[en] The range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview of NGS capacities on DBS-extracted DNA but did not focus on the identification of specific disorders. We thus aimed to demonstrate that NGS was reliable for detecting pathogenic mutations on genomic material extracted from DBS. Assuming the future implementation of NGS technologies into newborn screening (NBS), we conducted a pilot study on fifteen patients with inherited metabolic disorders. Blood was collected from DBS. Whole-exome sequencing was performed, and sequences were analyzed with a specific focus on genes related to NBS. Results were compared to the known pathogenic mutations previously identified by Sanger sequencing. Causal mutations were readily characterized, and multiple polymorphisms have been identified. According to variant database prediction, an unexplained homozygote pathogenic mutation, unrelated to patient's disorder, was also found in one sample. While amount and quality of DBS-extracted DNA are adequate to identify causal mutations by NGS, bioinformatics analysis revealed critical drawbacks: coverage fluctuations between regions, difficulties in identifying insertions/deletions, and inconsistent reliability of database-referenced variants. Nevertheless, results of this study lead us to consider future perspectives regarding "next-generation" NBS.
Disciplines :
Genetics & genetic processes
Author, co-author :
BOEMER, François ; Centre Hospitalier Universitaire de Liège - CHU > Service de génétique
Fasquelle, Corinne ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > GIGA-R : Génétique humaine
D'OTREPPE DE BOUVETTE, Stéphanie ; Centre Hospitalier Universitaire de Liège - CHU > Frais communs Biologie clinique - Pool assistants
JOSSE, Claire ; Centre Hospitalier Universitaire de Liège - CHU > Service d'oncologie médicale
DIDEBERG, Vinciane ; Centre Hospitalier Universitaire de Liège - CHU > Service de génétique
SEGERS, Karin ; Centre Hospitalier Universitaire de Liège - CHU > Service de génétique
GUISSARD, Valérie ; Centre Hospitalier Universitaire de Liège - CHU > Service de génétique
CAPRARO, Valérie ; Centre Hospitalier Universitaire de Liège - CHU > Secteur commun biologie moléculaire
Debray, François-Guillaume ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Maladies métaboliques d'origine génétique
Bours, Vincent ; Université de Liège - ULiège > Département des sciences biomédicales et précliniques > GIGA-R : Génétique humaine
Language :
English
Title :
A next-generation newborn screening pilot study: NGS on dried blood spots detects causal mutations in patients with inherited metabolic diseases.
Beale, S., Sanderson, D., Sanniti, A., Dundar, Y. & Boland, A. A scoping study to explore the cost-effectiveness of next-generation sequencing compared with traditional genetic testing for the diagnosis of learning disabilities in children. Heal. Technol Assess 19, 1-90 (2015).
Tang, W. et al. DNA extraction from formalin-fixed, paraffin-embedded tissue. Cold Spring Harb Protoc 2009, pdbprot5138 (2009).
Butler, J. M. The future of forensic DNAanalysis. Philos Trans R Soc L. B Biol Sci 370, (2015).
CLSI. Blood Collection on Filter Paper for Newborn Screening Programs; Approved Standard-Sixth Edition. Clin. Lab. Stand. Inst. Doc. 33, (2013).
Schrynemackers-Pitance, P. & Schoos-Barbette, S. Determination of aromatic and neutral aminoacids by HPLC in blood specimens collected on filter paper. Clin Chim Acta 166, 91-97 (1987).
Shokati, T. et al. Quantification of the Immunosuppressant Tacrolimus on Dried Blood Spots Using LC-MS/MS. J Vis Exp https://doi.org/10.3791/52424 (2015).
Tretzel, L. et al. Use of dried blood spots in doping control analysis of anabolic steroid esters. J Pharm Biomed Anal 5, 21-30 (2014).
Napierala Mavedzenge, S. et al. Finger Prick Dried Blood Spots for HIV Viral Load Measurement in Field Conditions in Zimbabwe. PLoS One 10, e0126878 (2015).
Barben, J. et al. Retrospective analysis of stored dried blood spots from children with cystic fibrosis and matched controls to assess the performance of a proposed newborn screening protocol in Switzerland. J Cyst Fibros 11, 332-336 (2012).
Hollegaard, M. V. et al. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-Targeted next-generation sequencing. Mol Genet Metab 110, 65-72 (2013).
Cantarel, B. L. et al. Analysis of archived residual newborn screening blood spots after whole genome amplification. BMC Genomics 16, 602 (2015).
Poulsen, J. B. et al. High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA. PLoS One 11, e0153253 (2016).
