Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations

Methods in Molecular Biology

Volumn 1015, Issue , 2013, Pages 127-146

  Londin, Eric ^a   Yadav, Priyanka ^a   Surrey, Saul ^a   Kricka, Larry J ^b   Fortina, Paolo ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Genome wide association study; Linkage analysis; Massively parallel sequencing; NGS applications; Pharmacogenomics

Indexed keywords

AMELOGENESIS IMPERFECTA; AMYOTROPHIC LATERAL SCLEROSIS; ARTHROGRYPOSIS; AUTISM; AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME; BARTTER SYNDROME; BONE DYSPLASIA; CARDIOMYOPATHY; CELIAC DISEASE; CHONDRODYSPLASIA; COLORECTAL CANCER; FACE MALFORMATION; GENE MUTATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC VARIABILITY; GENOME; GILLES DE LA TOURETTE SYNDROME; HAJDU CHENEY SYNDROME; HEREDITARY MOTOR SENSORY NEUROPATHY; HODGKIN DISEASE; HUMAN; HYPERCHOLESTEROLEMIA; HYPOTRICHOSIS; IMMUNE DEFICIENCY; KABUKI MAKEUP SYNDROME; LEUKODYSTROPHY; LINKAGE ANALYSIS; LYMPHEDEMA; MELANOMA; MENTAL DEFICIENCY; OSTEOGENESIS IMPERFECTA; PRIORITY JOURNAL; PROMYELOCYTIC LEUKEMIA; PYROSEQUENCING; RETINITIS PIGMENTOSA; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

GENETIC LINKAGE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION;

EID: 84880339190     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-435-7_8     Document Type: Review

References (80)

