Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability

Genetics in Medicine

Volumn 18, Issue 9, 2016, Pages 949-956

  Monroe, Glen R ^a   Frederix, Gerardus W ^b   Savelberg, Sanne M C ^a   De Vries, Tamar I ^a   Duran, Karen J ^a   Van Der Smagt, Jasper J ^a   Terhal, Paulien A ^a   Van Hasselt, Peter M ^c   Kroes, Hester Y ^a   Verhoeven Duif, Nanda M ^a   Nijman, Isaäc J ^a   Carbo, Ellen C ^a   Van Gassen, Koen L ^a   Knoers, Nine V ^a   Hövels, Anke M ^b   Van Haelst, Mieke M ^a   Visser, Gepke ^c   Van Haaften, Gijs ^a  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

clinical management; cost analysis; intellectual disability; whole exome sequencing

Indexed keywords

ARTICLE; CHILD; CLINICAL ARTICLE; COST BENEFIT ANALYSIS; COST CONTROL; EXOME; FEMALE; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; INTELLECTUAL IMPAIRMENT; MALE; MEDICAL RECORD REVIEW; MOLECULAR DIAGNOSIS; RETROSPECTIVE STUDY; COST; DNA SEQUENCE; ECONOMICS; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; WHOLE EXOME SEQUENCING;

COSTS AND COST ANALYSIS; EXOME; FEMALE; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTELLECTUAL DISABILITY; MALE; SEQUENCE ANALYSIS, DNA; WHOLE EXOME SEQUENCING;

EID: 84985041034     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2015.200     Document Type: Article

References (36)

1. Ng SB, Buckingham KJ, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010; 42: 30-35
2. 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: 19096-19101
3. 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: 121-127
4. Hall JG, Powers EK, Mcllvaine RT, Ean VH. The frequency, and financial burden of genetic disease in a pediatric hospital. Am J Med Genet 1978; 1: 417-436
5. Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. Exome sequencing can improve diagnosis, and alter patient management. Sci Transl Med 2012; 4: 138ra78
6. Farwell KD, Shahmirzadi L, El-Khechen D, et al. Enhanced utility of familycentered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med 2015; 17: 578-586
7. Lee H, Deignan JL, Dorrani N, et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 2014; 312: 1880-1887
8. Srivastava S, Cohen JS, Vernon H, et al. Clinical whole exome sequencing in child neurology practice. Ann Neurol 2014; 76: 473-483
9. Iglesias A, Anyane-Yeboa K, Wynn J, et al. The usefulness of whole-exome sequencing in routine clinical practice. Genet Med 2014; 16: 922-931
10. Engbers HM, Berger R, van Hasselt P, et al. Yield of additional metabolic studies in neurodevelopmental disorders. Ann Neurol 2008; 64: 212-217
11. Strømme P. Aetiology in severe, and mild mental retardation: a population-based study of Norwegian children. Dev Med Child Neurol 2000; 42: 76-86
12. Phillips KA, Ann Sakowski J, Trosman J, Douglas MP, Liang SY, Neumann P. The economic value of personalized medicine tests: what we know, and what we need to know. Genet Med 2014; 16: 251-257
13. van Nimwegen KJ, Schieving JH, Willemsen MA, et al. The diagnostic pathway in complex paediatric neurology: a cost analysis. Eur J Paediatr Neurol 2015; 19: 233-239
14. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014; 46: 310-315
15. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A; NISC Comparative Sequencing Program. Distribution, and intensity of constraint in mammalian genomic sequence. Genome Res 2005; 15: 901-913
16. Adzhubei IA, Schmidt S, Peshkin L, et al. A method, and server for predicting damaging missense mutations. Nat Methods 2010; 7: 248-249
17. 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: 1073-1081
18. Tan SS, Bouwmans CA, Rutten FF, Hakkaart-van Roijen L. Update of the Dutch manual for costing in economic evaluations. Int J Technol Assess Health Care 2012; 28: 152-158
19. Hamdan FF, Srour M, Capo-Chichi JM, et al. De novo mutations in moderate or severe intellectual disability. PLoS Genet 2014; 10: e1004772
20. Rauch A, Wieczorek D, Graf E, et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 2012; 380: 1674-1682
21. Kuechler A, Willemsen MH, Albrecht B, et al. De novo mutations in beta-catenin (CTNNB1) appear to be a frequent cause of intellectual disability: expanding the mutational, and clinical spectrum. Hum Genet 2015; 134: 97-109
22. Ockeloen CW, Willemsen MH, De Munnik S, et al. Further delineation of the KBG syndrome phenotype caused by ANKRD11 aberrations. Eur J Hum Genet 2015; 23: 1176-1185
23. Bragin E, Chatzimichali EA, Wright CF, et al. DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence, and copy-number variation. Nucleic Acids Res 2014; 42(Database issue): D993-D1000
24. Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature 2015; 519: 223-228
25. Firth HV, Richards SM, Bevan AP, et al. DECIPHER: Database of Chromosomal Imbalance, and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet 2009; 84: 524-533
26. Henderson LB, Applegate CD, Wohler E, Sheridan MB, Hoover-Fong J, Batista DA. The impact of chromosomal microarray on clinical management: a retrospective analysis. Genet Med 2014; 16: 657-664
27. Hochstenbach R, van Binsbergen E, Engelen J, et al. Array analysis, and karyotyping: workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands. Eur J Med Genet 2009; 52: 161-169
28. 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
29. Wright CF, Fitzgerald TW, Jones WD, et al. DDD study. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet 2015; 385: 1305-1314
30. Yang Y, Muzny DM, Xia F, et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 2014; 312: 1870-1879
31. Atwal PS, Brennan ML, Cox R, et al. Clinical whole-exome sequencing: are we there yet? Genet Med 2014; 16: 717-719
32. Need AC, Shashi V, Hitomi Y, et al. Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 2012; 49: 353-361
33. 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
34. Soden SE, Saunders CJ, Willig LK, et al. Effectiveness of exome, and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 2014; 6: 265ra168
35. Campeau PM, Kasperaviciute D, Lu JT, et al. The genetic basis of DOORS syndrome: an exome-sequencing study. Lancet Neurol 2014; 13: 44-58
36. Patton MA, Krywawych S, Winter RM, Brenton DP, Baraitser M. DOOR syndrome (deafness, onycho-osteodystrophy, and mental retardation): elevated plasma, and urinary 2-oxoglutarate in three unrelated patients. Am J Med Genet 1987; 26: 207-215