Рекомендации Российского общества медицинских генетиков по хромосомному микроматричному анализу
https://doi.org/10.25557/2073-7998.2023.10.3-47
Аннотация
Хромосомный микроматричный анализ представляет наиболее динамично развиваемую область современной клинической цитогенетики, обеспечивая эффективную и высокоразрешающую диагностику несбалансированных микроструктурных хромосомных перестроек. Настоящие рекомендации определяют показания к назначению хромосомного микроматричного анализа для постнатальной и пренатальной диагностики конститутивных хромосомных аномалий, а также рассматривают вопросы интерпретации клинической значимости выявляемых хромосомных вариантов, и медико-генетического консультирования семей пациентов с хромосомными болезнями. Делаются акценты на приоритетности экспертного мнения и необходимости диалога молекулярного цитогенетика и врача-генетика в оценке патогенетической значимости хромосомных вариантов и тактики дальнейшего лабораторного обследования пациента.
Об авторах
И. Н. ЛебедевРоссия
634050, г. Томск, ул. Набережная реки Ушайки, д. 10
Н. В. Шилова
Россия
115522, г. Москва, ул. Москворечье, д. 1
И. Ю. Юров
Россия
115522, г. Москва, Россия, Каширское шоссе, д. 34
125412, г. Москва, ул. Талдомская, д. 2
О. В. Малышева
Россия
199034, г. Санкт-Петербург, Менделеевская линия, д.3
А. А. Твеленева
Россия
119333, г. Москва, ул. Губкина, д. 3, корп.1
М. Е. Миньженкова
Россия
115522, г. Москва, ул. Москворечье, д. 1
Ж. Г. Маркова
Россия
115522, г. Москва, ул. Москворечье, д. 1
Е. Н. Толмачева
Россия
634050, г. Томск, ул. Набережная реки Ушайки, д. 10
А. А. Кашеварова
Россия
634050, г. Томск, ул. Набережная реки Ушайки, д. 10
Список литературы
1. Miller D.T., Adam M.P., Aradhya S. et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749-764.
2. Bi W., Borgan C., Pursley A. et al. Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosomal analysis in today’s genomic array era? Genetics in Medicine. 2013;15:450-457.
3. Kallioniemi A., Kallioniemi O.P., Sudar D. et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258(5083):818-821.
4. Vermeesch J.R., Melotte C., Froyen G. et al. Molecular karyotyping: Array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem. 2005;53(3):413-422.
5. Bélanger S.A., Caron J. Evaluation of the child with global developmental delay and intellectual disability. Pediatr. Child Heal. 2018;23(6):403-410.
6. Jang W., Kim Y., Han E. et al. Chromosomal microarray analysis as a first-tier clinical diagnostic test in patients with developmental delay/intellectual disability, autism spectrum disorders, and multiple congenital anomalies: a prospective multicenter study in Korea. Ann Lab Med. 2019;39(3):299-310.
7. Koolen D.A., de Vries B.B.A. Newly recognized mental retardation microdeletion/duplication syndromes. Monogr Hum Genet. Basel, Karger, 2010;18:101-113.
8. Vissers E.L.M.L., Stankiewicz P. Microdeletion and microduplication syndromes. Lars Feuk (ed.). Genomic Structural Variants: Methods and Protocols. Methods Mol Biol. 2012;238:29-75.
9. Nevado J., Mergener R., Palomares-Bralo M. et al. New microdeletion and microduplication syndromes: A comprehensive review. Genet Mol Biol. 2014;37(1 suppl):210-219.
10. Goldenberg P. An update on common chromosome microdeletion and microduplication syndromes. Pediatr Ann. 2018;47(5):e198-e203.
11. Manning M., Hudgins L., Professional Practice and Guidelines Committee. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med. 2010;12(11):742-745.
12. Kearney H.M., South S.T., Wolff D.J. et al., American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med. 2011;13(7):676-679.
13. Kearney H.M., Thorland E.C., Brown K.K. et al. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 2011;13(7):680-685.
14. Hastings R., Howell R., Bricarelli F.D. et al. Specific constitutional cytogenetic guidelines. A common European framework for quality assessment for constitutional, acquired and molecular cytogenetic investigations. European Cytogeneticists Association Newsletter. No 30. Jul 2012: 11-19.
15. South S.T., Lee C., Lamb A.N. et al. ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 2013;15(11):901-909.
16. American College of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 446: Array comparative genomic hybridization in prenatal diagnosis. Obstet Gynecol. 2009;114(5):1161-1163.
