Нови геномни технологии при диагностиката на вродени аномалии
Keywords:
вродени аномалии, секвениране от следващо поколение, микрочипова СГХ
Abstract
Вродените малформации и интелектуалният дефицит (ВМ/ИД) представляват сериозен проблем, поради тяхната висока честота (3-5%). ВМ/ИД са причина за 33% от неонаталната смъртност. В приблизително 40% от случаите генетичният дефект остава неясен. Много от тях имат хетерогенна етиология и затова те са трудни за диагностициране. Цитогенетичният метод не е достатъчен за поставяне на диагноза при голям процент от ВМ/ИД, които остават без уточнена етиология.
В пост–геномната ера новите диагностични подходи ще позволят по-добро разбиране на молекулните основи на вродените аномалии. Два от най-информативните методи за диагноза са микрочиповата сравнителна геномна хибридизация (array CGH, СГХ) и секвениране от следващо поколение (NGS). Тенденцията през последните години е тези технологии да се използват за откриване на кандидат гени за ВМ/ИД и диагностициране на пациенти с неуточнена клинична картина.
References
Zlotina A, Nikulina T, Yany N et al. Ring chromosome 18 in combination with 18q12.1 (DTNA) interstitial microdeletion in a patient with multiple congenital defects. Mol Cytogenet. 2016;9(18.
de Ravel TJ, Devriendt K, Fryns JP et al. What's new in karyotyping? The move towards array comparative genomic hybridisation (CGH). Eur J Pediatr. 2007;166(7):637-43.
Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7(2):85-97.
Friedman JM, Baross Б, Delaney AD et al. Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation. The American Journal of Human Genetics. 2006;79(3):500-13.
Ishkanian AS, Malloff CA, Watson SK et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004;36(3):299-303.
Menten B, Maas N, Thienpont B et al. Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet. 2006;43(8):625-33.
Sanlaville D, Lapierre JM, Turleau C et al. Molecular karyotyping in human constitutional cytogenetics. Eur J Med Genet. 2005;48(3):214-31.
Sebat J, Lakshmi B, Malhotra D et al. Strong association of de novo copy number mutations with autism. Science. 2007;316(5823):445-9.
Shaffer LG, Bejjani BA. Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res. 2006;115(3-4):303-9.
Хаджидекова С. Микроструктурни геномни аберации при пациенти с вродени малформации. Дисертация при Катедра по Медицинска генетика, Медицински Факултет, Медицински Университет – София. 2011.
Avdjieva-Tzavella D, Hadjidekova S, Rukova B et al. Detection of genomic imbalances by array-based comparative genomic hybridization in Bulgarian patients with autism spectrum disorders. Biotechnol & Biotechnol Eq. 2012;26(6):3389-93.
Avdjieva-Тzavellа D, Todorov T, Todorova A et al. Analysis of the genes encoding neuroligins NLGN3 and NLGN4 in bulgarian patients with autism. Genetic counseling. 2012;23(4):505-11.
Авджиева Д, Хаджидекова С, Рукова Б et al. Генетична характеристика на пациенти от аутистичния спектър. Педиатрия. 2012;4(20-26.
Cappuccio G, Vitiello F, Casertano A et al. New insights in the interpretation of array-CGH: autism spectrum disorder and positive family history for intellectual disability predict the detection of pathogenic variants. Ital J Pediatr. 2016;42(1):39.
Solinas-Toldo S, Lampel S, Stilgenbauer S et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997;20(4):399-407.
Pinkel D, Segraves R, Sudar D et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998;20(2):207-11.
Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36(9):949-51.
Erdogan F, Ullmann R, Chen W et al. Characterization of a 5.3 Mb deletion in 15q14 by comparative genomic hybridization using a whole genome "tiling path" BAC array in a girl with heart defect, cleft palate, and developmental delay. Am J Med Genet A. 2007;143(2):172-8.
Barber JC, Maloney VK, Huang S et al. 8p23.1 duplication syndrome; a novel genomic condition with unexpected complexity revealed by array CGH. Eur J Hum Genet. 2008;16(1):18-27.
