Deep sequencing of patient genomes for disease diagnosis: When will it become routine?

Science Translational Medicine

Volumn 3, Issue 87, 2011, Pages

  Kingsmore, Stephen F ^a,b   Saunders, Carol J ^b  

^a NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^b CHILDREN S MERCY HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COST BENEFIT ANALYSIS; DIAGNOSTIC ACCURACY; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HEREDITARY MOTOR SENSORY NEUROPATHY; HUMAN; HUMAN GENOME; MOLECULAR DIAGNOSIS; PRIORITY JOURNAL; REVIEW; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; TRANSLATIONAL RESEARCH; ARTICLE; DIFFERENTIAL DIAGNOSIS; DNA SEQUENCE; ECONOMICS; FORECASTING; GENOME; HIGH THROUGHPUT SEQUENCING; UTILIZATION REVIEW;

DIAGNOSIS, DIFFERENTIAL; FORECASTING; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 79959309141     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.3002695     Document Type: Review

References (32)

1. Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD). http://www.ncbi.nlm. nih.gov/omim.
2. T. Lialiaris, E. Mantadakis, D. Kareli, P. Mpountoukas, A. Tsalkidis, A. Chatzimichail, Frequency of genetic diseases and health coverage of children requiring admission in a general pediatric clinic of northern Greece. Ital. J. Pediatr. 36, 9 (2010).
3. T. Costa, C. R. Scriver, B. Childs, J. M. Opitz, J. F. Reynolds, The effect of Mendelian disease on human health: A measurement. Am. J. Med. Genet. 21, 231-242 (1985).
4. S. E. McCandless, J. W. Brunger, S. B. Cassidy, The burden of genetic disease on inpatient care in a children's hospital. Am. J. Hum. Genet. 74, 121-127 (2004).
5. A. Maddalena, S. Bale, S. Das, W. Grody, S. Richards; ACMG Laboratory Quality Assurance Committee, Technical standards and guidelines: Molecular genetic testing for ultra-rare disorders. Genet. Med. 7, 571-583 (2005).
6. American Society of Human Genetics Board of Directors-American College of Medical Genetics Board of Directors, Points to consider: Ethical, legal, and psychosocial implications of genetic testing in children and adolescents. Am. J. Hum. Genet. 57, 1233-1241 (1995).
7. M. A. Zoccoli, M. Chan, J. C. Erker, A. Ferreira-Gonzolas, I. M. Lubin, Nucleic Acid sequencing methods in diagnostic laboratory medicine; Approved guideline. NCCLS document MM9-A [ISBN 1-56238-558-5]. (NCCLS, Wayne, PA, 2004).
8. C. S. Richards, S. Bale, D. B. Bellissimo, S. Das, W. W. Grody, M. R. Hegde, E. Lyon, B. E. Ward; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee, ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet. Med. 10, 294-300 (2008).
9. K. Jensen, F. Murray, Intellectual property landscape of the human genome. Science 310, 239-240 (2005).
10. J. R. Lupski, J. G. Reid, C. Gonzaga-Jauregui, D. Rio Deiros, D. C. Chen, L. Nazareth, M. Bainbridge, H. Dinh, C. Jing, D. A. Wheeler, A. L. McGuire, F. Zhang, P. Stankiewicz, J. J. Halperin, C. Yang, C. Gehman, D. Guo, R. K. Irikat, W. Tom, N. J. Fantin, D. M. Muzny, R. A. Gibbs, Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362, 1181-1191 (2010).
11. M. N. Bainbridge, W. Wiszniewski, D. R. Murdock, J. Friedman, C. Gonzaga-Jauregui, I. Newsham, J. G. Reid, J. K. Fink, M. B. Morgan, M.-C. Gingras, D. M. Muzny, L. D. Hoang, S. Yousaf, J. R. Lupski, R. A. Gibbs, Whole-genome sequencing for optimized patient management. Sci. Transl. Med. 3, 87re3 (2011).
