Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing

Genetics in Medicine

Volumn 17, Issue 5, 2015, Pages 337-347

  Bhattacharjee, Arindam ^a   Sokolsky, Tanya ^a   Wyman, Stacia K ^a   Reese, Martin G ^b   Puffenberger, Erik ^c   Strauss, Kevin ^c   Morton, Holmes ^c   Parad, Richard B ^d   Naylor, Edwin W ^a,e  

^a Parabase Genomics   (United States)

^b Clinic for Special Children ^*  (United States)

^c The Clinic for Special Children   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Neonate; newborn screening; next generation sequencing; second tier testing

Indexed keywords

DNA;

ARTICLE; BLOOD ANALYSIS; CLINICAL ARTICLE; DIAGNOSTIC TEST; DNA ISOLATION; DNA SEQUENCE; EXOME; GENE MUTATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HUMAN; NEWBORN; NEWBORN DISEASE; NEWBORN SCREENING; NEXT GENERATION SEQUENCING; PARALLEL DESIGN; QUALITY CONTROL; RETROSPECTIVE STUDY; SENSITIVITY ANALYSIS; ALGORITHM; BIOLOGY; GENETIC VARIATION; HIGH THROUGHPUT SEQUENCING; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; WORKFLOW;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENETIC TESTING; GENETIC VARIATION; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT, NEWBORN; NEONATAL SCREENING; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; WORKFLOW;

EID: 84928898166     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2014.117     Document Type: Article

References (40)