Veltman JA, de Vries BB. Diagnostic genome profiling: unbiased whole genome or targeted analysis? J Mol Diagn. 2006;8(5):534-7; discussion 37-9.
Vianna GS, Medeiros PF, Alves AF et al. Array-CGH analysis in patients with intellectual disability and/or congenital malformations in Brazil. Genet Mol Res. 2016;15(1):
Quail MA, Smith M, Coupland P et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(341.
Rehm HL, Bale SJ, Bayrak-Toydemir P et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15(9):733-47.
Grada A, Weinbrecht K. Next-generation sequencing: methodology and application. J Invest Dermatol. 2013;133(8):e11.
Renkema KY, Stokman MF, Giles RH et al. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. 2014;
Renkema KY, Stokman MF, Giles RH et al. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. 2014;10(8):433-44.
Bamshad MJ, Shendure JA, Valle D et al. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A. 2012;158A(7):1523-5.
Shen P, Wang W, Krishnakumar S et al. High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A. 2011;108(16):6549-54.
Lai-Cheong JE, McGrath JA. Next-generation diagnostics for inherited skin disorders. J Invest Dermatol. 2011;131(10):1971-3.
Rauch A, Wieczorek D, Graf E et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet. 2012;380(9854):1674-82.
Brett M, McPherson J, Zang ZJ et al. Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel. PLoS One. 2014;9(4):e93409.
Cullinane AR, Vilboux T, O'Brien K et al. Homozygosity mapping and wholeexome sequencing to detect SLC45A2 and G6PC3 mutations in a single patient with oculocutaneous albinism and neutropenia. J Invest Dermatol. 2011;131(10):2017-25.
Gogol-Doring A, Chen W. An overview of the analysis of next generation sequencing data. Methods Mol Biol. 2012;802(249-57.
Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
Danecek P, Auton A, Abecasis G et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-8.
McKenna A, Hanna M, Banks E et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.
Bamshad MJ, Ng SB, Bigham AW et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745-55.
Manary MJ, Singhakul SS, Flannery EL et al. Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics. 2014;15(63.
Zhang X. Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med. 2014;8(1):42-57.
Altshuler DM, Gibbs RA, Peltonen L et al. Integrating common and rare genetic variation in diverse human populations. Nature. 2010;467(7311):52-8.
Petrovski S, Wang Q, Heinzen EL et al. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013;9(8):e1003709.
Abecasis GR, Auton A, Brooks LD et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56-65.
Raychaudhuri S, Iartchouk O, Chin K et al. A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet. 2011;43(12):1232-6.
Momozawa Y, Mni M, Nakamura K et al. Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet. 2011;43(1):43-7.
Sanna S, Li B, Mulas A et al. Fine mapping of five loci associated with lowdensity lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet. 2011;7(7):e1002198.
Dorschner MO, Amendola LM, Turner EH et al. Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet. 2013;93(4):631-40.
Christenhusz GM, Devriendt K, Dierickx K. To tell or not to tell? A systematic review of ethical reflections on incidental findings arising in genetics contexts. Eur J Hum Genet. 2013;21(3):248-55.
Kahrizi K, Hu CH, Garshasbi M et al. Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3. Eur J Hum Genet. 2011;19(1):115-7.
Grozeva D, Carss K, Spasic-Boskovic O et al. De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability. Am J Hum Genet. 2014;94(4):618-24.
Lepri FR, Scavelli R, Digilio MC et al. Diagnosis of Noonan syndrome and related disorders using target next generation sequencing. BMC Med Genet. 2014;15(14.
Lapunzina P, Lopez RO, Rodriguez-Laguna L et al. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies. Genet Mol Biol. 2014;37(1 Suppl):241-9.
Zhang R, Chen X, Li P et al. Molecular characterization of a novel ring 6 chromosome using next generation sequencing. Mol Cytogenet. 2016;9(33.