12. K. A. Wetterstrand, DNA sequencing costs: Data from the NHGRI large-scale genome sequencing program. www.genome.gov/sequencingcosts.
13. C. J. Bell, D. L. Dinwiddie, N. A. Miller, S. L. Hateley, E. E. Ganusova, J. Mudge, R. J. Langley, L. Zhang, C. C. Lee, F. D. Schilkey, V. Sheth, J. E. Woodward, H. E. Peckham, G. P. Schroth, R. W. Kim, S. F. Kingsmore, Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci. Transl. Med. 3, 65ra4 (2011).
14. N. L. Sobreira, E. T. Cirulli, D. Avramopoulos, E. Wohler, G. L. Oswald, E. L. Stevens, D. Ge, K. V. Shianna, J. P. Smith, J. M. Maia, C. E. Gumbs, J. Pevsner, G. Thomas, D. Valle, J. E. Hoover-Fong, D. B. Goldstein, Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet. 6, e1000991 (2010).
15. A. Bolze, M. Byun, D. McDonald, N. V. Morgan, A. Abhyankar, L. Premkumar, A. Puel, C. M. Bacon, F. Rieux-Laucat, K. Pang, A. Britland, L. Abel, A. Cant, E. R. Maher, S. J. Riedl, S. Hambleton, J. L. Casanova, Whole-exome- sequencingbased discovery of human FADD deficiency. Am. J. Hum. Genet. 87, 873-881 (2010).
16. S. Zühner, J. Dallman, R. Wen, G. Beecham, A. Naj, A. Farooq, M. A. Kohli, P. L. Whitehead, W. Hulme, I. Konidari, Y. J. Edwards, G. Cai, I. Peter, D. Seo, J. D. Buxbaum, J. L. Haines, S. Blanton, J. Young, E. Alfonso, J. M. Vance, B. L. Lam, M. A. Peričak-Vance, Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa. Am. J. Hum. Genet. 88, 201-206 (2011).
17. K. Bilgüar, A. K. Oztük, A. Louvi, K. Y. Kwan, M. Choi, B. Tatli, D. Yalnizoǧlu, B. Tüysüz, A. O. Caǧlayan, S. Gökben, H. Kaymakçalan, T. Barak, M. Bakircioǧlu, K. Yasuno, W. Ho, S. Sanders, Y. Zhu, S. Yilmaz, A. Dinçer, M. H. Johnson, R. A. Bronen, N. Koçer, H. Per, S. Mane, M. N. Pamir, C. Yalçinkaya, S. Kumandaş, M. Topçu, M. Ozmen, N. Sestan, R. P. Lifton, M. W. State, M. Günel, Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 467, 207-210 (2010).
18. T. Walsh, H. Shahin, T. Elkan-Miller, M. K. Lee, A. M. Thornton, W. Roeb, A. Abu Rayyan, S. Loulus, K. B. Avraham, M. C. King, M. Kanaan, Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am. J. Hum. Genet. 87, 90-94 (2010).
19. J. L. Wang, X. Yang, K. Xia, Z. M. Hu, L. Weng, X. Jin, H. Jiang, P. Zhang, L. Shen, J. F. Guo, N. Li, Y. R. Li, L. F. Lei, J. Zhou, J. Du, Y. F. Zhou, Q. Pan, J. Wang, J. Wang, R. Q. Li, B. S. Tang, TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 133, 3510-3518 (2010).
20. M. A. Simpson, M. D. Irving, E. Asilmaz, M. J. Gray, D. Dafou, F. V. Elmslie, S. Mansour, S. E. Holder, C. E. Brain, B. K. Burton, K. H. Kim, R. M. Pauli, S. Aftimos, H. Stewart, C. A. Kim, M. Holder-Espinasse, S. P. Robertson, W. M. Drake, R. C. Trembath, Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat. Genet. 43, 303-305 (2011).
21. E. A. Worthey, A. N. Mayer, G. D. Syverson, D. Helbling, B. B. Bonacci, B. Decker, J. M. Serpe, T. Dasu, M. R. Tschannen, R. L. Veith, M. J. Basehore, U. Broeckel, A. Tomita- Mitchell, M. J. Arca, J. T. Casper, D. A. Margolis, D. P. Bick, M. J. Hessner, J. M. Routes, J. W. Verbsky, H. J. Jacob, D. P. Dimmock, Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13, 255-262 (2011).
22. M. Choi, U. I. Scholl, W. Ji, T. Liu, I. R. Tikhonova, P. Zumbo, A. Nayir, A. Bakkaloǧlu, S. Ozen, S. Sanjad, C. Nelson-Williams, A. Farhi, S. Mane, R. P. Lifton, Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl. Acad. Sci. U.S.A. 106, 19096-19101 (2009).
