Challenges of Bringing Next Generation Sequencing Technologies to Clinical Molecular Diagnostic Laboratories

Neurotherapeutics

Volumn 10, Issue 2, 2013, Pages 262-272

  Wong, Lee Jun C ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

Massively parallel sequencing; Mitochondrial disorders; mtDNA deletion; mtDNA multiple deletions; mtDNA point mutations; Next generation sequencing

Indexed keywords

DNA; MITOCHONDRIAL DNA; NUCLEAR PROTEIN; RNA;

ARRAY COMPARATIVE GENOME HYBRIDIZATION; BIOINFORMATICS; BIOTECHNOLOGY; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; DIAGNOSTIC TEST; DNA PROBE; DNA SEQUENCE; GENE DELETION; GENE EXPRESSION; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC DISORDER; HEALTH CARE QUALITY; HETEROPLASMY; HISTOPATHOLOGY; HUMAN; LABORATORY; LABORATORY DEVICE; LAW; MASSIVELLY PARALLEL SEQUENCING; MITOCHONDRIAL DNA DISORDER; MITOCHONDRIAL GENOME; MITOCHONDRIAL RESPIRATION; MOLECULAR DIAGNOSIS; NEXT GENERATION SEQUENCING; NUCLEAR MITOCHONDRIAL SEQUENCE; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; RNA PROBE; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY;

EID: 84876185252     PISSN: 19337213     EISSN: 18787479     Source Type: Journal    
DOI: 10.1007/s13311-012-0170-5     Document Type: Review

References (74)

