Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization

npj Genomic Medicine

Volumn 3, Issue 1, 2018, Pages

  Farnaes, Lauge ^a,b   Hildreth, Amber ^a,b   Sweeney, Nathaly M ^a,b   Clark, Michelle M ^a   Chowdhury, Shimul ^a   Nahas, Shareef ^a   Cakici, Julie A ^a   Benson, Wendy ^a   Kaplan, Robert H ^c   Kronick, Richard ^d   Bainbridge, Matthew N ^a   Friedman, Jennifer ^a,b,e   Gold, Jeffrey J ^a,e   Ding, Yan ^a   Veeraraghavan, Narayanan ^a   Dimmock, David ^a   Kingsmore, Stephen F ^a  

^a RADY CHILDREN S INSTITUTE FOR GENOMIC MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c TorreyPines Therapeutics Inc   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTELY ILL PATIENT; ARTICLE; CHILDHOOD MORTALITY; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; COST CONTROL; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; FEMALE; GENETIC SCREENING; HOSPITALIZATION COST; HUMAN; INFANT; INFANT DISEASE; MALE; MORTALITY RISK; PALLIATIVE THERAPY; PRIORITY JOURNAL; RAPID WHOLE GENOME SEQUENCING; RETROSPECTIVE STUDY; RISK REDUCTION; SENSITIVITY AND SPECIFICITY; WHOLE GENOME SEQUENCING;

EID: 85044962474     PISSN: None     EISSN: 20567944     Source Type: Journal    
DOI: 10.1038/s41525-018-0049-4     Document Type: Article

References (35)