17. American College of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No 581: The use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol. 2013;122(6):1374-1377.
18. Committee on Genetics and the Society for Maternal-Fetal Medicine. Committee Opinion No 682: Microarrays and next-generation sequencing technology: the use of advanced genetic diagnostic tools in obstetrics and gynecology. Obstet Gynecol. 2016;128(6):e262-e268.
19. Silva M., de Leeuw N., Mann K. et al. European guidelines for constitutional cytogenomic analysis. Eur J Hum Genet. 2019;27(1):1-16.
20. Riggs E.R., Andersen E.F., Cherry A.M. 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. 2020;22(2):245-257.
21. Brandt T., Sack L.M., Arjona D. et al. Adapting ACMG/AMP sequence variant classification guidelines for single-gene copy number variants. Genet Med. 2020;22(2):336-344.
22. Gonzales P.R., Andersen E.F., Brown T.R. et al. Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American Colleague of Medical Genetics and Genomics (ACMG). Genet. Med. 2022;24(2):255-261.
23. Deans Z.C., Ahn J.W., Carreira I.M. et al. Recommendations for reporting results of diagnostic genomic testing. Eur J Hum Genet. 2022;30(9):1011-1016.
24. Levy B., Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril. 2018;109(2):201-212.
25. Wapner R.J., Martin C.L., Levy B. et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012;367(23):2175-2184.
26. Shaffer L.G., Dabell M.P., Fisher A.J. et al. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn. 2012; 32(10):976-985.
27. Srebniak M.I., Diderich K.E., Joosten M. et al. Prenatal SNP array testing in 1000 fetuses with ultrasound anomalies: causative, unexpected and susceptibility CNVs. Eur J Hum Genet. 2016; 24(5);645651.
28. Donnelly J.C., Platt L.D,. Rebarber A. et al. Association of copy number variants with specific ultrasonographically detected fetal anomalies. Obstet Gynecol. 2014;124(1):83-90.
29. Greenbaum L., Maya I., Sagi-Dain L. et al. Chromosomal microarray analysis in pregnancies with corpus callosum and posterior fossa anomalies. Neurol Genet. 2021;7(3):e585.30. Hilger A.C., Dworschak G.C., Reutter H.M. Lessons learned from CNV analysis of major birth defects. Int J Mol Sci. 2020; 21(21):8247.
30. Mastromoro G., Guadagnolo D., Khaleghi Hashemian N. et al. Molecular approaches in fetal malformations, dynamic anomalies and soft markers: diagnostic rates and challenges – systematic review of the literature and meta-analysis. Diagnostics (Basel). 2022;12(3):575.
31. Lebedev I.N., Karamysheva T.V., Elisaphenko E.A. et al. Prenatal diagnosis of small supernumerary marker chromosome 10 by array-based comparative genomic hybridization and microdissected chromosome sequencing. Biomedicines. 2021;9(8):1030.
32. Peng G., Zhou Q., Chai H. et al. Estimation on risk of spontaneous abortions by genomic disorders from a meta-analysis of microarray results on large series of pregnancy losses. Mol Genet Genomic Med. 2023;11(8):e2181.
33. Handyside A.H., Harton G.L., Mariani B. et al. Karyomapping: a universal method for genome wide analysis of genetic diseases based on mapping crossovers between parental haplotypes. J Med Genet. 2010;47(10):651-8.
34. Zamani Esteki M., Dimitriadou E., Mateiu L. et al. Concurrent whole-genome haplotyping and copy-number profiling of single cells. Am J Hum Genet. 2015;96(6):894-912.
35. Stuppia L., Antonucci I., Palka G., Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci. 2012;13(3):3245-76.
36. Кашеварова А.А., Лопаткина М.Е., Беляева Е.О. и др. Распространенность и спектр моногенных CNV у пациентов с нарушениями интеллектуального развития. Медицинская генетика. 2021;20(10):44-46.
37. An International System for Human Cytogenomic Nomenclature (2020) Ed. McGovan-Jordan J., Hastings R.J., Moore S. Karger. 2020. Reprint from Cytogenet Genome Res. 2020;160:341-503.
38. Scott S.A., Cohen N., Brandt T. et al. Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med. 2010;12(2):85-92.
39. Pham J., Shaw C., Pursley A. et al. Somatic mosaicism detected by exon-targeted, high-resolution aCGH in 10,362 consecutive cases. Eur J Hum Genet. 2014;22(8):969-978.
