2015 / 04

Следующая статья

ОБЗОР

Количественный и безошибочный анализ данных массированного секвенирования с использованием молекулярного баркодирования

Е. С. Егоров1,2, М. А. Израельсон2, С. А. Касацкая2, Д. М. Чудаков1,2, С. А. Лукьянов1,2
Информация об авторах

1 Российский национальный исследовательский медицинский университет имени Н. И. Пирогова, Москва, Россия

2 Группа структурной организации Т-клеточного иммунитета, отдел геномики адаптивного иммунитета, Федеральное государственное бюджетное учреждение науки Институт биоорганической химии им. академиков М.М. Шемякина и Ю.А. Овчинникова Российской академии наук, Москва

Для корреспонденции: Дмитрий Михайлович Чудаков
117997, Москва, ул. Островитянова, д. 1; ur.liam@mdvokaduhc

Информация о статье

Финансирование: работа поддержана Российским научным фондом, грант №14-35-00105.

Статья получена: 28.09.2015 Статья принята к печати: 22.10.2015 Опубликовано online: 05.01.2017
|
  1. Diehl F, Schmidt K, Durkee KH, Moore KJ, Goodman SN, Shuber AP, et al. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology. 2008; 135: 489–98.
  2. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci USA. 2008; 105: 16266–71.
  3. Burrell RA, Swanton C. The evolution of the unstable cancer genome. Curr Opin Genet Dev 2014; 24: 6–7.
  4. Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, et al. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One. 2015; 10: e0126626.
  5. Van Laethem K, Theys K, Vandamme AM. HIV-1 genotypic drug resistance testing: digging deep, reaching wide? Curr Opin Virol. 2015; 14: 16–23.
  6. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science. 2013; 341: 1237439.
  7. Barrick JE, Lenski RE. Genome dynamics during experimental evolution. Nat Rev Genet. 2013; 14: 827–39.
  8. Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc Natl Acad Sci USA. 2013; 110: 13463–8.
  9. Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J Immunol. 2014; 192: 2689–98.
  10. Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, Mamedov IZ, Tuganbaev TR, et al. Towards error-free profiling of immune repertoires. Nat Methods. 2014; 11: 653–5.
  11. He L, Sok D, Azadnia P, Hsueh J, Landais E, Simek M, et al. Toward a more accurate view of human B-cell repertoire by next-generation sequencing, unbiased repertoire capture and single-molecule barcoding. Sci Rep. 2014; 4: 6778.
  12. Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, et al. Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers. J Immunol. 2015; 194: 6155–63.
  13. Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol. 2015; 26: 1715–22.
  14. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA. 2005; 102: 16368–73.
  15. Fleischhacker M, Schmidt B. Circulating nucleic acids (CNAs) and cancer--a survey. Biochim Biophys Acta. 2007; 1775: 181–232.
  16. Chen Z, Feng J, Buzin CH, Liu Q, Weiss L, Kernstine K, et al. Analysis of cancer mutation signatures in blood by a novel ultra-sensitive assay: monitoring of therapy or recurrence in non-metastatic breast cancer. PLoS One. 2009; 4: e7220.
  17. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014; 6 (224): 224ra224.
  18. Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014; 20: 548–54.
  19. Nguyen P, Ma J, Pei D, Obert C, Cheng C, Geiger TL. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire. BMC Genomics. 2011; 12: 106.
  20. Bolotin DA, Mamedov IZ, Britanova OV, Zvyagin IV, Shagin D, Ustyugova SV, et al. Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur J Immunol. 2012; 42: 3073–83.
  21. Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, et al. PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data. PLoS One. 2013; 8: e70388.
  22. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012; 22: 568–76.
