15; 25 (14): 1754–60. DOI: 10.1093/bioinformatics/btp324.
  8. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15; 25 (16): 2078–9. DOI: 10.1093/bioinformatics/btp352.
  9. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013 Mar; 31 (3) :213–9. DOI: 10.1038/nbt.2514.
  10. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012 Apr-Jun; 6 (2): 80–92. DOI: 10.4161/fly.19695.
  11. Forbes SA, Beare D, Bindal N, Bamford S, Ward S, Cole CG et al. COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer. Curr Protoc Hum Genet. 2016 Oct 11; 91: 10.11.1-10.11.37. DOI: 10.1002/cphg.21.
  12. Liu X, Wu C, Li C, Boerwinkle E. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. Hum Mutat. 2016 Mar; 37 (3): 235–41. DOI: 10.1002/humu.22932.
  13. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1; 31 (13): 3812–4.
  14. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013 Jan; Chapter 7: Unit7.20. DOI: 10.1002/0471142905.hg0720s76.
  15. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO et al. A global reference for human genetic variation. Nature. 2015 Oct 1; 526 (7571): 68–74. DOI: 10.1038/nature15393.
  16. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18; 536 (7616): 285–91. DOI: 10.1038/nature19057.
  17. Grishina KA, Muzaffarova TA, Khaylenko VA, Karpukhin AV. [Molecular genetic markers of breast cancer].  Tumors of female reproductive system. 2016; 12 (3): 36–42. DOI: 10.17650/1994-4098-2016-12-3-26-42. Russian.