Missing genetic risk in neural tube defects: Can exome sequencing yield an insight?

Birth Defects Research Part A - Clinical and Molecular Teratology

Volumn 100, Issue 8, 2014, Pages 642-646

  Krupp, Deidre R ^a   Soldano, Karen L ^b   Garrett, Melanie E ^b   Cope, Heidi ^b   Ashley Koch, Allison E ^b   Gregory, Simon G ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

Compound heterozygosity; De novo, rare and common variation; Next generation exome sequencing

Indexed keywords

ARTICLE; EXOME; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CODE; GENETIC RISK; GENETIC VARIABILITY; GENOME; HUMAN; MULTIGENE FAMILY; NEURAL TUBE DEFECT; PRIORITY JOURNAL; DNA SEQUENCE; EMBRYOLOGY; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; NEURAL TUBE; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; EXOME; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEURAL TUBE; NEURAL TUBE DEFECTS; SEQUENCE ANALYSIS, DNA;

EID: 84906486678     PISSN: 15420752     EISSN: 15420760     Source Type: Journal    
DOI: 10.1002/bdra.23276     Document Type: Article

References (48)

1. Adzhubei I, Jordan DM, Sunyaev SR. 2013. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet Chapter 7:Unit7.20.
2. Arrington CB, Bleyl SB, Matsunami N, et al. 2012. Exome analysis of a family with pleiotropic congenital heart disease. Circ Cardiovasc Genet 5:175-182.
3. Bentley DR, Balasubramanian S, Swerdlow HP, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
4. Biesecker LG, Burke W, Kohane I, et al. 2012. Next-generation sequencing in the clinic: are we ready? Nat Rev Genet 13:818-824.
5. Bilguvar K, Ozturk AK, Louvi A, et al. 2010. Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations. Nature 427:207-210.
6. Cherkas Y, Raghavan N, Francke S, et al. 2011. Rare variant collapsing in conjunction with mean log p-value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data. BMC Proc 5(Suppl 9):S94.
7. Choi M, Scholl UI, Ji W, et al. 2009. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S Am 106:19096-19101.
8. Choi Y, Sims GE, Murphy S, et al. 2012. Predicting the functional effect of amino acid substitutions and indels. PloS One 7:e46688.
9. Cong L, Ran FA, Cox D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819-823.
10. Demenais F, Le Merrer M, Briard ML, Elston RC. 1982. Neural tube defects in France: segregation analysis. Am J Med Genet 11:287-298.
11. Desmet FO, Hamroun D, Lalande M, et al. 2009. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67.
12. Divina P, Kvitkovicova A, Buratti E, Vorechovsky I. 2009. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 17:759-765.
13. Do R, Kathiresan S, Abecasis GR. 2012. Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet 21:R1-R9.
14. Fineman RM, Jorde LB, Martin RA, et al. 1982. Spinal dysraphia as an autosomal dominant defect in four families. Am J Med Genet 12:457-464.
15. Genomes Project C, Abecasis GR, Auton A, et al. 2012. An integrated map of genetic variation from 1, 092 human genomes. Nature 491:56-65.
16. Harris MJ, Juriloff DM. 2010. An update to the list of mouse mutants with neural tube closure defects and advances toward a complete genetic perspective of neural tube closure. Birth defects Res A Clin Mol Teratol 88:653-669.
17. Harrow J, Frankish A, Gonzalez JM, et al. 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22:1760-1774.
18. Hindorff LA, Sethupathy P, Junkins HA, et al. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106:9362-9367.
19. Hoischen A, van Bon BW, Gilissen C, et al. 2010. De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42:483-485.
20. Johnson JO, Mandrioli J, Benatar M, et al. 2010. Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 68:857-864.
21. Kibar Z, Bosoi CM, Kooistra M, et al. 2009. Novel mutations in VANGL1 in neural tube defects. Hum Mutat 30:E706-E715.
22. Kibar Z, Torban E, McDearmid JR, et al. 2007. Mutations in VANGL1 associated with neural-tube defects. N Engl J Med 356:1432-1437.
23. Krawitz PM, Schweiger MR, Rodelsperger C, et al. 2010. Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nat Genet 42:827-829.
24. Leck I. 1974. Causation of neural tube defects: clues from epidemiology. Br Med Bull 30:158-163.
25. Lei YP, Zhang T, Li H, et al. 2010. VANGL2 mutations in human cranial neural-tube defects. N Engl J Med 362:2232-2235.
26. Li B, Leal SM. 2008. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321.
27. Li H, Homer N. 2010. A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473-483.
28. Lim KH, Ferraris L, Filloux ME, et al. 2011. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci U S A 108:11093-11098.
29. Manolio TA, Collins FS, Cox NJ, et al. 2009. Finding the missing heritability of complex diseases. Nature 461:747-753.
30. Mardis ER. 2013. Next-generation sequencing platforms. Annu Rev Anal Chem 6:287-303.
31. Margulies M, Egholm M, Altman WE, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.
32. Marini NJ, Hoffmann TJ, Lammer EJ, et al. 2011. A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PloS One 6:e28408.
33. Ng SB, Bigham AW, Buckingham KJ, et al. 2010a. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42:790-793.
34. Ng SB, Buckingham KJ, Lee C, et al. 2010b. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42:30-35.
35. Ng SB, Turner EH, Robertson PD, et al. 2009. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276.
36. Otto EA, Hurd TW, Airik R, et al. 2010. Candidate exome capture identifies mutation of SDCCAG8 as the cause of a retinal-renal ciliopathy. Nat Genet 42:840-850.
37. Pierce SB, Walsh T, Chisholm KM, et al. 2010. Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault Syndrome. Am J Hum Genet 87:282-288.
38. Raffan E, Hurst LA, Turki SA, et al. 2011. Early diagnosis of Werner's syndrome using exome-wide sequencing in a single, atypical patient. Front Endocrinol (Lausanne) 2:8.
39. Rios J, Stein E, Shendure J, et al. 2010. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet 19:4313-4318.
40. Robinson A, Escuin S, Doudney K, et al. 2012. Mutations in the planar cell polarity genes CELSR1 and SCRIB are associated with the severe neural tube defect craniorachischisis. Hum Mutat 33:440-447.
41. Rothberg JM, Hinz W, Rearick TM, et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348-352.
42. Sanger F, Coulson AR. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 94:441-448.
43. Smigielski EM, Sirotkin K, Ward M, Sherry ST. 2000. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28:352-355.
44. Stitziel NO, Kiezun A, Sunyaev S. 2011. Computational and statistical approaches to analyzing variants identified by exome sequencing. Genome Biol 12:227.
45. Stratton MR, Campbell PJ, Futreal PA. 2009. The cancer genome. Nature 458:719-724.
46. Summerton J. 1999. Morpholino antisense oligomers: the case for an RNase H-independent structural type. Biochimica et biophysica acta 1489:141-158.
47. Tennessen JA, Bigham AW, O'Connor TD, et al. 2012. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69.
48. Wu G, Zhi D. 2013. Pathway-based approaches for sequencing-based genome-wide association studies. Genet Epidemiol 37:478-494.