  23. 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; 31: 213–19.
  24. Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulus SK, et al. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol. 2011; 12: R124.
  25. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci USA. 2011; 108: 9530–35.
  26. Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2012; 9: 72–4.
  27. Ross MG, Russ C, Costello M, Hollinger A, Lennon NJ, Hegarty R, et al. Characterizing and measuring bias in sequence data. Genome Biol. 2013; 14: R51.
  28. Casbon JA, Osborne RJ, Brenner S, Lichtenstein CP. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res. 2011; 39: e81.
  29. Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, et al. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res. 2014; 42: e129.
  30. Faham M, Zheng J, Moorhead M, Carlton VE, Stow P, Coustan-Smith E, et al. Deep-sequencing approach for minimal residual disease detection in acute lymphoblastic leukemia. Blood. 2012; 120: 5173–80.
  31. Wu D, Sherwood A, Fromm JR, Winter SS, Dunsmore KP, Loh ML, et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci Transl Med. 2012; 4: 134ra163.
  32. Martinez-Lopez J, Lahuerta JJ, Pepin F, Gonzalez M, Barrio S, Ayala R, et al. Prognostic value of deep sequencing method for minimal residual disease detection in multiple myeloma. Blood. 2014; 123: 3073–79.
  33. Ladetto M, Bruggemann M, Monitillo L, Ferrero S, Pepin F, Drandi D, et al. Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders. Leukemia. 2014; 28: 1299–1307.
  34. Logan AC, Vashi N, Faham M, Carlton V, Kong K, Buno I, et al. Immunoglobulin and T Cell Receptor Gene High-Throughput Sequencing Quantifies Minimal Residual Disease in Acute Lymphoblastic Leukemia and Predicts Post-Transplantation Relapse and Survival. Biol Blood Marrow Transplant. 2014; 20 (9): 1307–13.
  35. Mamedov IZ, Britanova OV, Bolotin DA, Chkalina AV, Staroverov DB, Zvyagin IV, et al. Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBO Mol Med. 2011; 3 (4): 201–7.
  36. Britanova OV, Bochkova AG, Staroverov DB, Fedorenko DA, Bolotin DA, Mamedov IZ, et al. First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy. Bone Marrow Transplant. 2012; 47: 1479–81.
  37. Muraro PA, Robins H, Malhotra S, Howell M, Phippard D, Desmarais C, et al. T cell repertoire following autologous stem cell transplantation for multiple sclerosis. J Clin Invest. 2014; 124: 1168–72.
  38. Emerson RO, Sherwood AM, Rieder MJ, Guenthoer J, Williamson DW, Carlson CS, et al. High-throughput sequencing of T-cell receptors reveals a homogeneous repertoire of tumour-infiltrating lymphocytes in ovarian cancer. J Pathol. 2013; 231: 433–40.
  39. Cha E, Klinger M, Hou Y, Cummings C, Ribas A, Faham M, et al. Improved Survival with T Cell Clonotype Stability After Anti-CTLA-4 Treatment in Cancer Patients. Sci Transl Med. 2014; 6: 238ra270.
  40. Dudley ME, Wunderlich JR, Robbins PF, Yang JC, Hwu P, Schwartzentruber DJ, et al. Cancer regression and autoimmunity in patients after clonal repopulation with antitumor lymphocytes. Science. 2002; 298: 850–4.
  41. Linnemann C, Mezzadra R, Schumacher TN. TCR repertoires of intratumoral T-cell subsets. Immunol Rev. 2014; 257: 72-82.
  42. Gros A, Robbins PF, Yao X, Li YF, Turcotte S, Tran E, et al. PD-1 identifies the patient-specific CD8(+) tumor-reactive repertoire infiltrating human tumors. J Clin Invest. 2014; 124: 2246–59.
  43. Grun D, Kester L, van Oudenaarden A. Validation of noise models for single-cell transcriptomics. Nat Methods. 2014; 11: 637–40.
  44. Gout JF, Thomas WK, Smith Z, Okamoto K, Lynch M. Large-scale detection of in vivo transcription errors. Proc Natl Acad Sci USA. 2013; 110: 18584–9.