1. Hindorff LA et al (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367
2. Rommens JM et al (1989) Identifi cation of the cystic fi brosis gene: Chromosome walking and jumping. Science 245:1059-1065
3. Riordan JR et al (1989) Identifi cation of the cystic fi brosis gene: Cloning and characterization of complementary DNA. Science 245:1066-1073
4. Kerem B et al (1989) Identifi cation of the cystic fi brosis gene: Genetic analysis. Science 245:1073-1080
5. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
6. Altmuller J et al (2001) Genomewide scans of complex human diseases: True linkage is hard to fi nd. Am J Hum Genet 69:936-950
7. Consortium IH (2005) A haplotype map of the human genome. Nature 437:1299-1320
8. Manolio TA et al (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753
9. Klein RJ et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308:385-389
10. Barrett JC et al (2008) Genome-wide association defi nes more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40:955-962
11. Lango AH et al (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467:832-838
12. Maller J et al (2006) Common variation in three genes, including a noncoding variant in CFH, strongly infl uences risk of age-related macular degeneration. Nat Genet 38:1055-1059
13. Jakobsdottir J et al (2009) Interpretation of genetic association studies: Markers with replicated highly signifi cant odds ratios may be poor classifi ers. PLoS Genet 5:e1000337
14. Rose SP (2006) Commentary: Heritability estimates-long past their sell-by date. Int J Epidemiol 35:525-527
15. A 1000 Genomes Project Consortium, Abecasis GR et al (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-1073
16. Venter JC et al (2001) The sequence of the human genome. Science 291:1304-1351
17. Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
18. Schloss JA (2008) How to get genomes at one ten-thousandth the cost. Nat Biotechnol 26:1113-1115
19. Hert DG, Fredlake CP, Barron AE (2008) Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618-4626
20. Pareek CS, Smoczynski R, Tretyn A (2011) Sequencing technologies and genome sequencing. J Appl Genet 52:413-435
21. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11:31-46
22. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387-402
23. Zheng Z et al (2010) Titration-free massively parallel pyrosequencing using trace amounts of starting material. Nucleic Acids Res 38:e137
24. Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380
25. Depristo MA et al (2011) A framework for variation discovery and genotyping using nextgeneration DNA sequencing data. Nat Genet 43:491-498
26. Ng SB et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276
27. Ng SB et al (2009) Exome sequencing identifi es the cause of a mendelian disorder. Nat Genet 42:30-35
28. Hoischen A et al (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42:483-485
29. Bansal V et al (2010) Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 11:773-785
30. Nalls MA et al (2011) Imputation of sequence variants for identifi cation of genetic risks for Parkinson's disease: A meta-analysis of genomewide association studies. Lancet 377:641-649
31. Su Z et al (2011) Next-generation sequencing and its applications in molecular diagnostics. Expert Rev Mol Diagn 11:333-343
32. Marian AJ (2011) Medical DNA sequencing. Curr Opin Cardiol 26:175-180
33. Diamandis EP (2009) Next-generation sequencing: A new revolution in molecular diagnostics? Clin Chem 55:2088-2092
34. Choi M et al (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106:19096-19101
35. Maxmen A (2011) Exome sequencing deciphers rare diseases. Cell 144:635-637
36. St HC et al (2011) NT5E mutations and arterial calcifi cations. N Engl J Med 364: 432-442
37. Daly AK (2010) Genome-wide association studies in pharmacogenomics. Nat Rev Genet 11:241-246
38. Dewey FE et al (2011) Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet 7:e1002280
39. Trapnell C, Salzberg SL (2009) How to map billions of short reads onto genomes. Nat Biotechnol 27:455-457
40. Nielsen R et al (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443-451
41. Hinchcliffe M, Webster P (2011) In silico analysis of the exome for gene discovery. Methods Mol Biol 760:109-128
42. Blaby-Haas CE, de Crecy-Lagard V (2011) Mining high-throughput experimental data to link gene and function. Trends Biotechnol 29:174-182
43. Nothnagel M et al (2011) Technology-specifi c error signatures in the 1000 Genomes Project data. Hum Genet 130:505-516
44. Al Badr W et al (2011) Exome capture and massively parallel sequencing identifi es a novel HPSE2 mutation in a Saudi Arabian child with Ochoa (urofacial) syndrome. J Pediatr Urol 7:569-573
45. Alvarado DM et al (2011) Exome sequencing identifi es an MYH3 mutation in a family with distal arthrogryposis type 1. J Bone Joint Surg Am 93:1045-1050
46. Barak T et al (2011) Recessive LAMC3 mutations cause malformations of occipital cortical development. Nat Genet 43:590-594
47. Becker J et al (2011) Exome sequencing identifi es truncating mutations in human SERPINF1 in autosomal-recessive osteogenesis imperfecta. Am J Hum Genet 88:362-371
48. Bolze A et al (2010) Whole-exomesequencing-based discovery of human FADD defi ciency. Am J Hum Genet 87:873-881
49. Caliskan M et al (2011) 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
50. de Greef JC et al (2011) Mutations in ZBTB24 are associated with immunodefi ciency, centromeric instability, and facial anomalies syndrome type 2. Am J Hum Genet 88:796-804
51. Erlich Y et al (2011) Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res 21:658-664
52. Gilissen C et al (2010) Exome sequencing identifi es WDR35 variants involved in Sensenbrenner syndrome. Am J Hum Genet 87:418-423
53. Glazov EA et al (2011) Whole-exome re- sequencing in a family quartet identifi es POP1 mutations as the cause of a novel skeletal dysplasia. PLoS Genet 7:e1002027
54. Gotz A et al (2011) Exome sequencing identifi es mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. Am J Hum Genet 88:635-642
55. Greif PA et al (2011) Somatic mutations in acute promyelocytic leukemia (APL) identifi ed by exome sequencing. Leukemia 25:1519-1522
56. Johnson JO et al (2010) Exome sequencing reveals VCP mutations as a cause of familial ALS. Neuron 68:857-864
57. Li Y et al (2010) Resequencing of 200 human exomes identifi es an excess of low-frequency non-synonymous coding variants. Nat Genet 42:969-972
58. Liu Y et al (2011) Confi rmation by exome sequencing of the pathogenic role of NCSTN mutations in acne inversa (hidradenitis suppurativa). J Invest Dermatol 131:1570-1572
59. Mondal K et al (2011) Targeted sequencing of the human X chromosome exome. Genomics 98:260-265
60. Montenegro G et al (2011) Exome sequencing allows for rapid gene identifi cation in a Charcot-Marie-Tooth family. Ann Neurol 69: 464-470
61. Ng SB et al (2010) Exome sequencing identifi es MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42:790-793
62. O'Roak BJ et al (2011) Exome sequencing in sporadic autism spectrum disorders identifi es severe de novo mutations. Nat Genet 43: 585-589
63. O'Sullivan J et al (2011) Whole-exome sequencing identifi es FAM20A mutations as a cause of amelogenesis imperfecta and gingival hyperplasia syndrome. Am J Hum Genet 88:616-620
64. Ostergaard P et al (2011) Rapid identifi cation of mutations in GJC2 in primary lymphoedema using whole exome sequencing combined with linkage analysis with delineation of the phenotype. J Med Genet 48:251-255
65. Puente XS et al (2011) Exome sequencing and functional analysis identifi es BANF1 mutation as the cause of a hereditary progeroid syndrome. Am J Hum Genet 88:650-656
66. Rios J et al (2010) Identifi cation by wholegenome resequencing of gene defect responsible for severe hypercholesterolemia. Hum Mol Genet 19:4313-4318
67. Saarinen S et al (2011) Exome sequencing reveals germline NPAT mutation as a candidate risk factor for Hodgkin lymphoma. Blood 118:493-498
68. Simpson MA et al (2011) Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Am J Hum Genet 43:303-305
69. Snape K et al (2011) Mutations in CEP57 cause mosaic variegated aneuploidy syndrome. Am J Hum Genet 43:527-529
70. Szperl AM et al (2011) Exome sequencing in a family segregating for celiac disease. Clin Genet 80:138-147
71. Sundaram SK et al (2011) Exome sequencing of a pedigree with tourette syndrome or chronic tic disorder. Ann Neurol 69:901-904
72. Timmermann B et al (2010) Somatic mutation profi les of MSI and MSS colorectal cancer identifi ed by whole exome next generation sequencing and bioinformatics analysis. PLoS One 5:e15661
73. Tsurusaki Y et al (2011) Exome sequencing of two patients in a family with atypical X-linked leukodystrophy. Clin Genet 80:161-166
74. Vissers LE et al (2010) A de novo paradigm for mental retardation. Am J Hum Genet 42:1109-1112
75. Vissers LE et al (2011) Chondrodysplasia and abnormal joint development associated with mutations in IMPAD1, encoding the Golgiresident nucleotide phosphatase, gPAPP. Am J Hum Genet 88:608-615
76. Wei X et al (2011) Exome sequencing identifi es GRIN2A as frequently mutated in melanoma. Nat Genet 43:442-446
77. Worthey EA et al (2011) Making a defi nitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable infl ammatory bowel disease. Genet Med 13:255-262
78. Yamaguchi T et al (2011) Exome resequencing combined with linkage analysis identifi es novel PTH1R variants in primary failure of tooth eruption in Japanese. J Bone Miner Res 26(7):1655-1661
79. Zhou C et al (2011) Mutation in ribosomal protein L21 underlies hereditary hypotrichosis simplex. Hum Mutat 32:710-714
80. Zuchner S et al (2011) Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa. Am J Hum Genet 88:201-206