Generic placeholder image

Current Pharmacogenomics and Personalized Medicine

Editor-in-Chief

ISSN (Print): 1875-6921
ISSN (Online): 1875-6913

Review Article

The Promise of Whole-exome Sequencing for Prenatal Genetic Diagnosis

Author(s): Jiun Kang*

Volume 17, Issue 1, 2020

Page: [25 - 31] Pages: 7

DOI: 10.2174/1875692117666191106105918

Price: $65

Abstract

Prenatal genetic diagnosis provides information for pregnancy and perinatal decision- making and management. Cytogenetic testing methods, including chromosomal microarray analysis and gene panels, have evolved to become a part of routine laboratory testing, providing valuable diagnostic and prognostic information for prenatal diagnoses. Despite this progress, however, cytogenetic analyses are limited by their resolution and diagnosis is only possible in around 40% of the dysmorphic fetuses. The advent of nextgeneration sequencing (NGS), whole-genome sequencing or whole-exome sequencing has revolutionized prenatal diagnosis and fetal medicine. These technologies have improved the identification of genetic disorders in fetuses with structural abnormalities and provide valuable diagnostic and prognostic information for the detection of genomic defects. Here, the potential future of prenatal genetic diagnosis, including a move toward NGS technologies, is discussed.

Keywords: Prenatal genetic diagnosis, next-generation sequencing, whole-genome sequencing, whole-exome sequencing, cytogenetic testing, genomic defects.

