Abstract
The present work describes the value of genetic analysis as a confirmatory measure following the detection of suspected inborn errors of metabolism in the Spanish newborn mass spectrometry screening program. One hundred and forty-one consecutive DNA samples were analyzed by next-generation sequencing using a customized exome sequencing panel. When required, the Illumina extended clinical exome panel was used, as was Sanger sequencing or transcriptional profiling. Biochemical tests were used to confirm the results of the genetic analysis. Using the customized panel, the metabolic disease suspected in 83 newborns (59%) was confirmed. In three further cases, two monoallelic variants were detected for two genes involved in the same biochemical pathway. In the remainder, either a single variant or no variant was identified. Given the persistent absence of biochemical alterations, carrier status was assigned in 39 cases. False positives were recorded for 11. In five cases in which the biochemical pattern was persistently altered, further genetic analysis allowed the detection of two variants affecting the function of BCAT2, ACSF3, and DNAJC12, as well as a second, deep intronic variant in ETFDH or PTS. The present results suggest that genetic analysis using extended next-generation sequencing panels can be used as a confirmatory test for suspected inborn errors of metabolism detected in newborn screening programs. Biochemical tests can be very helpful when a diagnosis is unclear. In summary, simultaneous genomic and metabolomic analyses can increase the number of inborn errors of metabolism that can be confirmed following suggestive newborn screening results.
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References
Pampols T. Inherited metabolic rare disease. Adv Exp Med Biol. 2010;686:397–431.
Morava E, Rahman S, Peters V, Baumgartner MR, Patterson M, Zschocke J. Quo vadis: the re-definition of "inborn metabolic diseases". J Inherit Metab Dis. 2015;38:1003–6.
Couce ML, Sanchez-Pintos P, Diogo L, Leao-Teles E, Martins E, Santos H, et al. Newborn screening for medium-chain acyl-CoA dehydrogenase deficiency: regional experience and high incidence of carnitine deficiency. Orphanet J Rare Dis. 2013;8:102.
Wilcken B. Newborn screening: how are we travelling, and where should we be going? J Inherit Metab Dis. 2011;34:569–74.
Martinez-Morillo E, Prieto Garcia B, Alvarez Menendez FV. Challenges for Worldwide Harmonization of Newborn Screening Programs. Clin Chem. 2016;62:689–98.
Vilarinho L, Rocha H, Sousa C, Marcao A, Fonseca H, Bogas M, et al. Four years of expanded newborn screening in Portugal with tandem mass spectrometry. J Inherit Metab Dis. 2010;33:Suppl 3:S133–138.
Blau N, Hennermann JB, Langenbeck U, Lichter-Konecki U. Diagnosis, classification, and genetics of phenylketonuria and tetrahydrobiopterin (BH4) deficiencies. Mol Genet Metab. 2011;104:Suppl,S2–9.
Fowler B, Leonard JV, Baumgartner MR. Causes of and diagnostic approach to methylmalonic acidurias. J Inherit Metab Dis. 2008;31:350–60.
Trujillano D, Ramos MD, Gonzalez J, Tornador C, Sotillo F, Escaramis G, et al. Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR. J Med Genet. 2013;50:455–62.
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.
Kleinberger J, Maloney KA, Pollin TI, Jeng LJ. An openly available online tool for implementing the ACMG/AMP standards and guidelines for the interpretation of sequence variants. Genet Med. 2016;18:1165.
Brasil S, Viecelli HM, Meili D, Rassi A, Desviat LR, Perez B, et al. Pseudoexon exclusion by antisense therapy in 6-pyruvoyl-tetrahydropterin synthase deficiency. Hum Mutat. 2011;32:1019–27.
Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thony B, Shen N, et al. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet. 2017;100:257–66.
Tondo M, Calpena E, Arriola G, Sanz P, Martorell L, Ormazabal A, et al. Clinical, biochemical, molecular and therapeutic aspects of 2 new cases of 2-aminoadipic semialdehyde synthase deficiency. Mol Genet Metab. 2013;110:231–6.
Merinero B, Alcaide P, Martin-Hernandez E, Morais A, Garcia-Silva MT, Quijada-Fraile P, et al. Four Years' Experience in the Diagnosis of Very Long-Chain Acyl-CoA Dehydrogenase Deficiency in Infants Detected in Three Spanish Newborn Screening Centers. JIMD Rep. 2018;39:63–74
Meili D, Kralovicova J, Zagalak J, Bonafe L, Fiori L, Blau N, et al. Disease-causing mutations improving the branch site and polypyrimidine tract: pseudoexon activation of LINE-2 and antisense Alu lacking the poly(T)-tail. Hum Mutat. 2009;30:823–31.