1. Calvo S, et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet 2006; 38(5): 576-582.
2. Scharfe C, et al. Mapping gene associations in human mitochondria using clinical disease phenotypes. PLoS Comput Biol 2009; 5(4): e1000374.
3. Dimmock D, et al. A quantitative evaluation of the mitochondrial DNA depletion syndrome. Clin Chem 2010; 56(7): 1119-27.
4. Shanske S, Wong LJ. Molecular analysis for mitochondrial DNA disorders. Mitochondrion 2004; 4(5-6): 403-15.
5. Wong LJ, Boles RG. Mitochondrial DNA analysis in clinical laboratory diagnostics. Clin Chim Acta 2005; 354(1-2): 1-20.
6. Wong L-JC. Molecular genetics of mitochondrial disorders. Dev Disabil Res Rev 2010; 16(2): 154-162.
7. Koopman WJ, Willems PH, Smeitink JA. Monogenic mitochondrial disorders. N Engl J Med 2012; 366(12): 1132-41.
8. Smeitink J, van den Heuvel L, DiMauro S. The genetics and pathology of oxidative phosphorylation. Nat Rev Genet 2001; 2(5): 342-52.
9. Calvo SE, et al. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 2012; 4(118): 118ra10.
10. Casey JP, et al. Identification of a mutation in LARS as a novel cause of infantile hepatopathy. Mol Genet Metab 2012; 106(3): 351-8.
11. Galmiche L, et al. Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy. Hum Mutat 2011; 32(11): 1225-31.
12. Gandre-Babbe S, van der Bliek AM. The novel tail-anchored membrane protein Mff controls mitochondrial and peroxisomal fission in mammalian cells. Mol Biol Cell 2008; 19(6): 2402-12.
13. Gerards M, et al. Riboflavin-responsive oxidative phosphorylation complex I deficiency caused by defective ACAD9: new function for an old gene. Brain 2011; 134(Pt 1): 210-9.
14. Ghezzi D, et al. Mutations of the mitochondrial-tRNA modifier MTO1 cause hypertrophic cardiomyopathy and lactic acidosis. Am J Hum Genet 2012; 90(6): 1079-87.
15. Glazov EA, et al. Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia. PLoS Genet 2011; 7(3): e1002027.
16. Gotz A, et al. Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. Am J Hum Genet 2011; 88(5): 635-42.
17. Haack TB, et al. Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency. Nat Genet 2010; 42(12): 1131-4.
18. Majczenko K, et al. Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores. Am J Hum Genet 2012; 91(2): 365-71.
19. Mayr JA, et al. Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome. Am J Hum Genet 2012; 90(2): 314-20.
20. Pierce SB, et al. Mutations in mitochondrial histidyl tRNA synthetase HARS2 cause ovarian dysgenesis and sensorineural hearing loss of Perrault syndrome. Proc Natl Acad Sci USA 2011; 108(16): 6543-8.
21. Rotig A. Human diseases with impaired mitochondrial protein synthesis. Biochim Biophys Acta 2011; 1807(9): 1198-205.
22. Sloan JL, et al. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet 2011; 43(9): 883-6.
23. Spiegel R et al. Infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aconitase, ACO2. Am J Hum Genet 2012; 90(3): 518-23.
24. Steenweg ME et al. Leukoencephalopathy with thalamus and brainstem involvement and high lactate 'LTBL' caused by EARS2 mutations. Brain 2012; 135(Pt 5): 1387-94.
25. Tucker EJ, et al. Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation. Cell Metab 2011; 14(3): 428-34.
26. Watkins D, et al. Novel inborn error of folate metabolism: identification by exome capture and sequencing of mutations in the MTHFD1 gene in a single proband. J Med Genet 2011; 48(9): 590-2.
27. Wortmann SB, et al. Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness. Nat Genet 2012; 44(7): 797-802.
28. Schrijver I, et al. Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the association for molecular pathology. J Mol Diagn 2012; 14(6): 525-40.
29. Zhang W, Cui H, Wong LJ. Application of Next Generation Sequencing to Molecular Diagnosis of Inherited Diseases. Top Curr Chem, 2012 PMID 22576358.
30. Zhang W, Cui H, Wong LJ. Comprehensive 1-step molecular analyses of mitochondrial genome by massively parallel sequencing. Clin Chem 2012; 58: 1322-31.
31. Gargis AS, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012; 30(11): 1033-6.
32. Tang S, et al. Analysis of common mitochondrial DNA mutations by allele-specific oligonucleotide and Southern blot hybridization. Methods Mol Biol 2012; 837: 259-79.
33. Bai RK, Wong LJ. Detection and quantification of heteroplasmic mutant mitochondrial DNA by real-time amplification refractory mutation system quantitative PCR analysis: a single-step approach. Clin Chem 2004; 50(6): 996-1001.
34. Venegas V, Halberg MC. Quantification of mtDNA mutation heteroplasmy (ARMS qPCR). Methods Mol Biol 2012; 837: 313-26.
35. Chinault AC, et al. Application of dual-genome oligonucleotide array-based comparative genomic hybridization to the molecular diagnosis of mitochondrial DNA deletion and depletion syndromes. Genet Med 2009; 11(7): 518-26.
36. Wang J, et al. Targeted array CGH as a valuable molecular diagnostic approach: experience in the diagnosis of mitochondrial and metabolic disorders. Mol Genet Metab 2012; 106(2): 221-30.