1. Christianson A, Howson CP, Modell B. Global Report on Birth Defects: The Hidden Toll of Dying and Disabled Children. March of Dimes Birth Defects Foundation: White Plains, NY, 2006.
2. Landau YE, Lichter-Konecki U, Levy HL. Genomics in newborn screening. J Pediatr 2014;164:14-19.
3. The President's Council on Bioethics. http://www.bioethics.gov/reports/newborn-screening/index.html. 2008. Accessed 28 August 2014.
4. Costa T, Scriver CR, Childs B. The effect of Mendelian disease on human health: a measurement. Am J Med Genet 1985;21:231-242.
5. Kumar P, Radhakrishnan J, Chowdhary MA, Giampietro PF. Prevalence and patterns of presentation of genetic disorders in a pediatric emergency department. Mayo Clin Proc 2001;76:777-783.
6. 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;4:154ra135.
7. Kaiser J. Genomics. Researchers to explore promise, risks of sequencing newborns' DNA. Science 2013;341:1163.
8. Ng SB, Turner EH, Robertson PD, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009;461:272-276.
9. de Ligt J, Willemsen MH, van Bon BW, et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 2012;367:1921-1929.
10. Shashi V, McConkie-Rosell A, Rosell B, et al. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders. Genet Med 2014;16:176-182.
11. Yang Y, Muzny DM, Reid JG, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369:1502-1511.
12. Guthrie R, Susi A. A simple phenylalanine method for detecting phenylketonuria in large populations of newborn infants. Pediatrics 1963;32:338-343.
13. Dussault JH, Laberge C. [Thyroxine (T4) determination by radioimmunological method in dried blood eluate: new diagnostic method of neonatal hypothyroidism?]. Union Med Can 1973;102:2062-2064.
14. Crossley JR, Elliott RB, Smith PA. Dried-blood spot screening for cystic fibrosis in the newborn. Lancet 1979;1:472-474.
15. Naylor EW. Recent developments in neonatal screening. Semin Perinatol 1985;9:232-249.
16. Pang SY, Wallace MA, Hofman L, et al. Worldwide experience in newborn screening for classical congenital adrenal hyperplasia due to 21-hydroxylase deficiency. Pediatrics 1988;81:866-874.
17. Naylor EW, Chace DH. Automated tandem mass spectrometry for mass newborn screening for disorders in fatty acid, organic acid, and amino acid metabolism. J Child Neurol 1999;14(suppl 1):S4-S8.
18. Chace DH, Kalas TA, Naylor EW. The application of tandem mass spectrometry to neonatal screening for inherited disorders of intermediary metabolism. Annu Rev Genomics Hum Genet 2002;3:17-45.
19. Herrmann MG, Dobrowolski SF, Wittwer CT. Rapid beta-globin genotyping by multiplexing probe melting temperature and color. Clin Chem 2000;46:425-428.
20. Spence WC, Paulus-Thomas J, Orenstein DM, Naylor EW. Neonatal screening for cystic fibrosis: addition of molecular diagnostics to increase specificity. Biochem Med Metab Biol 1993;49:200-211.
21. Comeau AM, Parad RB, Dorkin HL, et al. Population-based newborn screening for genetic disorders when multiple mutation DNA testing is incorporated: a cystic fibrosis newborn screening model demonstrating increased sensitivity but more carrier detections. Pediatrics 2004;113:1573-1581.
22. Andresen BS, Dobrowolski SF, O'Reilly L, et al. Medium-chain acyl-CoA dehydrogenase (MCAD) mutations identified by MS/MS-based prospective screening of newborns differ from those observed in patients with clinical symptoms: identification and characterization of a new, prevalent mutation that results in mild MCAD deficiency. Am J Hum Genet 2001;68:1408-1418.
23. Naylor EW, Hoffman EP, Paulus-Thomas J, et al. Neonatal screening for Duchenne muscular dystrophy: reconsideration based on molecular diagnosis and potential therapeutics. Screening 1992;1:99-113.
24. Dobrowolski SF, Banas RA, Suzow JG, Berkley M, Naylor EW. Analysis of common mutations in the galactose-1-phosphate uridyl transferase gene: new assays to increase the sensitivity and specificity of newborn screening for galactosemia. J Mol Diagn 2003;5:42-47.
25. Puck JM. Neonatal screening for severe combined immune deficiency. Curr Opin Allergy Clin Immunol 2007;7:522-527.
26. Saavedra-Matiz CA, Isabelle JT, Biski CK, et al. Cost-effective and scalable DNA extraction method from dried blood spots. Clin Chem 2013;59:1045-1051.
27. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-1760.
28. 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;20:1297-1303.
29. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011;43:491-498.
30. Richards CS, Bale S, Bellissimo DB, et al.; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 2008;10:294-300.
31. Beyan H, Down TA, Ramagopalan SV, et al. Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans. Genome Res 2012;22:2138-2145.
32. Aberg KA, Xie LY, Nerella S, Copeland WE, Costello EJ, van den Oord EJ. High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot. Epigenetics 2013;8: 542-547.
33. Hollegaard MV, Grauholm J, Nielsen R, Grove J, Mandrup S, Hougaard DM. Archived neonatal dried blood spot samples can be used for accurate whole genome and exome-targeted next-generation sequencing. Mol Genet Metab 2013;110:65-72.
34. Meynert AM, Bicknell LS, Hurles ME, Jackson AP, Taylor MS. Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 2013;14:195.
35. Ajay SS, Parker SC, Abaan HO, Fajardo KV, Margulies EH. Accurate and comprehensive sequencing of personal genomes. Genome Res 2011;21:1498-1505.
36. Green RC, Berg JS, Grody WW, et al.; American College of Medical Genetics and Genomics. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-574.
37. Prach L, Koepke R, Kharrazi M, et al.; California Cystic Fibrosis Newborn Screening Consortium. Novel CFTR variants identified during the first 3 years of cystic fibrosis newborn screening in California. J Mol Diagn 2013;15: 710-722.
38. Dewey FE, Grove ME, Pan C, et al. Clinical interpretation and implications of whole-genome sequencing. JAMA 2014;311:1035-1045.
39. Singleton MV, Guthery SL, Voelkerding KV, et al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet 2014;94:599-610.
40. Mueller PW, Lyons J, Kerr G, Haase CP, Isett RB. Standard enrichment methods for targeted next-generation sequencing in high-repeat genomic regions. Genet Med 2013;15:910-911.