Sequence capture and next-generation resequencing of multiple tagged nucleic acid samples for mutation screening of urea cycle disorders

Clinical Chemistry

Volumn 57, Issue 1, 2011, Pages 102-111

  Amstutz, Ursula ^a,b   Andrey Zürcher, Gisela ^a   Suciu, Dominic ^c   Jaggi, Rolf ^a   Häberle, Johannes ^d   Largiadér, Carlo R ^a  

^a UNIVERSITY OF BERN   (Switzerland)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c CustomArray Incorporated   (United States)

^d UNIVERSITY CHILDREN S HOSPITAL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CARBAMOYL PHOSPHATE SYNTHASE; GLUTAMATE ACETYLTRANSFERASE; NUCLEIC ACID; ORNITHINE CARBAMOYLTRANSFERASE;

ARTICLE; CONTROLLED STUDY; DNA BARCODING; DNA MICROARRAY; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENETIC SCREENING; HETEROZYGOTE; HOMOZYGOTE; HUMAN; MITOCHONDRION; NUCLEIC ACID ANALYSIS; OLIGONUCLEOTIDE PROBE; PROMOTER REGION; SCREENING; UREA CYCLE; UREA CYCLE DISORDER;

AMINO-ACID N-ACETYLTRANSFERASE; CARBAMOYL-PHOSPHATE SYNTHASE (AMMONIA); DNA; FALSE POSITIVE REACTIONS; GENOME, HUMAN; HUMANS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORNITHINE CARBAMOYLTRANSFERASE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES; UREA CYCLE DISORDERS, INBORN;

EID: 78650979991     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2010.150706     Document Type: Article

References (32)

1. Mian A, Lee B. Urea-cycle disorders as a paradigm for inborn errors of hepatocyte metabolism. Trends Mol Med 2002;8:583-9.
2. Endo F, Matsuura T, Yanagita K, Matsuda I. Clinical manifestations of inborn errors of the urea cycle and related metabolic disorders during childhood. J Nutr 2004;134:1605S-9S.
3. Yamaguchi S, Brailey LL, Morizono H, Bale AE, Tuchman M. Mutations and polymorphisms in the human ornithine transcarbamylase (OTC) gene. Hum Mutat 2006;27:626-32.
4. Engel K, Nuoffer J-M, Mü hlhausen C, Klaus V, Largiadér CR, Tsiekas K, et al. Analysis of mRNA transcripts improves the success rate of molecular genetic testing in OTC deficiency. Mol Genet Metab 2008;94:292-7.
5. Ogino W, Takeshima Y, Nishiyama A, Akizuka Y, Yagi M, Tsuneishi S, et al. Mutation analysis of the ornithine transcarbamylase (OTC) gene in five Japanese OTC deficiency patients revealed two known and three novel mutations including a deep intronic mutation. Kobe J Med Sci 2007;53: 229-40.
6. Azevedo L, Soares PA, Quental R, Vilarinho L, Teles EL, Martins E, et al. Mutational spectrum and linkage disequilibrium patterns at the ornithine transcarbamylase gene (OTC). Ann Hum Genet 2006;70:797-801.
7. Mak CM, Siu T-SS, Lam C-WW, Chan GC, Poon GW, Wong K-YY, et al. Complete recovery from acute encephalopathy of late-onset ornithine transcarbamylase deficiency in a 3-year-old boy. J Inherit Metab Dis 2007;30:981.
8. Scaglia F, Zheng Q, O'Brien WE, Henry J, Rosenberger J, Reeds P, Lee B. An integrated approach to the diagnosis and prospective management of partial ornithine transcarbamylase deficiency. Pediatrics 2002;109:150-2.
9. Häberle J, Denecke J, Schmidt E, Koch HG. Diagnosis of N-acetylglutamate synthase deficiency by use of cultured fibroblasts and avoidance of nonsense-mediated mRNA decay. J Inherit Metab Dis 2003;26:601-5.
10. Häberle J, Koch HG. Genetic approach to prenatal diagnosis in urea cycle defects. Prenat Diagn 2004;24:378-83.
11. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 2008;18: 1638-42.
12. Chou L-S, Liu C-SJ, Boese B, Zhang X, Mao R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: Neurofibromatosis type 1 gene as a model. Clin Chem 2010;56: 62-72.
13. ten Bosch JR, Grody WW. Keeping up with the next generation: Massively parallel sequencing in clinical diagnostics. J Mol Diagn 2008;10: 484-92.
14. Raca G, Jackson C, Warman B, Bair T, Schimmenti LA. Next generation sequencing in research and diagnostics of ocular birth defects. Mol Genet Metab 2010;100:184-92.
15. Vasta V, Ng SB, Turner EH, Shendure J, Hahn SH. Next generation sequence analysis for mitochondrial disorders. Genome Med 2009;1:100.
16. Hoischen A, Gilissen C, Arts P, Wieskamp N, van der Vliet W, Vermeer S, et al. Massively parallel sequencing of ataxia genes after array-based enrichment. Hum Mutat 2010;31:494-9.
17. Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 2007;4:903-5.
18. Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, Hoheisel JD, et al. Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays. Anal Bioanal Chem 2009;393:171-5.
19. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007;4:907-9.
20. Gnirke A, Melnikov A, Maguire J, Rogov P, Le- Proust EM, Brockman W, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009;27:183-9.
21. Meyer M, Stenzel U, Myles S, Prufer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res 2007;35:e97.
22. D'Ascenzo M, Meacham C, Kitzman J, Middle C, Knight J, Winer R, et al. Mutation discovery in the mouse using genetically guided array capture and resequencing. Mamm Genome 2009;20:424-36.
23. Strömberg M, Lee W-P. MOSAIK [computer software]. Version 1.0.1370. http://bioinformatics. bc.edu/marthlab/Mosaik (Accessed January 2010).
24. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; 2009.
25. Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E, Sirotkin K. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308-11.
26. Biesecker LG. Exome sequencing makes medical genomics a reality. Nat Genet 2010;42:13-4.
27. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009;323:133-8.
28. Summerer D, Wu H, Haase B, Cheng Y, Schracke N, Stähler CF, et al. Microarray-based multicycleenrichment of genomic subsets for targeted nextgeneration sequencing. Genome Res 2009;19: 1616-21.
29. Hoppman-Chaney N, Peterson LM, Klee EW, Middha S, Courteau LK, Ferber MJ. Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics. Clin Chem 2010;56:1297-306.
30. Carletti E, Guerra E, Alberti S. The forgotten variables of DNA array hybridization. Trends Biotechnol 2006;24:443-8.
31. Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, et al. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 2006;314:1930 -3.
32. Lee H, O'Connor BD, Merriman B, Funari VA, Homer N, Chen Z, et al. Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing. BMC Genomics 2009;10:646.