ОБЗОР

Неинвазивный пренатальный молекулярный скрининг: особенности внедрения в клиническую практику

Информация об авторах

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

2 ООО «Генотек», Москва, Россия

Для корреспонденции: Дмитрий Олегович Коростин
Наставнический переулок, д. 17, к. 1, г. Москва, 105120; moc.liamg@nitsorok.d

Информация о статье

Благодарности: авторы очень признательны сотруднице ФГБУ «НМИЦ АГП имени В. И. Кулакова» Екатерине Шубиной за ценные замечания и реко- мендации, которые она давала в ходе подготовки обзора.

Вклад авторов в работу: Д. О. Коростин — идея и план публикации, общее руководство подготовкой публикации; Д. А. Плахина — подготовка разделов о внДНК и о законодательстве, редактирование рукописи; В. А. Белова — подготовка разделов о НИПС с помощью MPS, подготовка раздела о законодательстве, редактирование рукописи.

Статья получена: 05.10.2018 Статья принята к печати: 10.05.2019 Опубликовано online: 23.05.2019
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  1. Hassold T, Hall H, Hunt P. The origin of human aneuploidy: where we have been, where we are going. Human molecular genetics. 2007; 16 (2): 203–8.
  2. Driscoll DA, Gross S. Prenatal screening for aneuploidy. New England Journal of Medicine. 2009; 360 (24): 2556–62.
  3. Nagaoka SI, Hassold TJ, Hunt PA. Human aneuploidy: mechanisms and new insights into an age-old problem. Nature Reviews Genetics. 2012; 13 (7): 493–504.
  4. Ehrich M, Deciu C, Zwiefelhofer T, Tynan JA, Cagasan L, Tim R, et al. Noninvasive detection of fetal trisomy 21 by sequencing of DNA in maternal blood: a study in a clinical setting. American journal of obstetrics and gynecology. 2011; 204 (3): 205–e1.
  5. Morris JK, Mutton DE, Alberman E. Revised estimates of the maternal age specific live birth prevalence of Down's syndrome. Journal of medical screening. 2002; 9 (1): 2–6.
  6. Buckley F, Buckley S. Wrongful deaths and rightful lives-screening for Down syndrome. Down Syndrome Research and Practice. 2008; 12 (2): 79–86.
  7. Wald NJ, Hackshaw AK. Combining ultrasound and biochemistry in first-trimester screening for Down's syndrome. Prenatal diagnosis. 1997; 17 (9): 821–9.
  8. Sillence KA, Madgett TE, Roberts LA, Overton TG, Avent ND. Non-invasive screening tools for Down’s syndrome: a review. Diagnostics. 2013; 3 (2): 291–314.
  9. Choy KW, Kwok YK, Cheng YKY, Wong KM, Wong HK, Leung KO, et al. Diagnostic accuracy of the BACs-on-Beads™ assay versus karyotyping for prenatal detection of chromosomal abnormalities: a retrospective consecutive case series. BJOG: An International Journal of Obstetrics & Gynaecology. 2014; 121 (10): 1245–52.
  10. Lo YD, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW, et al. Presence of fetal DNA in maternal plasma and serum. The lancet. 1997; 350 (9076): 485–7.
  11. Lo YD, Hjelm NM, Fidler C, Sargent IL, Murphy MF, Chamberlain PF, et al. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. New England Journal of Medicine. 1998; 339 (24): 1734–8.
  12. Farina A, Caramelli E, Concu M, Sekizawa A, Ruggeri R, Bovicelli L, et al. Testing normality of fetal DNA concentration in maternal plasma at 10–12 completed weeks' gestation: a preliminary approach to a new marker for genetic screening. Prenatal Diagnosis: Published in Affiliation With the International Society for Prenatal Diagnosis. 2002; 22 (2): 148–52.
  13. Bischoff FZ, Lewis DE, Simpson JL. Cell-free fetal DNA in maternal blood: kinetics, source and structure. Human reproduction update. 2005; 11 (1): 59–67.
  14. Wang E, Batey A, Struble C, Musci T, Song K, Oliphant A. Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma. Prenatal diagnosis. 2013; 33 (7): 662–6.