Graphical Abstract
[1]
Best S, Wou K, Vora N, Van der Veyver IB, Wapner R, Chitty LS. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn 2018; 38(1): 10-9.
[http://dx.doi.org/10.1002/pd.5102] [PMID: 28654730]
[2]
Kang JU. Overview of cytogenetic technologies. Korean J Clin Lab Sci 2018; 50: 375-81.
[http://dx.doi.org/10.15324/kjcls.2018.50.4.375]
[3]
Van den Veyver IB. Recent advances in prenatal genetic screening and testing. F1000 Res 2016; 5: 2591.
[http://dx.doi.org/10.12688/f1000research.9215.1] [PMID: 27853526]
[4]
Hayward J, Chitty LS. Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23(2): 94-101.
[http://dx.doi.org/10.1016/j.siny.2017.12.002] [PMID: 29305293]
[5]
Maciejewski JP, Mufti GJ. Whole genome scanning as a cytogenetic tool in hematologic malignancies. Blood 2008; 112(4): 965-74.
[http://dx.doi.org/10.1182/blood-2008-02-130435] [PMID: 18505780]
[6]
Peters DG, Yatsenko SA, Surti U, Rajkovic A. Recent advances of genomic testing in perinatal medicine. Semin Perinatol 2015; 39(1): 44-54.
[http://dx.doi.org/10.1053/j.semperi.2014.10.009] [PMID: 25444417]
[7]
MacDorman MF, Kirmeyer S. Fetal and perinatal mortality, United States, 2005. Natl Vital Stat Rep 2009; 57(8): 1-19.
[PMID: 19294965]
[8]
Brackley KJ, Kilby MD, Morton J, Whittle MJ, Knight SJ, Flint J. A case of recurrent congenital fetal anomalies associated with a familial subtelomeric translocation. Prenat Diagn 1999; 19(6): 570-4.
[http://dx.doi.org/10.1002/(SICI)1097-0223(199906)19:6<570:AID-PD582>3.0.CO;2-Q] [PMID: 10416976]
[9]
Bejjani BA, Saleki R, Ballif BC, et al. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: is less more? Am J Med Genet A 2005; 134(3): 259-67.
[http://dx.doi.org/10.1002/ajmg.a.30621] [PMID: 15723295]
[10]
Shaffer LG, Bejjani BA. Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res 2006; 115(3-4): 303-9.
[http://dx.doi.org/10.1159/000095928] [PMID: 17124414]
[11]
Shaffer LG, Bejjani BA. Medical applications of array CGH and the transformation of clinical cytogenetics. Cytogenet Genome Res 2006; 115(3-4): 303-9.
[http://dx.doi.org/10.1159/000095928] [PMID: 17124414]
[12]
Carvalho CM, Zhang F, Lupski JR. Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci USA 2010; 107(Suppl. 1): 1765-71.
[http://dx.doi.org/10.1073/pnas.0906222107] [PMID: 20080665]
[13]
Kang JU. Chromosome 8q as the most frequent target for amplification in early gastric carcinoma. Oncol Lett 2014; 7(4): 1139-43.
[http://dx.doi.org/10.3892/ol.2014.1849] [PMID: 24944681]
[14]
Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012; 367(23): 2175-84.
[http://dx.doi.org/10.1056/NEJMoa1203382] [PMID: 23215555]
[15]
McGillivray G, Rosenfeld JA, McKinlay Gardner RJ, Gillam LH. Genetic counselling and ethical issues with chromosome microarray analysis in prenatal testing. Prenat Diagn 2012; 32(4): 389-95.
[http://dx.doi.org/10.1002/pd.3849] [PMID: 22467169]
[16]
Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril 2018; 109(2): 201-12.
[http://dx.doi.org/10.1016/j.fertnstert.2018.01.005] [PMID: 29447663]
[17]
Xuan J, Yu Y, Qing T, Guo L, Shi L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett 2013; 340(2): 284-95.
[http://dx.doi.org/10.1016/j.canlet.2012.11.025] [PMID: 23174106]
[18]
Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16(9): 987-99.
[http://dx.doi.org/10.1080/14737159.2016.1209411] [PMID: 27388938]
[19]
Borghesi A, Mencarelli MA, Memo L, et al. Intersociety policy statement on the use of whole-exome sequencing in the critically ill newborn infant. Ital J Pediatr 2017; 43(1): 100.
[http://dx.doi.org/10.1186/s13052-017-0418-0] [PMID: 29100554]
[20]
Milos PM. Emergence of single-molecule sequencing and potential for molecular diagnostic applications. Expert Rev Mol Diagn 2009; 9(7): 659-66.
[http://dx.doi.org/10.1586/erm.09.50] [PMID: 19817551]
[21]
Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell 2013; 155(1): 27-38.
[http://dx.doi.org/10.1016/j.cell.2013.09.006] [PMID: 24074859]
[22]
Sawyer SL, Hartley T, Dyment DA, et al. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet 2016; 89(3): 275-84.