Burgard, P. et al. Newborn screening programmes in Europe; arguments and efforts regarding harmonization. Part 2-From screening laboratory results to treatment, follow-up and quality assurance. in. Journal of Inherited Metabolic Disease 35, 613-625 (2012).
Loeber, J. G. et al. Newborn screening programmes in Europe; arguments and efforts regarding harmonization. Part 1-From blood spot to screening result. in. Journal of Inherited Metabolic Disease 35, 603-611 (2012).
Moat, S. J., Bradley, D. M., Salmon, R., Clarke, A. & Hartley, L. Newborn bloodspot screening for Duchenne muscular dystrophy: 21 years experience in Wales (UK). Eur. J. Hum. Genet. 21, 1049-53 (2013).
Phan, H. C., Taylor, J. L., Hannon, H. & Howell, R. Newborn screening for spinal muscular atrophy: Anticipating an imminent need. Semin. Perinatol. 39, 217-229 (2015).
Strauss, K., Puffenberger, E. & Morton, D. Maple Syrup Urine Disease. (GeneReviews® [Internet]. University of Washington, 2013).
Yang, H. & Wang, K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc 10, 1556-1566 (2015).
NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 44, D7-D19 (2015).
Schwarz, J. M., Rödelsperger, C., Schuelke, M. & Seelow, D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat. Methods 7, 575-576 (2010).
Moreno, J. C. et al. Inactivating Mutations in the Gene for Thyroid Oxidase 2 (THOX2) and Congenital Hypothyroidism. N. Engl. J. Med. 347, 95-102 (2002).
Grasberger, H. Defects of thyroidal hydrogen peroxide generation in congenital hypothyroidism. Molecular and Cellular Endocrinology 322, 99-106 (2010).
Meienberg, J., Bruggmann, R., Oexle, K. & Matyas, G. Clinical sequencing: is WGS the better WES? Hum. Genet. 135, 359-362 (2016).
Chace, D. H., Kalas, T. A. & Naylor, E. W. The application of tandem mass spectrometry to neonatal screening for inherited disorders of intermediary metabolism. Annu Rev Genomics Hum Genet 3, 17-45 (2002).
Kronn, D., Mofidi, S., Braverman, N. & Harris, K. Diagnostic guidelines for newborns who screen positive in newborn screening. Genet Med 12, S251-5 (2010).
Ombrone, D., Giocaliere, E., Forni, G., Malvagia, S. & la Marca, G. Expanded newborn screening by mass spectrometry: New tests, future perspectives. Mass Spectrom Rev 35, 71-84 (2016).
Wilson, J. M. G. & Jungner, G. Principles and practice of screening for disease. (WHO, 1968).
Francescatto, L. & Katsanis, N. Newborn screening and the era of medical genomics. Semin Perinatol 39, 617-622 (2015).
Qian, J. et al. Applying targeted next generation sequencing to dried blood spot specimens from suspicious cases identified by tandem mass spectrometry-based newborn screening. J. Pediatr. Endocrinol. Metab. https://doi.org/10.1515/jpem-2017-0003 (2017).
Zurynski, Y. et al. Australian children living with rare diseases: experiences of diagnosis and perceived consequences of diagnostic delays. Orphanet J. Rare Dis. 12, 68 (2017).
Bailey, D. B. Jr. & Gehtland, L. Newborn screening: evolving challenges in an era of rapid discovery. JAMA 313, 1511-1512 (2015).
Lewis, M. A. et al. Supporting Parental Decisions About Genomic Sequencing for Newborn Screening: The NC NEXUS Decision Aid. Pediatrics 137(Suppl), S16-23 (2016).
Howard, H. C. et al. Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. Eur J Hum Genet 23, 1593-1600 (2015).
Almannai, M., Marom, R. & Sutton, V. R. Newborn screening: A review of history, recent advancements, and future perspectives in the era of next generation sequencing. Curr Opin Pediatr 28, 694-699 (2016).
Knoppers, B. M., Senecal, K., Borry, P. & Avard, D. Whole-genome sequencing in newborn screening programs. Sci Transl Med 6, 229cm2 (2014).
Botkin, J. R. & Rothwell, E. Whole Genome Sequencing and Newborn Screening. Curr Genet Med Rep 4, 1-6 (2016).
McEwen, J. E. et al. The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: reflections on an ongoing experiment. Annu Rev Genomics Hum Genet 15, 481-505 (2014).
St Julien, K. R. et al. High quality genome-wide genotyping from archived dried blood spots without DNA amplification. PLoS One 8, e64710 (2013).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-8 (2011).
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44, W3-W10 (2016).
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Br. Bioinform 14, 178-192 (2013).