  15. Curnow KJ, Gross SJ, Hall MP, Stosic M, Demko Z, Zimmermann B, et al. Clinical experience and follow-up with large scale single-nucleotide polymorphism–based noninvasive prenatal aneuploidy testing. American journal of obstetrics and gynecology. 2014; 211 (5): 527–e1.
  16. Tjoa ML, Cindrova-Davies T, Spasic-Boskovic O, Bianchi DW, Burton GJ. Trophoblastic oxidative stress and the release of cell-free feto-placental DNA. The American journal of pathology. 2006; 169 (2): 400–4.
  17. Alberry M, Maddocks D, Jones M, Abdel Hadi M, Abdel-Fattah S, Avent N, Soothill PW. Free fetal DNA in maternal plasma in anembryonic pregnancies: confirmation that the origin is the trophoblast. Prenatal Diagnosis: Published in Affiliation With the International Society for Prenatal Diagnosis. 2007; 27 (5): 415–8.
  18. Gardner RM, Sutherland GR, Shaffer LG. Chromosome abnormalities and genetic counseling. Oxford University Press USA. 2011; (61).
  19. Lo YD, Chan KA, Sun H, Chen EZ, Jiang P, Lun FM, et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Science translational medicine. 2010; 2 (61): 61ra91–61ra91.
  20. Ivanov M, Baranova A, Butler T, Spellman P, Mileyko V. Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. BMC genomics. 2015; 16 (13): S1.
  21. Sancho M, Diani E, Beato M, Jordan A. Depletion of human histone H1 variants uncovers specific roles in gene expression and cell growth. PLoS genetics. 2008; 4 (10): e1000227.
  22. Jiang P, Lo YMD. The long and short of circulating cell-free DNA and the ins and outs of molecular diagnostics. Trends in Genetics. 2016; 32 (6): 360–71.
  23. Geiman TM, Muegge K. DNA methylation in early development. Molecular Reproduction and Development: Incorporating Gamete Research. 2010; 77 (2): 105–13.
  24. Sun K, et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proceedings of the National Academy of Sciences. 2015; 112 (40): E5503–E5512.
  25. Sun K, Jiang P, Wong AI, Cheng YK, Cheng SH, Zhang H, et al. Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing. Proceedings of the National Academy of Sciences. 2018; 115 (22): E5106–E5114.
  26. Tamminga S, van Maarle M, Henneman L, Oudejans CB, Cornel MC, Sistermans EA. Maternal plasma DNA and RNA sequencing for prenatal testing. Advances in clinical chemistry. 2016; (74): 63–102.
  27. Ashoor G, Poon L, Syngelaki A, Mosimann B, Nicolaides KH. Fetal fraction in maternal plasma cell-free DNA at 11–13 weeks’ gestation: effect of maternal and fetal factors. Fetal diagnosis and therapy. 2012; 31 (4): 237–43.
  28. Canick JA, et al. The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies. Prenatal diagnosis. 2013; 33 (7): 667–74.
  29. Wright D, Syngelaki A, Bradbury I, Akolekar R, Nicolaides KH. First-trimester screening for trisomies 21, 18 and 13 by ultrasound and biochemical testing. Fetal diagnosis and therapy. 2014; 35 (2): 118–26.
  30. Kim SK, Hannum G, Geis J, Tynan J, Hogg G, Zhao C, et al. Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts. Prenatal diagnosis. 2015; 35 (8): 810–15.
  31. Jiang P, Peng X, Su X, Sun K, Stephanie CY, Chu WI, et al. FetalQuant SD: accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA. NPJ genomic medicine. 2016; (1): 16013.
  32. Peng XL, Jiang P. Bioinformatics approaches for fetal DNA fraction estimation in noninvasive prenatal testing. International journal of molecular sciences. 2017; 18 (2): 453.
  33. Zimmermann B, Hill M, Gemelos G, Demko Z, Banjevic M, Baner J, et al. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci. Prenatal diagnosis. 2012; 32 (13): 1233–41.
  34. Lun FM, Chiu RW, Sun K, Leung TY, Jiang P, Chan KA, et al. Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clinical chemistry. DOI: 10.1373/clinchem.2013.212274.
  35. Yu SC, et al. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing. Proceedings of the National Academy of Sciences. 2014; 111 (23): 8583–8.