[http://dx.doi.org/10.1111/cge.12654] [PMID: 26283276]
[23]
Mellis R, Chandler N, Chitty LS. Next-generation sequencing and the impact on prenatal diagnosis. Expert Rev Mol Diagn 2018; 18(8): 689-99.
[http://dx.doi.org/10.1080/14737159.2018.1493924] [PMID: 29962246]
[24]
Vora NL, Hui L. Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development. Genet Med 2018; 20(8): 791-9.
[http://dx.doi.org/10.1038/s41436-018-0087-4] [PMID: 30032162]
[25]
Willig LK, Petrikin JE, Smith LD, et al. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir Med 2015; 3(5): 377-87.
[http://dx.doi.org/10.1016/S2213-2600(15)00139-3] [PMID: 25937001]
[26]
Desbats MA, Vetro A, Limongelli I, et al. Primary coenzyme Q10 deficiency presenting as fatal neonatal multiorgan failure. Eur J Hum Genet 2015; 23(9): 1254-8.
[http://dx.doi.org/10.1038/ejhg.2014.277] [PMID: 25564041]
[27]
Liu Y, Wang L, Yang YK, et al. Prenatal diagnosis of fetal skeletal dysplasia using targeted next-generation sequencing: an analysis of 30 cases. Diagn Pathol 2019; 14(1): 76.
[http://dx.doi.org/10.1186/s13000-019-0853-x] [PMID: 31299979]
[28]
Talkowski ME, Ordulu Z, Pillalamarri V, et al. Clinical diagnosis by whole-genome sequencing of a prenatal sample. N Engl J Med 2012; 367(23): 2226-32.
[http://dx.doi.org/10.1056/NEJMoa1208594] [PMID: 23215558]
[29]
Choi M, Scholl UI, Ji W, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 2009; 106(45): 19096-101.
[http://dx.doi.org/10.1073/pnas.0910672106] [PMID: 19861545]
[30]
Ng SB, Buckingham KJ, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010; 42(1): 30-5.
[http://dx.doi.org/10.1038/ng.499] [PMID: 19915526]
[31]
Xue Y, Zhao G, Li H, et al. Non-invasive prenatal testing to detect chromosome aneuploidies in 57,204 pregnancies. Mol Cytogenet 2019; 12: 29.
[http://dx.doi.org/10.1186/s13039-019-0441-5] [PMID: 31249627]
[32]
Tetreault M, Bareke E, Nadaf J, Alirezaie N, Majewski J. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities. Expert Rev Mol Diagn 2015; 15(6): 749-60.
[http://dx.doi.org/10.1586/14737159.2015.1039516] [PMID: 25959410]
[33]
Srivastava S, Cohen JS, Vernon H, et al. Clinical whole exome sequencing in child neurology practice. Ann Neurol 2014; 76(4): 473-83.
[http://dx.doi.org/10.1002/ana.24251] [PMID: 25131622]
[34]
Sullivan HK, Bayefsky M, Wakim PG, et al. Noninvasive prenatal whole genome sequencing: Pregnant women’s views and preferences. Obstet Gynecol 2019; 133(3): 525-32.
[http://dx.doi.org/10.1097/AOG.0000000000003121] [PMID: 30741804]
[35]
Kitzman JO, Snyder MW, Ventura M, et al. Non‐invasive whole genome sequencing of a human fetus. Sci Transl 2012; 4(137) 137ra76
[36]
Wellcome trust sanger institute. Prenatal Assessment Of Genomes And Exomes (PAGE). Available from:. http://www.sanger.ac.uk/science/collaboration/prenatalassessment- genomes-and-exomes-page [Accessed February 21, 2017]
[37]
Horn R, Parker M. Opening Pandora’s box?: ethical issues in prenatal whole genome and exome sequencing. Prenat Diagn 2018; 38(1): 20-5.
[http://dx.doi.org/10.1002/pd.5114] [PMID: 28695688]
[38]
Hillman SC, Willams D, Carss KJ, McMullan DJ, Hurles ME, Kilby MD. Prenatal exome sequencing for fetuses with structural abnormalities: the next step. Ultrasound Obstet Gynecol 2015; 45(1): 4-9.
[http://dx.doi.org/10.1002/uog.14653] [PMID: 25157891]
[39]
Aristidou C, Theodosiou A, Ketoni A, et al. Cryptic breakpoint identified by whole-genome mate-pair sequencing in a rare paternally inherited complex chromosomal rearrangement. Mol Cytogenet 2018; 11: 34.
[http://dx.doi.org/10.1186/s13039-018-0384-2] [PMID: 29930709]
[40]
Yadava SM, Ashkinadze E. 125: Whole exome sequencing (WES) in prenatal diagnosis for carefully selected cases. Am J Obstet Gynecol 2017; 216: S87-8.
[http://dx.doi.org/10.1016/j.ajog.2016.11.029]
[41]
Jelin AC, Vora N. Whole exome sequencing: Applications in prenatal genetics. Obstet Gynecol Clin North Am 2018; 45(1): 69-81.
[http://dx.doi.org/10.1016/j.ogc.2017.10.003] [PMID: 29428287]
[42]