1. March of Dimes Foundation Data Book for Policy Makers. Maternal, Infant, and Child Health in the United States 2016. http://www.marchofdimes.org/March-of-Dimes-2016-Databook.pdf. Accessed 27 May 2016.
2. Xu, J., Murphy, S. L., Kochanek, K. D. & Arias, E. Mortality in the United States, 2015. NCHS Data Brief 267, 1-8 (2016).
3. Yoon, P. W. et al. Contribution of birth defects and genetic diseases to pediatric hospitalizations. A population-based study. Arch. Pediatr. Adolesc. Med. 151, 1096-1103 (1997).
4. O'Malley, M. & Hutcheon, R. G. Genetic disorders and congenital malformations in pediatric long-term care. J. Am. Med. Dir. Assoc. 8, 332-334 (2007).
5. Berry, M. A., Shah, P. S., Brouillette, R. T. & Hellmann, J. Predictors of mortality and length of stay for neonates admitted to children's hospital neonatal intensive care units. J. Perinatol. 28, 297-302 (2008).
6. Petrikin, J. E., Willig, L. K., Smith, L. D. & Kingsmore, S. F. Rapid whole genome sequencing and precision neonatology. Semin. Perinatol. 39, 623-631 (2015).
7. Daoud, H. et al. Next-generation sequencing for diagnosis of rare diseases in the neonatal intensive care unit. CMAJ 188, E254-E260 (2016).
8. Phillips, K. A. et al. Making genomic medicine evidence-based and patient-centered: a structured review and landscape analysis of comparative effectiveness research. Genet. Med. 19, 1081-1091 (2017).
9. Willig, L. K. et al. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir. Med. 3, 377-387 (2015).
10. Wymer, K. M., Anderson, B. B., Wilkens, A. A. & Gundeti, M. S. Megacystis microcolon intestinal hypoperistalsis syndrome: case series and updated review of the literature with an emphasis on urologic management. J. Pediatr. Surg. 51, 1565-1573 (2016).
11. Raphael, B. P. et al. Cisapride improves enteral tolerance in pediatric short-bowel syndrome with dysmotility. J. Pediatr. Gastroenterol. Nutr. 52, 590-594 (2011).
12. Hayeems, R. Z. et al. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur. J. Hum. Genet. 25, 1303-1312 (2017).
13. Hildreth, A. et al. Rapid whole-genome sequencing identifies a novel homozygous NPC1 variant associated with Niemann-Pick type C1 disease in a 7-weekold male with cholestasis. Cold Spring Harb Mol Case Stud. 3 (2017).
14. Lam, V., Kain, N., Joynt, C. & van Manen, M. A. A descriptive report of end-of-life care practices occurring in two neonatal intensive care units. Palliat. Med. 30, 971-978 (2016).
15. Oberender, F. & Tibballs, J. Withdrawal of life-support in paediatric intensive care-a study of time intervals between discussion, decision and death. BMC Pediatr. 11, 39 (2016).
16. Lee, H. P. et al. Outcome of Alagille syndrome patients who had previously received Kasai operation during infancy: a single center study. Pediatr. Gastroenterol. Hepatol. Nutr. 18, 175-179 (2015).
17. Kaye, A. J. et al. Effect of Kasai procedure on hepatic outcome in Alagille syndrome. J. Pediatr. Gastroenterol. Nutr. 51, 319-321 (2010).
18. Emerick, K. M. et al. Features of Alagille syndrome in 92 patients: frequency and relation to prognosis. Hepatology 29, 822-829 (1999).
19. Milliman. 2017 US Organ and Tissue Transplant Cost. http://www.milliman.com/uploadedFiles/insight/2017/2017-Transplant-Report.pdf.
20. Pisano, T. et al. Early and effective treatment of KCNQ2 encephalopathy. Epilepsia 56, 685-691 (2015).
21. Numis, A. L. et al. KCNQ2 encephalopathy: delineation of the electroclinical phenotype and treatment response. Neurology 82, 368-370 (2014).
22. Kato, M. et al. Clinical spectrum of early onset epileptic encephalopathies caused by KCNQ2 mutation. Epilepsia 54, 1282-1287 (2013).
23. Milh, M. et al. Similar early characteristics but variable neurological outcome of patients with a de novo mutation of KCNQ2. Orphanet. J. Rare Dis. 8, 80 (2013).
24. Joshi, C. et al. Reducing the cost of the diagnostic odyssey in early onset epileptic encephalopathies. Biomed. Res. Int. 2016, 6421039 (2016).
25. Stanley, C. A. et al. Preoperative evaluation of infants with focal or diffuse congenital hyperinsulinism by intravenous acute insulin response tests and selective pancreatic arterial calcium stimulation. J. Clin. Endocrinol. Metab. 89, 288-296 (2004).
26. Hussain, K., Blankenstein, O., De Lonlay, P. & Christesen, H. T. Hyperinsulinaemic hypoglycaemia: biochemical basis and the importance of maintaining normoglycaemia during management. Arch. Dis. Child. 92, 568-570 (2007).
27. Menni, F. et al. Neurologic outcomes of 90 neonates and infants with persistent hyperinsulinemic hypoglycemia. Pediatrics 107, 476-479 (2001).
28. Farnaes L. et al. Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome. Cold Spring Harb. Mol. Case Stud. 3, https://doi.org/10.1101/mcs.a001776 (2017)
29. Lionel A. C. et al. Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test. Genet Med. https://doi.org/10.1038/gim.2017.119 (2017)
30. Stavropoulos, D. J. et al. Whole genome sequencing expands diagnostic utility and improves clinical management in pediatric medicine. NPJ Genom. Med. 1, 15012 (2016).
31. Stark, Z. et al. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genet. Med. 18, 1090-1096 (2016).
32. Stark, Z. et al. Prospective comparison of the cost-effectiveness of clinical wholeexome sequencing with that of usual care overwhelmingly supports early use and reimbursement. Genet. Med. 19, 867-874 (2017).
33. Chen, X. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 32, 1220-1222 (2016).
34. Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984 (2011).
35. Helmer-Hirschberg O. Analysis of the Future: The Delphi Method (RAND Corporation, Santa Monica, CA, 1967).