  36. Cirigliano V, Ordoñez E, Rueda L, Syngelaki A, Nicolaides KH. Performance of the neoBona test: a new paired-end massively parallel shotgun sequencing approach for cell-free DNA-based aneuploidy screening. Ultrasound in Obstetrics & Gynecology. 2017; 49 (4): 460–4.
  37. Straver R, Oudejans C, Sistermans EA, Reinders MJ. Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles. Prenatal diagnosis. 2016; 36 (7): 614–21.
  38. Kim SK, Hannum G, Geis J, Tynan J, Hogg G, Zhao C, Boom D. Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts. Prenatal diagnosis. 2015; 35 (8): 810–5.
  39. Chen S, Lau TK, Zhang C, Xu C, Xu Z, Hu P, et al. A method for noninvasive detection of fetal large deletions/duplications by low coverage massively parallel sequencing. Prenatal diagnosis. 2013; 33 (6): 584–90.
  40. Van den Veyver IB. Recent advances in prenatal genetic screening and testing. F1000 Research. 2016; 5 (F1000 Faculty Rev): 2591.
  41. Peters D, Chu T, Yatsenko SA, Hendrix N, Hogge WA, Surti U, et al. Noninvasive prenatal diagnosis of a fetal microdeletion syndrome. New England Journal of Medicine. 2011; 365 (19): 1847–8.
  42. Jensen TJ, Dzakula Z, Deciu C, van den Boom D, Ehrich M. Detection of microdeletion 22q11. 2 in a fetus by next-generation sequencing of maternal plasma. Clinical chemistry. 2012; 58 (7): 1148–51.
  43. Srinivasan A, Bianchi DW, Huang H, Sehnert AJ, Rava RP. Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma. The American Journal of Human Genetics. 2013; 92 (2): 167–76.
  44. Lefkowitz RB, Tynan JA, Liu T, Wu Y, Mazloom AR, Almasri E, et al. Clinical validation of a noninvasive prenatal test for genomewide detection of fetal copy number variants. American journal of obstetrics and gynecology. 2016; 215 (2): 227–e1.
  45. Straver R, Sistermans EA, Holstege H, Visser A, Oudejans CB, Reinders MJ. WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme. Nucleic acids research. 2013; 42 (5): e31–e31.
  46. Zhao C, Tynan J, Ehrich M, Hannum G, McCullough R, Saldivar JS, Deciu C. Detection of fetal subchromosomal abnormalities by sequencing circulating cell-free DNA from maternal plasma. Clinical chemistry. 2015.
  47. Nicolaides KH, Syngelaki A, Gil M, Atanasova V, Markova D. Validation of targeted sequencing of single-nucleotide polymorphisms for non-invasive prenatal detection of aneuploidy of chromosomes 13, 18, 21, X, and Y. Prenatal diagnosis. 2013; 33 (6): 575–9.
  48. Wapner RJ, Babiarz JE, Levy B, Stosic M, Zimmermann B, Sigurjonsson S, Hu J. Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes. American journal of obstetrics and gynecology. 2015; 212 (3): 332–e1.
  49. Costa JM, Benachi A, Gautier E. New strategy for prenatal diagnosis of X-linked disorders. New England Journal of Medicine. 2002; 346 (19): 1502.
  50. Lo YD, Hjelm NM, Fidler C, Sargent IL, Murphy MF, Chamberlain PF, et al. Prenatal diagnosis of fetal RhD status by molecular analysis of maternal plasma. New England Journal of Medicine. 1998; 339 (24): 1734–8.
  51. Tang NL, Leung TN, Zhang J, Lau TK, Lo YD. Detection of fetal-derived paternally inherited X-chromosome polymorphisms in maternal plasma. Clinical chemistry. 1999; 45 (11): 2033–5.
  52. Bustamante-Aragonés A, de Alba MR, Perlado S, Trujillo-Tiebas MJ, Arranz JP, Díaz-Recasens J, et al. Non-invasive prenatal diagnosis of single-gene disorders from maternal blood. Gene. 2012; 504 (1): 144–9.
  53. Amicucci P, Gennarelli M, Novelli G, Dallapiccola B. Prenatal diagnosis of myotonic dystrophy using fetal DNA obtained from maternal plasma. Clinical chemistry. 2000; 46 (2): 301–2.
  54. Vermeulen C, Geeven G, de Wit E, Verstegen MJ, Jansen RP, van Kranenburg M, et al. Sensitive monogenic noninvasive prenatal diagnosis by targeted haplotyping. The American Journal of Human Genetics. 2017; 101 (3): 326–39.