40. Happe S., Shen X., Truong N., Maran V., Agilent Technologies, Inc. High-Performance aberration detection from low DNA input and mosaic samples with the Agilent SureTag Labeling Kit and CGH Microarray. https://www.agilent.com/cs/library/applications/application-lowdna-input-mosaic-samples-surtag-cgh-microarrays-5994-2722enagilent.pdf?elqTrackId=58f21e7c88344aa2829f4bf886ca3a94&elqaid=4951&elqat=2
41. Nurk S., Koren S., Rhie A. et al. A complete sequence of a human genome. Science. 2022;376(6588):44-53.
42. Collins R.L., Glessner J.T., Porcu E. et al. A cross-disorder dosage sensitivity map of the human genome. Cell. 2022;185(16):30413055.e25.
43. Adam M.P., Justice A.N., Schelley S. et al. Clinical utility of array comparative genomic hybridization: uncovering tumor susceptibility in individuals with developmental delay. J Pediatr. 2009;154(1):143-146.
44. Vogt P.H. Genomic heterogeneity and instability of the AZF locus on the human Y chromosome. Mol Cell Endocrinol. 2004;224(1-2):1-9.
45. Boone P.M., Soens Z.T., Campbell I.M. et al. Incidental copynumber variants identified by routine genome testing in a clinical population. Genet Med. 2013;15(1):45-54.
46. Kalia S.S., Adelman K., Bale S.J. et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017;19(2):249-255.
47. Richards S., Aziz N., Bale S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation on the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424.
48. Newman S., Hermetz K.E., Weckselblatt B., Rudd M.K. Nextgeneration sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. Am J Hum Genet. 2015;96:208–220.
49. Richardson M.E., Chong H., Mu W. et al. DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes. Genet Med. 2018;21:683–693.
50. MacDonald J.R., Ziman R., Yuen R.K. et al. The database of genomic variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014;42(D1):D986–92.
51. Juan-Mateau J., Gonzalez-Quereda L., Rodriquez M.J. et al. DMD mutations in 576 dystrophinopathy families: a step forward in genotype-phenotype correlations. PLoS One. 2015;10:e0135189.
52. Gijsbers A.C., Schoumans J., Ruivenkamp .. Interpretation of array comparative genome hybridization data: a major challenge. Cytogenet Genome Res. 2011;135(3-4):222-227.
53. Iourov I.Y., Vorsanova S.G., Korostelev S.A. et al. Long contiguous stretches of homozygosity spanning shortly the imprinted loci are associated with intellectual disability, autism and/or epilepsy. Mol Cytogenet. 2015;8:77.
54. Kurinnaia O.S., Vasin K.S., Zelenova M.A. et al. Outcomes of ROHs (runs of homozygosity)/LCSHs (long contiguous stretches of homozygosity) spanning the imprinted loci of chromosomes 7, 11 and 15 among children with neurodevelopmental disorders. Res Results Biomed. 2023;9(3):312-321.
55. Шилова Н.В., Миньженкова М.Е. Интерпретация клинически значимых вариаций числа копий ДНК. Медицинская генетика. 2018;10:40-44.
56. Миньженкова М.Е., Антоненко В.Г., Шилова Н.В. Международная система цитогеномной номенклатуры человека (ISCN 2020): Дополнения и изменения записи результатов флуоресцентной in situ гибридизации и хромосомного микроматричного анализа при конститутивных нарушениях. Медицинская генетика. 2023;22(4):11-16.
Рецензия
Для цитирования:
Лебедев И.Н., Шилова Н.В., Юров И.Ю., Малышева О.В., Твеленева А.А., Миньженкова М.Е., Маркова Ж.Г., Толмачева Е.Н., Кашеварова А.А. Рекомендации Российского общества медицинских генетиков по хромосомному микроматричному анализу. Медицинская генетика. 2023;22(10):3-47. https://doi.org/10.25557/2073-7998.2023.10.3-47
For citation:
Lebedev I.N., Shilova N.V., Iourov I.Yu., Malysheva O.V., Tveleneva A.A., Minzhenkova M.E., Markova Zh.G., Tolmacheva E.N., Kashevarova A.A. Guidelines of the Russian Society of Medical Geneticists for Chromosomal Microarray Analysis. Medical Genetics. 2023;22(10):3-47. (In Russ.) https://doi.org/10.25557/2073-7998.2023.10.3-47