Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate

1. MerikangasKR, LowNC (2004) The epidemiology of mood disorders. Curr Psychiatry Rep 6: 411–421.

2. SerrettiA, MandelliL (2008) The genetics of bipolar disorder: genome ‘hot regions,’ genes, new potential candidates and future directions. Mol Psychiatry 13: 742–771.

3. BadnerJA, KollerD, ForoudT, EdenbergH, NurnbergerJIJr, et al. (2012) Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms. Mol Psychiatry 17: 818–826.

4. WTCC (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661–678.

5. SklarP, SmollerJW, FanJ, FerreiraMA, PerlisRH, et al. (2008) Whole-genome association study of bipolar disorder. Mol Psychiatry 13: 558–569.

6. FerreiraMA, O'DonovanMC, MengYA, JonesIR, RuderferDM, et al. (2008) Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Nat Genet 40: 1056–1058.

7. McMahonFJ, AkulaN, SchulzeTG, MugliaP, TozziF, et al. (2010) Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1. Nat Genet 42: 128–131.

8. Psychiatric GWAS Consortium (2011) Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 43: 977–983.

9. ScottLJ, MugliaP, KongXQ, GuanW, FlickingerM, et al. (2009) Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. Proc Natl Acad Sci U S A 106: 7501–7506.

10. CraddockN, SklarP (2009) Genetics of bipolar disorder: successful start to a long journey. Trends Genet 25: 99–105.

11. CarrollLS, OwenMJ (2009) Genetic overlap between autism, schizophrenia and bipolar disorder. Genome Med 1: 102.

12. LanderES, BotsteinD (1987) Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 236: 1567–1570.

13. PeltonenL, PalotieA, LangeK (2000) Use of population isolates for mapping complex traits. Nat Rev Genet 1: 182–190.

14. TuysuzB, BayrakliF, DiLunaML, BilguvarK, BayriY, et al. (2008) Novel NTRK1 mutations cause hereditary sensory and autonomic neuropathy type IV: demonstration of a founder mutation in the Turkish population. Neurogenetics 9: 119–125.

15. MorrowEM, YooSY, FlavellSW, KimTK, LinY, et al. (2008) Identifying autism loci and genes by tracing recent shared ancestry. Science 321: 218–223.

16. Hostetler JA (1993) Amish society. Baltimore: Johns Hopkins University Press.

17. HostetterAM, EgelandJA, EndicottJ (1983) Amish Study, II: Consensus diagnoses and reliability results. Am J Psychiatry 140: 62–66.

18. Egeland JA (1994) An epidemiologic and genetic study of affective disorders among the Old Order Amish In: Papolos DF, Lachman HM, editors. Genetic Studies in Affective Disorders. New York: J. Wiley. Chap 4: : 70–90 pp.

19. PaulsDL, MortonLA, EgelandJA (1992) Risks of affective illness among first-degree relatives of bipolar I Old Order Amish probands. Arch Gen Psychiatry 49: 703–708.

20. EgelandJA, GerhardDS, PaulsDL, SussexJN, KiddKK, et al. (1987) Bipolar affective disorders linked to DNA markers on chromosome 11. Nature 325: 783–787.

21. KelsoeJR, GinnsEI, EgelandJA, GerhardDS, GoldsteinAM, et al. (1989) Re-evaluation of the linkage relationship between chromosome 11p loci and the gene for bipolar affective disorder in the Old Order Amish. Nature 342: 238–243.

22. GinnsEI, OttJ, EgelandJA, AllenCR, FannCS, et al. (1996) A genome-wide search for chromosomal loci linked to bipolar affective disorder in the Old Order Amish. Nat Genet 12: 431–435.

23. SpitzerRL, EndicottJ, RobinsE (1978) Research diagnostic criteria: rationale and reliability. Arch Gen Psychiatry 35: 773–782.

24. American Psychiatric Association (1994) Diagnostic and Statistical Manual of Mental Disorders 4th ed.

25. WangK, LiM, HadleyD, LiuR, GlessnerJ, et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17: 1665–1674.

26. DrmanacR, SparksAB, CallowMJ, HalpernAL, BurnsNL, et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327: 78–81.

27. AlmasyL, BlangeroJ (1998) Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62: 1198–1211.

28. ManichaikulA, MychaleckyjJC, RichSS, DalyK, SaleM, et al. (2010) Robust relationship inference in genome-wide association studies. Bioinformatics 26: 2867–2873.

29. AdzhubeiIA, SchmidtS, PeshkinL, RamenskyVE, GerasimovaA, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248–249.

30. KumarP, HenikoffS, NgPC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073–1081.

31. CooperGM, StoneEA, AsimenosG, GreenED, BatzoglouS, et al. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901–913.

32. KangHM, SulJH, ServiceSK, ZaitlenNA, KongSY, et al. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42: 348–354.

33. LairdNM, HorvathS, XuX (2000) Implementing a unified approach to family-based tests of association. Genet Epidemiol 19 Suppl 1: S36–42.

34. SpielmanRS, McGinnisRE, EwensWJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52: 506–516.

35. Belmonte MahonP, PiroozniaM, GoesFS, SeifuddinF, SteeleJ, et al. (2011) Genome-wide association analysis of age at onset and psychotic symptoms in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 156B: 370–378.

36. RipkeS, O'DushlaineC, ChambertK, MoranJL, KahlerAK, et al. (2013) Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet

37. DeG, YipWK, Ionita-LazaI, LairdN (2013) Rare variant analysis for family-based design. PLoS One 8: e48495.

38. FingerlinTE, BoehnkeM, AbecasisGR (2004) Increasing the power and efficiency of disease-marker case-control association studies through use of allele-sharing information. Am J Hum Genet 74: 432–443.