  55. Tong YK, Jin S, Chiu RW, Ding C, Chan KA, Leung TY, et al. Noninvasive prenatal detection of trisomy 21 by an epigenetic– genetic chromosome-dosage approach. Clinical chemistry. 2010; 56 (1): 90–8.
  56. Tsui DW, Lam YD, Lee WS, Leung TY, Lau TK, Lau ET, et al. Systematic identification of placental epigenetic signatures for the noninvasive prenatal detection of Edwards syndrome. PloS one. 2010; 5 (11): e15069.
  57. Yuen RK, Penaherrera MS, Von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. European Journal of Human Genetics. 2010; 18 (9): 1006.
  58. Blair JD, Yuen RK, Lim BK, McFadden DE, von Dadelszen P, Robinson WP. Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia. Molecular human reproduction. 2013; 19 (10): 697–708.
  59. Chu T, Bunce K, Shaw P, Shridhar V, Althouse A, Hubel C, et al. Comprehensive analysis of preeclampsia-associated DNA methylation in the placenta. PLoS One. 2014; 9 (9): e107318.
  60. Hahn S, Rusterholz C, Hösli I, Lapaire O. Cell-free nucleic acids as potential markers for preeclampsia. Placenta. 2011; (32): S17–S20.
  61. Bianchi DW, Parker RL, Wentworth J, Madankumar R, Saffer C, Das AF, et al. DNA sequencing versus standard prenatal aneuploidy screening. New England journal of medicine. 2014; 370 (9): 799–808.
  62. Norton ME, Jacobsson B, Swamy GK, Laurent LC, Ranzini AC, Brar H, et al. Cell-free DNA analysis for noninvasive examination of trisomy. New England Journal of Medicine. 2015; 372 (17): 1589–97.
  63. Wataganara T, Peter I, Messerlian GM, Borgatta L, Bianchi DW. Inverse correlation between maternal weight and second trimester circulating cell-free fetal DNA levels. Obstetrics & Gynecology. 2004; 104 (3): 545–50.
  64. Румянцев А. Г., Курцер М. А., Мареева Ю. М., Мисюрин А. В., Румянцев С. А., Устюгов А. Ю. Клиническое значение фетального микрохимеризма у матери. Гены и клетки. 2012; 7 (2): 103–111.
  65. Wang Y, et al. Maternal mosaicism is a significant contributor to discordant sex chromosomal aneuploidies associated with noninvasive prenatal testing. Clinical chemistry. 2014; 60 (1): 251–9.
  66. Bianchi DW. Cherchez la femme: maternal incidental findings can explain discordant prenatal cell-free DNA sequencing results. Genetics in Medicine. 2017; DOI: 10.1038/gim.2017.219.
  67. Hartwig TS, Ambye L, Sørensen S, Jørgensen FS. Discordant non-invasive prenatal testing (NIPT)–a systematic review. Prenatal diagnosis. 2017; 37 (6): 527–39.
  68. Attilakos G, Maddocks DG, Davies T, Hunt LP, Avent ND, Soothill PW, et al. Quantification of free fetal DNA in multiple pregnancies and relationship with chorionicity. Prenatal diagnosis. 2011; 31 (10): 967–72.
  69. Bevilacqua E, Gil MM, Nicolaides KH, Ordoñez E, Cirigliano V, Dierickx H, et al. Performance of screening for aneuploidies by cell-free DNA analysis of maternal blood in twin pregnancies. Ultrasound in Obstetrics & Gynecology. 2015; 45 (1): 61–6.
  70. Curnow KJ, Wilkins-Haug L, Ryan A, Kırkızlar E, Stosic M, Hall MP, et al. Detection of triploid, molar, and vanishing twin pregnancies by a single-nucleotide polymorphism–based noninvasive prenatal test. American journal of obstetrics and gynecology. 2015; 212 (1): 79–e1.
  71. Gil MM, Quezada MS, Revello R, Akolekar R, Nicolaides KH. Analysis of cell-free DNA in maternal blood in screening for fetal aneuploidies: updated meta-analysis. Ultrasound in obstetrics & gynecology. 2015; 45 (3): 249–66.
  72. Zhang H, Gao Y, Jiang F, Fu M, Yuan Y, Guo Y, et al. Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146 958 pregnancies. Ultrasound in Obstetrics & Gynecology. 2015; 45 (5): 530–8.
  73. Russell LM, Strike P, Browne CE, Jacobs PA. X chromosome loss and ageing. Cytogenetic and genome research. 2007; 116 (3): 181–5.