37. Wong LJ, et al. Utility of oligonucleotide array-based comparative genomic hybridization for detection of target gene deletions. Clin Chem 2008; 54(7): 1141-8.
38. Landsverk ML, Cornwell ME, Palculict ME. Sequence analysis of the whole mitochondrial genome and nuclear genes causing mitochondrial disorders. Methods Mol Biol 2012; 837: 281-300.
39. Ware SM, et al. Infantile cardiomyopathy caused by a mutation in the overlapping region of mitochondrial ATPase 6 and 8 genes. J Med Genet 2009; 46(5): 308-14.
40. Lacbawan F, et al. Clinical heterogeneity in mitochondrial DNA deletion disorders: a diagnostic challenge of Pearson syndrome. Am J Med Genet 2000; 95(3): 266-8.
41. Brautbar A, et al. The mitochondrial 13513G&A mutation is associated with Leigh disease phenotypes independent of complex I deficiency in muscle. Mol Genet Metab 2008; 94(4): 485-90.
42. Wang J, et al. Two mtDNA mutations 14487T&C (M63V, ND6) and 12297T&C (tRNA Leu) in a Leigh syndrome family. Mol Genet Metab 2009; 96(2): 59-65.
43. Kara B, et al. Whole mitochondrial genome analysis of a family with NARP/MILS caused by m. 8993T&C mutation in the MT-ATP6 gene. Mol Genet Metab, 2012; 107: 389-93.
44. Zaragoza MV, et al. Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing. PLoS One 2010; 5(8): e12295.
45. Cui H, et al. Comprehensive next generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders. Genetics in Medicine, 2012. (in press).
46. Gnirke A, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009; 27(2): 182-9.
47. Hirano M, et al. Apparent mtDNA heteroplasmy in Alzheimer's disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. Proc Natl Acad Sci USA 1997; 94(26): 14894-9.
48. Parfait B, et al. Co-amplification of nuclear pseudogenes and assessment of heteroplasmy of mitochondrial DNA mutations. Biochem Biophys Res Commun 1998; 247(1): 57-9.
49. Bennett ST, et al. Toward the $1000 human genome. Pharmacogenomics 2005; 6(4): 373-382.
50. Margulies M, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437(7057): 376-380.
51. Rothberg JM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475(7356): 348-352.
52. Shendure J, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309(5741): 1728-1732.
53. Haas RH, et al. Mitochondrial disease: a practical approach for primary care physicians. Pediatrics 2007; 120(6): 1326-33.
54. Haas RH, et al. The in-depth evaluation of suspected mitochondrial disease. Mol Genet Metab 2008; 94(1): 16-37.
55. Wong L-JC, et al. Current molecular diagnostic algorithm for mitochondrial disorders. Mol Genet Metab 2010; 100(2): 111-117.
56. Wang J, et al. An integrated approach for classifying mitochondrial DNA variants: one clinical diagnostic laboratory's experience. Genet Med 2012; 14(6): 620-6.
57. Zhang VW, Wang J. Determination of the clinical significance of an unclassified variant. Methods Mol Biol 2012; 837: 337-48.
58. Tang S, et al. Left ventricular noncompaction is associated with mutations in the mitochondrial genome. Mitochondrion 2010; 10(4): 350-7.
59. Goto H, et al. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol 2011; 12(6): R59.
60. He Y, et al. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature 2010; 464(7288): 610-4.
61. Li M, et al. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 2010; 87(2): 237-49.
62. Schonberg A, et al. High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences. Eur J Hum Genet 2011; 19(9): 988-94.
63. Calvo SE, et al. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet 2010; 42(10): 851-8.
64. Vasta V, et al. Next-generation sequencing for mitochondrial diseases: A wide diagnostic spectrum. Pediatr Int 2012; 54(5): 585-601.
65. Tucker EJ, et al. Next-generation sequencing in molecular diagnosis: NUBPL mutations highlight the challenges of variant detection and interpretation. Hum Mutat 2012; 33(2): 411-8.
66. Richards CS, et al. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 2008; 10(4): 294-300.
67. MacArthur DG, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012; 335(6070): 823-8.
68. Landsverk ML, et al. Diagnostic approaches to apparent homozygosity. Genet Med 2012; 14(10): 877-82.
69. Milone M, Benarroch EE, Wong LJ. POLG-related disorders: defects of the nuclear and mitochondrial genome interaction. Neurology 2011; 77(20): 1847-52.
70. Tang S., et al. Mitochondrial DNA polymerase gamma mutations: an ever expanding molecular and clinical spectrum. J Med Genet 2011; 48(10): 669-81.
71. Milone M, et al. Novel POLG splice site mutation and optic atrophy. Arch Neurol 2011; 68(6): 806-11.
72. Milone M, et al. Mitochondrial disorder with OPA1 mutation lacking optic atrophy. Mitochondrion 2009; 9(4): 279-81.
73. Milone M, et al. Sensory ataxic neuropathy with ophthalmoparesis caused by POLG mutations. Neuromuscul Disord 2008; 18(8): 626-32.
74. Yarham JW, et al. A comparative analysis approach to determining the pathogenicity of mitochondrial tRNA mutations. Hum Mutat 2011; 32(11): 1319-25.