Kamalapathy P, Fonda Allen JS, Macri CJ, Lawrence AK, Regier DS, Rubio EI. Whole-exome sequencing for diagnosis of Peters-plus syndrome after prenatal diagnosis of recurrent low PAPP-A and multiple fetal anomalies in two consecutive pregnancies. J Neonatal Perinatal Med 2019; 12(3): 333-8.
[http://dx.doi.org/10.3233/NPM-1854] [PMID: 31476172]
[43]
Greenbaum L, Pode-Shakked B, Eisenberg-Barzilai S, et al. Evaluation of diagnostic yield in fetal whole-exome sequencing: A report on 45 consecutive families. Front Genet 2019; 10: 425.
[http://dx.doi.org/10.3389/fgene.2019.00425] [PMID: 31428121]
[44]
Drury S, Williams H, Trump N, et al. Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities. Prenat Diagn 2015; 35(10): 1010-7.
[http://dx.doi.org/10.1002/pd.4675] [PMID: 26275891]
[45]
Mone F, Quinlan-Jones E, Ewer AK, Kilby MD. Exome sequencing in the assessment of congenital malformations in the fetus and neonate. Arch Dis Child Fetal Neonatal Ed 2019; 104(4): F452-6.
[http://dx.doi.org/10.1136/archdischild-2018-316352] [PMID: 30816854]
[46]
Pangalos C, Hagnefelt B, Lilakos K, Konialis C. First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects. PeerJ 2016; 4 e1955
[http://dx.doi.org/10.7717/peerj.1955] [PMID: 27168972]
[47]
Carss KJ, Hillman SC, Parthiban V, et al. Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound. Hum Mol Genet 2014; 23(12): 3269-77.
[http://dx.doi.org/10.1093/hmg/ddu038] [PMID: 24476948]
[48]
Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. What can exome sequencing do for you? J Med Genet 2011; 48(9): 580-9.
[http://dx.doi.org/10.1136/jmedgenet-2011-100223] [PMID: 21730106]
[49]
Yang Y, Muzny DM, Xia F, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 2014; 312(18): 1870-9.
[http://dx.doi.org/10.1001/jama.2014.14601] [PMID: 25326635]
[50]
Vora NL, Hui L. Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development. Genet Med 2018; 20(8): 791-9.
[http://dx.doi.org/10.1038/s41436-018-0087-4] [PMID: 30032162]
[51]
McMullan DJ, Lord J, Eberhardt R, et al. Exome sequencing of 406 parental/fetal trios with structural abnormalities revealed by ultrasound in the UK prenatal assessment of genomes and exomes (PAGE) project. Available From:. https://www.conferences.com.au/2exome sequencing-of-406-parentalfetal-trios-with-structural-abnormalities-revealed-by ultrasound-in-the-uk-prenatal-assessment-of-genomes-and-exomes-page-project/ [Accessed February 27, 2017]
[52]
Petrovski S, Aggarwal V, Giordano JL, et al. Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study. Lancet 2019; 393(10173): 758-67.
[http://dx.doi.org/10.1016/S0140-6736(18)32042-7] [PMID: 30712878]
[53]
Ng SB, Turner EH, Robertson PD, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009; 461(7261): 272-6.
[http://dx.doi.org/10.1038/nature08250] [PMID: 19684571]
[54]
Rosenfeld JA, Mason CE, Smith TM. Limitations of the human reference genome for personalized genomics. PLoS One 2012; 7(7) e40294
[http://dx.doi.org/10.1371/journal.pone.0040294] [PMID: 22811759]
[55]
Noavar S, Behroozi S, Tatarcheh T, Parvini F, Foroutan M, Fahimi H. A novel homozygous frame-shift mutation in the SLC29A3 gene: a new case report and review of literature. BMC Med Genet 2019; 20(1): 147.
[http://dx.doi.org/10.1186/s12881-019-0879-7] [PMID: 31464584]
[56]
Saunders CJ, Miller NA, Soden SE, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 2012; 4(154) 154ra135
[http://dx.doi.org/10.1126/scitranslmed.3004041] [PMID: 23035047]
[57]
Wong FC, Lo YM. Prenatal diagnosis innovation: Genome sequencing of maternal plasma. Annu Rev Med 2016; 67: 419-32.
[http://dx.doi.org/10.1146/annurev-med-091014-115715] [PMID: 26473414]
[58]
Yohe S, Thyagarajan B. Review of clinical next-generation sequencing. Arch Pathol Lab Med 2017; 141(11): 1544-57.
[http://dx.doi.org/10.5858/arpa.2016-0501-RA] [PMID: 28782984]
[59]
Lord J, McMullan DJ, Eberhardt RY, et al. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet 2019; 393(10173): 747-57.
[http://dx.doi.org/10.1016/S0140-6736(18)31940-8] [PMID: 30712880]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy