Genetic testing strategies in the newborn.


Journal

Journal of perinatology : official journal of the California Perinatal Association
ISSN: 1476-5543
Titre abrégé: J Perinatol
Pays: United States
ID NLM: 8501884

Informations de publication

Date de publication:
07 2020
Historique:
received: 27 11 2019
accepted: 19 05 2020
revised: 30 04 2020
pubmed: 31 5 2020
medline: 1 9 2021
entrez: 31 5 2020
Statut: ppublish

Résumé

Genetic disorders presenting in the neonatal period can have a significant impact on morbidity and mortality. Early diagnosis can facilitate timely prognostic counseling to families and possibility of precision care, which could improve outcome. As availability of diagnostic testing expands, the required knowledge base of the neonatologist must also expand to include proper application and understanding of genetic testing modalities, especially where availability of clinical genetics consultation is limited. Herein, we review genetic tests utilized in the neonatal intensive care unit (NICU) providing background on the technology, clinical indications, advantages, and limitations of the tests. This review will span from classic cytogenetics to the evolving role of next generation sequencing and its impact on the management of neonatal disease.

Identifiants

pubmed: 32472107
doi: 10.1038/s41372-020-0697-y
pii: 10.1038/s41372-020-0697-y
doi:

Types de publication

Journal Article Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

1007-1016

Références

Yang L, Liu X, Li Z, Zhang P, Wu B, Wang H, et al. Genetic aetiology of early infant deaths in a neonatal intensive care unit. J Med Genet. 2019. https://doi.org/10.1136/jmedgenet-2019-106221 .
McCandless SE, Brunger JW, Cassidy SB. The burden of genetic disease on inpatient care in a children’s hospital. Am J Hum Genet. 2004;74:121–7.
pubmed: 14681831 pmcid: 14681831 doi: 10.1086/381053
French CE, Delon I, Dolling H, Sanchis-Juan A, Shamardina O, Mégy K, et al. Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children. Intensive Care Med. 2019;45:627–36.
pubmed: 30847515 pmcid: 6483967 doi: 10.1007/s00134-019-05552-x
Petrikin JE, Willig LK, Smith LD, Kingsmore SF. Rapid whole genome sequencing and precision neonatology. Semin Perinatol. 2015;39:623–31.
pubmed: 26521050 pmcid: 4657860 doi: 10.1053/j.semperi.2015.09.009
Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, et al. Whole-genome sequencing for optimized patient management. Sci Transl Med. 2011;3:87re3.
pubmed: 21677200 pmcid: 3314311 doi: 10.1126/scitranslmed.3002243
Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, et al. Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization. NPJ Genom Med. 2018;3:10.
pubmed: 29644095 pmcid: 5884823 doi: 10.1038/s41525-018-0049-4
Tjio JH, Levan A. The chromosome number of man. Hereditas. 1956;42:1–6.
doi: 10.1111/j.1601-5223.1956.tb03010.x
Pasquier L, Fradin M, Chérot E, Martin-Coignard D, Colin E, Journel H, et al. Karyotype is not dead (yet)! Eur J Med Genet. 2016;59:11–15.
pubmed: 26691665 doi: 10.1016/j.ejmg.2015.11.016
Huber D, Voith von Voithenberg L, Kaigala GV. Fluorescence in situ hybridization (FISH): history, limitations and what to expect from micro-scale FISH? Micro Nano Eng. 2018;1:15–24.
doi: 10.1016/j.mne.2018.10.006
Cui C, Shu W, Li P. Fluorescence in situ hybridization: cell-based genetic diagnostic and research applications. Front Cell Dev Biol. 2016;4. https://doi.org/10.3389/fcell.2016.00089 .
McDonald-McGinn DM, Sullivan KE, Marino B, Philip N, Swillen A, Vorstman JAS, et al. 22q11.2 deletion syndrome. Nat Rev Dis Prim. 2015;1:1–19.
Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, 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. 2019. https://doi.org/10.1038/s41436-019-0686-8 .
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;12:742–5.
pubmed: 20962661 pmcid: 3111046 doi: 10.1097/GIM.0b013e3181f8baad
Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, 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;86:749–64.
pubmed: 20466091 pmcid: 20466091 doi: 10.1016/j.ajhg.2010.04.006
Wang J-C, Ross L, Mahon LW, Owen R, Hemmat M, Wang BT, et al. Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility. Eur J Hum Genet. 2015;23:663–71.
pubmed: 25118026 doi: 10.1038/ejhg.2014.153
Ballif BC, Rorem EA, Sundin K, Lincicum M, Gaskin S, Coppinger J, et al. Detection of low-level mosaicism by array CGH in routine diagnostic specimens. Am J Med Genet A. 2006;140:2757–67.
pubmed: 17103431 doi: 10.1002/ajmg.a.31539
Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, et al. College of American Pathologists’ laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med. 2015;139:481–93.
pubmed: 25152313 doi: 10.5858/arpa.2014-0250-CP
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA. 1977;74:5463–7.
pubmed: 271968 doi: 10.1073/pnas.74.12.5463
Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17:333–51.
doi: 10.1038/nrg.2016.49 pubmed: 27184599
Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009;461:272–6.
pubmed: 19684571 pmcid: 2844771 doi: 10.1038/nature08250
Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet. 2010;11:31–46.
pubmed: 19997069 pmcid: 19997069 doi: 10.1038/nrg2626
Mardis ER. Next-generation sequencing platforms. Annu Rev Anal Chem. 2013;6:287–303.
doi: 10.1146/annurev-anchem-062012-092628
Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91.
pubmed: 27535533 pmcid: 27535533 doi: 10.1038/nature19057
Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001;11:863–74.
pubmed: 11337480 pmcid: 311071 doi: 10.1101/gr.176601
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073–81.
pubmed: 19561590 doi: 10.1038/nprot.2009.86
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.
pubmed: 2855889 pmcid: 2855889 doi: 10.1038/nmeth0410-248
Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980–5.
pubmed: 24234437 doi: 10.1093/nar/gkt1113
Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2016;44:D862–8.
pubmed: 26582918 doi: 10.1093/nar/gkv1222
Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46:D1062–7.
pubmed: 29165669 doi: 10.1093/nar/gkx1153
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.
pubmed: 25741868 pmcid: 25741868 doi: 10.1038/gim.2015.30
Lincoln SE, Truty R, Lin C-F, Zook JM, Paul J, Ramey VH, et al. A rigorous interlaboratory examination of the need to confirm next-generation sequencing–detected variants with an orthogonal method in clinical genetic testing. J Mol Diagn. 2019;21:318–29.
pubmed: 30610921 pmcid: 6629256 doi: 10.1016/j.jmoldx.2018.10.009
Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15:733–47.
pubmed: 23887774 pmcid: 4098820 doi: 10.1038/gim.2013.92
Kalia SS, Adelman K, Bale SJ, Chung WK, Eng C, Evans JP, 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;19:249–55.
pubmed: 27854360 doi: 10.1038/gim.2016.190
Baruch S, Hudson K. Civilian and military genetics: nondiscrimination policy in a post-GINA world. Am J Hum Genet. 2008;83:435–44.
pubmed: 18940308 pmcid: 2561935 doi: 10.1016/j.ajhg.2008.09.003
Hellwig LD, Turner C, Manolio TA, Haigney M, James CA, Murray B, et al. Return of secondary findings in genomic sequencing: Military implications. Mol Genet Genom Med. 2019;7:e00483.
doi: 10.1002/mgg3.483
De Castro M, Biesecker LG, Turner C, Brenner R, Witkop C, Mehlman M, et al. Genomic medicine in the military. NPJ Genom Med. 2016;1:15008.
pubmed: 29263806 pmcid: 5685294 doi: 10.1038/npjgenmed.2015.8
ACMG Board of Directors Points to consider for informed consent for genome/exome sequencing. Genet Med. 2013;15:748–9.
doi: 10.1038/gim.2013.94
Shellhaas RA, Wusthoff CJ, Tsuchida TN, Glass HC, Chu CJ, Massey SL, et al. Profile of neonatal epilepsies: characteristics of a prospective US cohort. Neurology. 2017;89:893–9.
pubmed: 28733343 pmcid: 5577964 doi: 10.1212/WNL.0000000000004284
Møller RS, Larsen LHG, Johannesen KM, Talvik I, Talvik T, Vaher U, et al. Gene panel testing in epileptic encephalopathies and familial epilepsies. Mol Syndromol. 2016;7:210–9.
pubmed: 27781031 pmcid: 5073625 doi: 10.1159/000448369
Kapoor RR, Flanagan SE, Arya VB, Shield JP, Ellard S, Hussain K. Clinical and molecular characterisation of 300 patients with congenital hyperinsulinism. Eur J Endocrinol. 2013;168:557–64.
pubmed: 23345197 pmcid: 3599069 doi: 10.1530/EJE-12-0673
Stanley CA. Perspective on the genetics and diagnosis of congenital hyperinsulinism disorders. J Clin Endocrinol Metab. 2016;101:815–26.
pubmed: 26908106 pmcid: 4803157 doi: 10.1210/jc.2015-3651
Togawa T, Sugiura T, Ito K, Endo T, Aoyama K, Ohashi K, et al. Molecular genetic dissection and neonatal/infantile intrahepatic cholestasis using targeted next-generation sequencing. J Pediatr. 2016;171:171–7.e1–4.
pubmed: 26858187 doi: 10.1016/j.jpeds.2016.01.006
Daoud H, Luco SM, Li R, Bareke E, Beaulieu C, Jarinova O, et al. Next-generation sequencing for diagnosis of rare diseases in the neonatal intensive care unit. Can Med Assoc J. 2016;188:E254–60.
doi: 10.1503/cmaj.150823
Brunelli L, Jenkins SM, Gudgeon JM, Bleyl SB, Miller CE, Tvrdik T, et al. Targeted gene panel sequencing for the rapid diagnosis of acutely ill infants. Mol Genet Genom Med. 2019;7:e00796.
Diemen CC, van, Kerstjens-Frederikse WS, Bergman KA, Koning TJ, de, Sikkema-Raddatz B, Velde JKvander, et al. Rapid targeted genomics in critically ill newborns. Pediatrics. 2017;140:e20162854.
pubmed: 28939701 doi: 10.1542/peds.2016-2854
Kernohan KD, Hartley T, Naumenko S, Armour CM, Graham GE, Nikkel SM, et al. Diagnostic clarity of exome sequencing following negative comprehensive panel testing in the neonatal intensive care unit. Am J Med Genet A. 2018;176:1688–91.
pubmed: 30160830 doi: 10.1002/ajmg.a.38838
Elliott AM, du Souich C, Lehman A, Guella I, Evans DM, Candido T, et al. RAPIDOMICS: rapid genome-wide sequencing in a neonatal intensive care unit-successes and challenges. Eur J Pediatr. 2019;178:1207–18.
pubmed: 31172278 doi: 10.1007/s00431-019-03399-4
Meng L, Pammi M, Saronwala A, Magoulas P, Ghazi AR, Vetrini F, et al. Use of exome sequencing for infants in intensive care units: ascertainment of severe single-gene disorders and effect on medical management. JAMA Pediatr. 2017;171:e173438.
pubmed: 28973083 pmcid: 6359927 doi: 10.1001/jamapediatrics.2017.3438
Powis Z, Hagman KDF, Speare V, Cain T, Blanco K, Mowlavi LS, et al. Exome sequencing in neonates: diagnostic rates, characteristics, and time to diagnosis. Genet Med. 2018;20:1468–71.
pubmed: 29565416 doi: 10.1038/gim.2018.11
Stark Z, Tan TY, Chong B, Brett GR, Yap P, Walsh M, et al. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genet Med. 2016;18:1090–6.
pubmed: 26938784 doi: 10.1038/gim.2016.1
Kingsmore SF, Cakici JA, Clark MM, Gaughran M, Feddock M, Batalov S, et al. A randomized, controlled trial of the analytic and diagnostic performance of singleton and trio, rapid genome and exome sequencing in ill infants. Am J Hum Genet. 2019;105:719–33.
pubmed: 31564432 pmcid: 6817534 doi: 10.1016/j.ajhg.2019.08.009
LaDuca H, Farwell KD, Vuong H, Lu H-M, Mu W, Shahmirzadi L, et al. Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels. PloS ONE. 2017;12:e0170843.
pubmed: 28152038 pmcid: 5289469 doi: 10.1371/journal.pone.0170843
Belkadi A, Bolze A, Itan Y, Cobat A, Vincent QB, Antipenko A, et al. Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci USA. 2015;112:5473–8.
pubmed: 25827230 doi: 10.1073/pnas.1418631112
Petrikin JE, Cakici JA, Clark MM, Willig LK, Sweeney NM, Farrow EG, et al. The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants. NPJ Genom Med. 2018;3:6.
pubmed: 29449963 pmcid: 5807510 doi: 10.1038/s41525-018-0045-8
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12:745–55.
pubmed: 21946919 doi: 10.1038/nrg3031
Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012;4:154ra135.
pubmed: 23035047 pmcid: 4283791 doi: 10.1126/scitranslmed.3004041

Auteurs

Jeanne Carroll (J)

Department of Pediatrics, University of California, La Jolla, CA, USA. jcarroll@rchsd.org.
Division of Neonatology, Rady Children's Hospital, San Diego, CA, USA. jcarroll@rchsd.org.
Rady Children's Institute for Genomic Medicine, San Diego, CA, USA. jcarroll@rchsd.org.

Kristen Wigby (K)

Department of Pediatrics, University of California, La Jolla, CA, USA.
Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
Division of Genetics/Dysmorphology, Rady Children's Hospital, San Diego, CA, USA.

Sarah Murray (S)

Department of Pathology, University of California San Diego, La Jolla, CA, USA.
Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA.

Articles similaires

Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C

Classifications MeSH