Next-Generation Diagnostics: Gene Panel, Exome, or Whole Genome?

Human Mutation

Volumn 36, Issue 6, 2015, Pages 648-655

  Sun, Yu ^a,c   Ruivenkamp, Claudia A L ^a   Hoffer, Mariëtte J V ^a   Vrijenhoek, Terry ^b   Kriek, Marjolein ^a   van Asperen, Christi J ^a   den Dunnen, Johan T ^a   Santen, Gijs W E ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

Exome sequencing; Genome sequencing; Intellectual disability; NGS

Indexed keywords

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; EXOME; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; GENE IDENTIFICATION; GENETIC LINKAGE; GENETIC VARIABILITY; HUMAN; INTELLECTUAL IMPAIRMENT; MOLECULAR DIAGNOSTICS; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL; SEQUENCE ANALYSIS; WHOLE EXOME SEQUENCING; WHOLE GENOME SEQUENCING; GENETIC SCREENING; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STANDARDS;

EXOME; GENETIC TESTING; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 84929512492     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22783     Document Type: Article

References (23)

1. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, et al. 2011. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 3:65ra4.
2. Berg JS, Amendola LM, Eng C, VanAllen E, Gray SW, Wagle N, Rehm HL, DeChene ET, Dulik MC, Hisama FM, Burke W, Spinner NB, et al. 2013. Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium. Genet Med 15:860-867.
3. deLigt J, Willemsen MH, vanBon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, deVries P, Gilissen C, Del Rosario M, Hoischen A, et al. 2012. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367:1921-1929.
4. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
5. Dorschner MO, Amendola LM, Turner EH, Robertson PD, Shirts BH, Gallego CJ, Bennett RL, Jones KL, Tokita MJ, Bennett JT, Kim JH, Rosenthal EA, et al. 2013. Actionable, pathogenic incidental findings in 1000 participants' exomes. Am J Hum Genet 93:631-640.
6. Gilissen C, Hehir-Kwa JY, Thung DT, vande Vorst M, vanBon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, et al. 2014. Genome sequencing identifies major causes of severe intellectual disability. Nature 511:344-347.
7. Hoischen A, vanBon BW, Rodriguez-Santiago B, Gilissen C, Vissers LE, deVries P, Janssen I, vanLier B, Hastings R, Smithson SF, Newbury-Ecob R, Kjaergaard S, et al. 2011. De novo nonsense mutations in ASXL1 cause Bohring-Opitz syndrome. Nat Genet 43:729-731.
8. Knoppers BM, Avard D, Senecal K, Zawati MH. 2014. Return of whole-genome sequencing results in paediatric research: a statement of the P3G international paediatrics platform. Eur J Hum Genet 22:3-5.
9. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
10. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079.
11. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303.
12. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, et al. 2010a. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42:790-793.
13. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. 2010b. Exome sequencing identifies the cause of a Mendelian disorder. Nat Genet 42:30-35.
14. Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, Wood NW, Hambleton S, Burns SO, Thrasher AJ, Kumararatne D, Doffinger R, et al. 2012. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 28:2747-2754.
15. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, et al. 2012. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380:1674-1682.
16. Rigter T, Henneman L, Kristoffersson U, Hall A, Yntema HG, Borry P, Tonnies H, Waisfisz Q, Elting MW, Dondorp WJ, Cornel MC. 2013. Reflecting on earlier experiences with unsolicited findings: points to consider for next-generation sequencing and informed consent in diagnostics. Hum Mutat 34:1322-1328.
17. Santen GW, Aten E, Sun Y, Almomani R, Gilissen C, Nielsen M, Kant SG, Snoeck IN, Peeters EA, Hilhorst-Hofstee Y, Wessels MW, den Hollander NS, et al. 2012. Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome. Nat Genet 44:379-380.
18. Swen JJ, Nijenhuis M, de BA, Grandia L, Maitland-van der Zee AH, Mulder H, Rongen GA, vanSchaik RH, Schalekamp T, Touw DJ, vander Weide J, Wilffert B, et al. 2011. Pharmacogenetics: from bench to byte-an update of guidelines. Clin Pharmacol Ther 89:662-673.
19. Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, et al. 2012. Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome. Nat Genet 44:376-378.
20. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. 2013. From FastQ Data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinform 43:11.10.1-11.10.33.
21. Vrijenhoek T, Kraaijeveld K, Elferink M, deLigt J, Kranendonck E, Santen GW, Nijman I, Butler D, Claes G, Costessi A, Dorlijn W, Eyndhoven W, et al. 2015. Next-generation sequencing-based genome diagnostics across clinical genetics centers-implementation choices and their effects. Eur J Hum Genet. doi: 10.1038/ejhg.2014.279 [Epub ahead of print]
22. Weiss MM, Vander Zwaag B, Jongbloed JD, Vogel MJ, Bruggenwirth HT, Lekanne Deprez RH, Mook O, Ruivenkamp CA, vanSlegtenhorst MA, vanden Wijngaard A, Waisfisz Q, Nelen MR, et al. 2013. Best practice guidelines for the use of next-ge sequencing applications in genome diagnostics: a national collaborative study of Dutch genome diagnostic laboratories. Hum Mutat 34:1313-1321.
23. Yu JH, Harrell TM, Jamal SM, Tabor HK, Bamshad MJ. 2014. Attitudes of genetics professionals toward the return of incidental results from exome and whole-genome sequencing. Am J Hum Genet 95:77-84.