  74. Samango-Sprouse C, Kırkızlar E, Hall MP, Lawson P, Demko Z, Zneimer SM, et al. Incidence of X and Y chromosomal aneuploidy in a large child bearing population. PloS One. 2016; 11 (8): e0161045.
  75. Shubina J, Trofimov DY, Barkov IY, Stupko OK, Goltsov AY, Mukosey IS, et al. In silico size selection is effective in reducing false positive NIPS cases of monosomy X that are due to maternal mosaic monosomy X. Prenatal diagnosis. 2017; 37 (13): 1305–10.
  76. Bianchi DW, Chudova D, Sehnert AJ, Bhatt S, Murray K, Prosen TL, et al. Noninvasive prenatal testing and incidental detection of occult maternal malignancies. Jama. 2015; 314 (2): 162–9.
  77. Ferguson-Smith MA. Placental mRNA in maternal plasma: prospects for fetal screening. Proceedings of the National Academy of Sciences. 2003; 100 (8): 4360–2.
  78. Chiu RW, Cantor CR, Lo YD. Non-invasive prenatal diagnosis by single molecule counting technologies. Trends in genetics. 2009; 25 (7): 324–31.
  79. ACOG Practice Bulletin № 77: screening for fetal chromosomal abnormalities. Obstet Gynecol. 2007; (109): 217–27.
  80. Benn P, Borrell A, Chiu RW, Cuckle H, Dugoff L, Faas B, et al. Position statement from the Chromosome Abnormality Screening Committee on behalf of the Board of the International Society for Prenatal Diagnosis. Prenatal diagnosis. 2015; 35 (8): 725–34.
  81. Кащеева Т. К., Кузнецова Т. В., Баранов В. С. Новые технологии и тенденции развития пренатальной диагностики. Журнал акушерства и женских болезней. 2017; 66 (2): 33–39.
  82. UK National Screening Committee. www.gov.uk URL. Available from: https://www.gov.uk/government/groups/uk-national-screening-committee-uk-nsc (дата обращения: 20.07.2018).
  83. Screening in the UK: making effective recommendations 2015 to 2016. Public Health England hosts the UK National Screening Committee URL. Available from: https://assets. publishing.service.gov.uk/government/uploads/system/uploads/ attachment_data/file/538524/Screening_in_the_UK___making_ effective_recommendations_2015_to_2016_180716_final.pdf (дата обращения: 20.07.2018).
  84. Analysis of foetal DNA in the woman's blood: non-invasive prenatal testing (NIPT) for trisomy 13, 18 and 21. SFOG Guidelines URL: http://www.nfog.org/files/guidelines/NIPT%202016%2006%20 05%20.pdf (дата обращения: 20.07.2018).
  85. Trisomie 21 : la HAS actualise ses recommandations concernant le dépistage prénatal de la trisomie 21. www.has-sante.fr URL. Available from: https://www.has-sante.fr/portail/jcms/c_2768535/fr/ trisomie-21-la-has-actualise-ses-recommandations-concernant-le-depistage-prenatal-de-la-trisomie-21 (дата обращения: 20.07.2018).
  86. Allyse M, Wick MJ. What do the new American College of Medical Genetics and Genomics (ACMG) guidelines mean for the provision of non-invasive prenatal genetic screening? Journal of Obstetrics and Gynaecology. 2017; 37 (6): 795–8.
  87. American College of Obstetricians and Gynecologists: Screening for fetal aneuploidy. Obstet Gynecol. 2016; 127 (5): e123–137.
  88. Prenatal cell-free DNA screening. National Society of Genetic Counselors. Available from: http://www.nsgc.org/p/bl/et/ blogaid=805#.WCTELTNR ftw.linkedin.
  89. Gregg AR, Skotko BG, Benkendorf JL, Monaghan KG, Bajaj K, Best RG, et al. Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics. Genetics in medicine. 2016; 18 (10): 1056–65.
  90. Информационно-методическое письмо Минздрава РФ от 19.03.2015 № 15-4/607. Доступно по ссылке: http://www. consultant.ru/document/cons_doc_LAW_177689/.
  91. Сухих Г. Т., Трофимов Д. Ю, Барков И. Ю., Донников А. Е., Шубина Е. С., Коростин Д. О. и др. Неинвазивный пренатальный ДНК-скрининг анеуплоидий плода по крови матери методом высокопроизводительного секвенирования. Клинические рекомендации. Акушерство и гинекология. 2016; (6): 3–22.