23. M. Çalişkan, J. X. Chong, L. Uricchio, R. Anderson, P. Chen, C. Sougnez, K. Garimella, S. B. Gabriel, M. A. dePristo, K. Shakir, D. Matern, S. Das, D. Waggoner, D. L. Nicolae, C. Ober, Exome sequencing reveals a novel mutation for autosomal recessive non-syndromic mental retardation in the TECR gene on chromosome 19p13. Hum. Mol. Genet. 20, 1285-1289 (2011).
24. S. B. Ng, A. W. Bigham, K. J. Buckingham, M. C. Hannibal, M. J. McMillin, H. I. Gildersleeve, A. E. Beck, H. K. Tabor, G. M. Cooper, H. C. Mefford, C. Lee, E. H. Turner, J. D. Smith, M. J. Rieder, K. Yoshiura, N. Matsumoto, T. Ohta, N. Niikawa, D. A. Nickerson, M. J. Bamshad, J. Shendure, Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790-793 (2010).
25. T. B. Haack, K. Danhauser, B. Haberberger, J. Hoser, V. Strecker, D. Boehm, G. Uziel, E. Lamantea, F. Invernizzi, J. Poulton, B. Rolinski, A. Iuso, S. Biskup, T. Schmidt, H. W. Mewes, I. Wittig, T. Meitinger, M. Zeviani, H. Prokisch, Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat. Genet. 42, 1131-1134 (2010).
26. J. I. Kim, Y. S. Ju, H. Park, S. Kim, S. Lee, J. H. Yi, J. Mudge, N. A. Miller, D. Hong, C. J. Bell, H. S. Kim, I. S. Chung, W. C. Lee, J. S. Lee, S. H. Seo, J. Y. Yun, H. N. Woo, H. Lee, D. Suh, S. Lee, H. J. Kim, M. Yavartanoo, M. Kwak, Y. Zheng, M. K. Lee, H. Park, J. Y. Kim, O. Gokcumen, R. E. Mills, A. W. Zaranek, J. Thakuria, X. Wu, R. W. Kim, J. J. Huntley, S. Luo, G. P. Schroth, T. D. Wu, H. Kim, K. S. Yang, W. Y. Park, H. Kim, G. M. Church, C. Lee, S. F. Kingsmore, J. S. Seo, A highly annotated whole-genome sequence of a Korean individual. Nature 460, 1011-1015 (2009).
27. Public Law 100-578, the Clinical Laboratory Improvement Amendment of 1988 [CLIA 1988].
28. S. B. Ng, E. H. Turner, P. D. Robertson, S. D. Flygare, A. W. Bigham, C. Lee, T. Shaffer, M. Wong, A. Bhattacharjee, E. E. Eichler, M. Bamshad, D. A. Nickerson, J. Shendure, Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-276 (2009).
29. P. M. Krawitz, M. R. Schweiger, C. Rödelsperger, C. Marcelis, U. Kölsch, C. Meisel, F. Stephani, T. Kinoshita, Y. Murakami, S. Bauer, M. Isau, A. Fischer, A. Dahl, M. Kerick, J. Hecht, S. Köhler, M. Jäger, J. Grünhagen, B. J. de Condor, S. Doelken, H. G. Brunner, P. Meinecke, E. Passarge, M. D. Thompson, D. E. Cole, D. Horn, T. Roscioli, S. Mundlos, P. N. Robinson, Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nat. Genet. 42, 827-829 (2010).
30. GeneTests: Medical Genetics Information Resource (database online). Copyright, University of Washington, Seattle. 1993-2011. http://www.genetests. org.
31. M. R. Kohonen-Corish, J. Y. Al-Aama, A. D. Auerbach, M. Axton, C. I. Barash, I. Bernstein, C. Béroud, J. Burn, F. Cunningham, G. R. Cutting, J. T. den Dunnen, M. S. Greenblatt, J. Kaput, M. Katz, A. Lindblom, F. Macrae, D. Maglott, G. Möslein, S. Povey, R. Ramesar, S. Richards, D. Seminara, M. J. Sobrido, S. Tavtigian, G. Taylor, M. Vihinen, I. Winship, R. G. Cotton; Human Variome Project Meeting, How to catch all those mutations - The report of the third Human Variome Project Meeting, UNESCO Paris, May 2010. Hum. Mutat. 31, 1374-1381 (2010).
32. Acknowledgments: We thank D. Dinwiddie, N. Miller, and S. Soden for their insights. This work was funded by the Beyond Batten Disease Foundation and Children's Mercy Hospital. A deo lumen, ab amicis auxilium. Competing interests: The authors declare no competing interests.