Zhu X, Li J, Ru T et al. Identification of copy number variations associated with congenital heart disease by chromosomal microarray analysis and nextgeneration sequencing. Prenat Diagn. 2016;36(4):321-7.
de Ravel TJ, Devriendt K, Fryns JP et al. What's new in karyotyping? The move towards array comparative genomic hybridisation (CGH). Eur J Pediatr. 2007;166(7):637-43.
Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7(2):85-97.
Friedman JM, Baross Б, Delaney AD et al. Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation. The American Journal of Human Genetics. 2006;79(3):500-13.
Ishkanian AS, Malloff CA, Watson SK et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004;36(3):299-303.
Menten B, Maas N, Thienpont B et al. Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet. 2006;43(8):625-33.
Sanlaville D, Lapierre JM, Turleau C et al. Molecular karyotyping in human constitutional cytogenetics. Eur J Med Genet. 2005;48(3):214-31.
Sebat J, Lakshmi B, Malhotra D et al. Strong association of de novo copy number mutations with autism. Science. 2007;316(5823):445-9.
Shaffer LG, Bejjani BA. Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res. 2006;115(3-4):303-9.
Хаджидекова С. Микроструктурни геномни аберации при пациенти с вродени малформации. Дисертация при Катедра по Медицинска генетика, Медицински Факултет, Медицински Университет – София. 2011.
Avdjieva-Tzavella D, Hadjidekova S, Rukova B et al. Detection of genomic imbalances by array-based comparative genomic hybridization in Bulgarian patients with autism spectrum disorders. Biotechnol & Biotechnol Eq. 2012;26(6):3389-93.
Avdjieva-Тzavellа D, Todorov T, Todorova A et al. Analysis of the genes encoding neuroligins NLGN3 and NLGN4 in bulgarian patients with autism. Genetic counseling. 2012;23(4):505-11.
Авджиева Д, Хаджидекова С, Рукова Б et al. Генетична характеристика на пациенти от аутистичния спектър. Педиатрия. 2012;4(20-26.
Cappuccio G, Vitiello F, Casertano A et al. New insights in the interpretation of array-CGH: autism spectrum disorder and positive family history for intellectual disability predict the detection of pathogenic variants. Ital J Pediatr. 2016;42(1):39.
Solinas-Toldo S, Lampel S, Stilgenbauer S et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997;20(4):399-407.
Pinkel D, Segraves R, Sudar D et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998;20(2):207-11.
Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat Genet. 2004;36(9):949-51.
Erdogan F, Ullmann R, Chen W et al. Characterization of a 5.3 Mb deletion in 15q14 by comparative genomic hybridization using a whole genome "tiling path" BAC array in a girl with heart defect, cleft palate, and developmental delay. Am J Med Genet A. 2007;143(2):172-8.
Barber JC, Maloney VK, Huang S et al. 8p23.1 duplication syndrome; a novel genomic condition with unexpected complexity revealed by array CGH. Eur J Hum Genet. 2008;16(1):18-27.
Veltman JA, de Vries BB. Diagnostic genome profiling: unbiased whole genome or targeted analysis? J Mol Diagn. 2006;8(5):534-7; discussion 37-9.
Vianna GS, Medeiros PF, Alves AF et al. Array-CGH analysis in patients with intellectual disability and/or congenital malformations in Brazil. Genet Mol Res. 2016;15(1):
Quail MA, Smith M, Coupland P et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13(341.
Rehm HL, Bale SJ, Bayrak-Toydemir P et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15(9):733-47.
Grada A, Weinbrecht K. Next-generation sequencing: methodology and application. J Invest Dermatol. 2013;133(8):e11.
Renkema KY, Stokman MF, Giles RH et al. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. 2014;
Renkema KY, Stokman MF, Giles RH et al. Next-generation sequencing for research and diagnostics in kidney disease. Nat Rev Nephrol. 2014;10(8):433-44.
Bamshad MJ, Shendure JA, Valle D et al. The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions. Am J Med Genet A. 2012;158A(7):1523-5.