Wilcken B. Recent advances in newborn screening. J Inherit Metab Dis. 2007;30:129–33.
Vockley J, Rinaldo P, Bennett MJ, Matern D, Vladutiu GD. Synergistic heterozygosity: disease resulting from multiple partial defects in one or more metabolic pathways. Mol Genet Metab. 2000;71:10–18.
Boneh A, Andresen BS, Gregersen N, Ibrahim M, Tzanakos N, Peters H, et al. VLCAD deficiency: pitfalls in newborn screening and confirmation of diagnosis by mutation analysis. Mol Genet Metab. 2006;88:166–70.
Nguyen MT, Charlebois K. The clinical utility of whole-exome sequencing in the context of rare diseases - the changing tides of medical practice. Clin Genet. 2015;88:313–9.
Yu HC, Sloan JL, Scharer G, Brebner A, Quintana AM, Achilly NP, et al. An X-linked cobalamin disorder caused by mutations in transcriptional coregulator HCFC1. Am J Hum Genet. 2013;93:506–14.
Pupavac M, Watkins D, Petrella F, Fahiminiya S, Janer A, Cheung W, et al. Inborn Error of Cobalamin Metabolism Associated with the Intracellular Accumulation of Transcobalamin-Bound Cobalamin and Mutations in ZNF143, Which Codes for a Transcriptional Activator. Hum Mutat. 2016.
Quintana AM, Yu HC, Brebner A, Pupavac M, Geiger EA, Watson A, et al. Mutations in THAP11 cause an inborn error of cobalamin metabolism and developmental abnormalities. Hum Mol Genet. 2017;26:2838–49.
Narravula A, Garber KB, Askree SH, Hegde M, Hall PL. Variants of uncertain significance in newborn screening disorders: implications for large-scale genomic sequencing. Genet Med. 2017;19:77–82.
Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L et al. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Genet Med. 2018.
Varela-Lema L, Paz-Valinas L, Atienza-Merino G, Zubizarreta-Alberdi R, Villares RV, Lopez-Garcia M. Appropriateness of newborn screening for classic galactosaemia: a systematic review. J Inherit Metab Dis. 2016;39:633–49.
Pavey AR, Bodian DL, Vilboux T, Khromykh A, Hauser NS, Huddleston K, et al. Utilization of genomic sequencing for population screening of immunodeficiencies in the newborn. Genet Med. 2017;19:1367–75.
Gueant JL, Chery C, Oussalah A, Nadaf J, Coelho D, Josse T, et al. APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients. Nat Commun. 2018;9:67.
Falkenberg KD, Braverman NE, Moser AB, Steinberg SJ, Klouwer FCC, Schluter A, et al. Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder. Am J Hum Genet. 2017;101:965–76.
Wevers RA, Blau N. Think big - think omics. J Inherit Metab Dis. 2018;41:281–3.
Del Mar Amador M, Colsch B, Lamari F, Jardel C, Ichou F, Rastetter A, et al. Targeted versus untargeted omics - the CAFSA story. J Inherit Metab Dis. 2018;41:447–56.
van Karnebeek CDM, Wortmann SB, Tarailo-Graovac M, Langeveld M, Ferreira CR, van de Kamp JM, et al. The role of the clinician in the multi-omics era: are you ready? J Inherit Metab Dis. 2018;41:571–82.
Schwarze K, Buchanan J, Taylor JC, Wordsworth S. Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature. Genet Med. 2018.
Acknowledgements
We thank the parents of the newborns for their kind collaboration in this work. We are also grateful to the newborn screening centers for the detection of infants with a suspected inborn error of metabolism. This work was funded in part by grant PI16/00573, B2017/BMD-3721, the Fundación Isabel Gemio and the Fundación La Caixa (LCF/PR/PR16/11110018), an institutional grant from the Fundación Ramón Areces to the Centro de Biología Molecular Severo Ochoa, and the European Regional Development Fund.
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Navarrete, R., Leal, F., Vega, A.I. et al. Value of genetic analysis for confirming inborn errors of metabolism detected through the Spanish neonatal screening program. Eur J Hum Genet 27, 556–562 (2019). https://doi.org/10.1038/s41431-018-0330-0
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DOI: https://doi.org/10.1038/s41431-018-0330-0
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