Shen P, Wang W, Krishnakumar S et al. High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A. 2011;108(16):6549-54.
Lai-Cheong JE, McGrath JA. Next-generation diagnostics for inherited skin disorders. J Invest Dermatol. 2011;131(10):1971-3.
Rauch A, Wieczorek D, Graf E et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet. 2012;380(9854):1674-82.
Brett M, McPherson J, Zang ZJ et al. Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel. PLoS One. 2014;9(4):e93409.
Cullinane AR, Vilboux T, O'Brien K et al. Homozygosity mapping and wholeexome sequencing to detect SLC45A2 and G6PC3 mutations in a single patient with oculocutaneous albinism and neutropenia. J Invest Dermatol. 2011;131(10):2017-25.
Gogol-Doring A, Chen W. An overview of the analysis of next generation sequencing data. Methods Mol Biol. 2012;802(249-57.
Li H, Handsaker B, Wysoker A et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-9.
Danecek P, Auton A, Abecasis G et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-8.
McKenna A, Hanna M, Banks E et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303.
Bamshad MJ, Ng SB, Bigham AW et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745-55.
Manary MJ, Singhakul SS, Flannery EL et al. Identification of pathogen genomic variants through an integrated pipeline. BMC Bioinformatics. 2014;15(63.
Zhang X. Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med. 2014;8(1):42-57.
Altshuler DM, Gibbs RA, Peltonen L et al. Integrating common and rare genetic variation in diverse human populations. Nature. 2010;467(7311):52-8.
Petrovski S, Wang Q, Heinzen EL et al. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013;9(8):e1003709.
Abecasis GR, Auton A, Brooks LD et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56-65.
Raychaudhuri S, Iartchouk O, Chin K et al. A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet. 2011;43(12):1232-6.
Momozawa Y, Mni M, Nakamura K et al. Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease. Nat Genet. 2011;43(1):43-7.
Sanna S, Li B, Mulas A et al. Fine mapping of five loci associated with lowdensity lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet. 2011;7(7):e1002198.
Dorschner MO, Amendola LM, Turner EH et al. Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet. 2013;93(4):631-40.
Christenhusz GM, Devriendt K, Dierickx K. To tell or not to tell? A systematic review of ethical reflections on incidental findings arising in genetics contexts. Eur J Hum Genet. 2013;21(3):248-55.
Kahrizi K, Hu CH, Garshasbi M et al. Next generation sequencing in a family with autosomal recessive Kahrizi syndrome (OMIM 612713) reveals a homozygous frameshift mutation in SRD5A3. Eur J Hum Genet. 2011;19(1):115-7.
Grozeva D, Carss K, Spasic-Boskovic O et al. De novo loss-of-function mutations in SETD5, encoding a methyltransferase in a 3p25 microdeletion syndrome critical region, cause intellectual disability. Am J Hum Genet. 2014;94(4):618-24.
Lepri FR, Scavelli R, Digilio MC et al. Diagnosis of Noonan syndrome and related disorders using target next generation sequencing. BMC Med Genet. 2014;15(14.
Lapunzina P, Lopez RO, Rodriguez-Laguna L et al. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies. Genet Mol Biol. 2014;37(1 Suppl):241-9.
Zhang R, Chen X, Li P et al. Molecular characterization of a novel ring 6 chromosome using next generation sequencing. Mol Cytogenet. 2016;9(33.
Zhu X, Li J, Ru T et al. Identification of copy number variations associated with congenital heart disease by chromosomal microarray analysis and nextgeneration sequencing. Prenat Diagn. 2016;36(4):321-7.
Published
2016-06-15
How to Cite
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Михайлова М, Тончева Д, Хаджидекова С. Нови геномни технологии при диагностиката на вродени аномалии. Редки болести и лекарства сираци [Internet]. 2016Jun.15 [cited 2024Apr.20];7(2):3-. Available from: https://journal.raredis.org/index.php/RBLS/article/view/50
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