39. AbecasisGR, ChernySS, CooksonWO, CardonLR (2002) Merlin–rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30: 97–101.

40. GreenbergDA, AbreuPC (2001) Determining trait locus position from multipoint analysis: accuracy and power of three different statistics. Genet Epidemiol 21: 299–314.

41. HodgeSE, VielandVJ, GreenbergDA (2002) HLODs remain powerful tools for detection of linkage in the presence of genetic heterogeneity. Am J Hum Genet 70: 556–559.

42. BadnerJA, GershonES (2002) Meta-analysis of whole-genome linkage scans of bipolar disorder and schizophrenia. Mol Psychiatry 7: 405–411.

43. VenkenT, AlaertsM, SoueryD, GoossensD, SluijsS, et al. (2008) Chromosome 10q harbors a susceptibility locus for bipolar disorder in Ashkenazi Jewish families. Mol Psychiatry 13: 442–450.

44. BerrettiniWH, FerraroTN, GoldinLR, WeeksDE, Detera-WadleighS, et al. (1994) Chromosome 18 DNA markers and manic-depressive illness: evidence for a susceptibility gene. Proc Natl Acad Sci U S A 91: 5918–5921.

45. StineOC, XuJ, KoskelaR, McMahonFJ, GschwendM, et al. (1995) Evidence for linkage of bipolar disorder to chromosome 18 with a parent-of-origin effect. Am J Hum Genet 57: 1384–1394.

46. LinPI, McInnisMG, PotashJB, WillourVL, MackinnonDF, et al. (2005) Assessment of the effect of age at onset on linkage to bipolar disorder: evidence on chromosomes 18p and 21q. Am J Hum Genet 77: 545–555.

47. Detera-WadleighSD, BadnerJA, BerrettiniWH, YoshikawaT, GoldinLR, et al. (1999) A high-density genome scan detects evidence for a bipolar-disorder susceptibility locus on 13q32 and other potential loci on 1q32 and 18p11.2. Proc Natl Acad Sci U S A 96: 5604–5609.

48. MulleJG, FallinMD, LasseterVK, McGrathJA, WolyniecPS, et al. (2007) Dense SNP association study for bipolar I disorder on chromosome 18p11 suggests two loci with excess paternal transmission. Mol Psychiatry 12: 367–375.

49. MeerabuxJM, OhbaH, IwayamaY, MaekawaM, Detera-WadleighSD, et al. (2009) Analysis of a t(18;21)(p11.1;p11.1) translocation in a family with schizophrenia. J Hum Genet 54: 386–391.

50. AlsTD, DahlHA, FlintTJ, WangAG, VangM, et al. (2004) Possible evidence for a common risk locus for bipolar affective disorder and schizophrenia on chromosome 4p16 in patients from the Faroe Islands. Mol Psychiatry 9: 93–98.

51. Le HellardS, LeeAJ, UnderwoodS, ThomsonPA, MorrisSW, et al. (2007) Haplotype analysis and a novel allele-sharing method refines a chromosome 4p locus linked to bipolar affective disorder. Biol Psychiatry 61: 797–805.

52. BlackwoodDH, HeL, MorrisSW, McLeanA, WhittonC, et al. (1996) A locus for bipolar affective disorder on chromosome 4p. Nat Genet 12: 427–430.

53. GinnsEI, St JeanP, PhilibertRA, GaldzickaM, Damschroder-WilliamsP, et al. (1998) A genome-wide search for chromosomal loci linked to mental health wellness in relatives at high risk for bipolar affective disorder among the Old Order Amish. Proc Natl Acad Sci U S A 95: 15531–15536.

54. BrownCD, MangraviteLM, EngelhardtBE (2013) Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. PLoS Genet 9: e1003649.

55. StoreyJD (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society Series B 479–498.

56. CorvinAP (2010) Neuronal cell adhesion genes: Key players in risk for schizophrenia, bipolar disorder and other neurodevelopmental brain disorders? Cell Adh Migr 4: 511–514.

57. O'DushlaineC, KennyE, HeronE, DonohoeG, GillM, et al. (2011) Molecular pathways involved in neuronal cell adhesion and membrane scaffolding contribute to schizophrenia and bipolar disorder susceptibility. Mol Psychiatry 16: 286–292.

58. HolmH, GudbjartssonDF, SulemP, MassonG, HelgadottirHT, et al. (2011) A rare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat Genet 43: 316–320.

59. SulemP, GudbjartssonDF, WaltersGB, HelgadottirHT, HelgasonA, et al. (2011) Identification of low-frequency variants associated with gout and serum uric acid levels. Nat Genet 43: 1127–1130.

60. StaceySN, SulemP, JonasdottirA, MassonG, GudmundssonJ, et al. (2011) A germline variant in the TP53 polyadenylation signal confers cancer susceptibility. Nat Genet 43: 1098–1103.

61. RafnarT, GudbjartssonDF, SulemP, JonasdottirA, SigurdssonA, et al. (2011) Mutations in BRIP1 confer high risk of ovarian cancer. Nat Genet 43: 1104–1107.

62. JonssonT, AtwalJK, SteinbergS, SnaedalJ, JonssonPV, et al. (2012) A mutation in APP protects against Alzheimer's disease and age-related cognitive decline. Nature 488: 96–99.

63. YalcinB, Willis-OwenSA, FullertonJ, MeesaqA, DeaconRM, et al. (2004) Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice. Nat Genet 36: 1197–1202.

64. BendeskyA, TsunozakiM, RockmanMV, KruglyakL, BargmannCI (2011) Catecholamine receptor polymorphisms affect decision-making in C. elegans. Nature 472: 313–318.

65. EdwardsAC, MackayTF (2009) Quantitative trait loci for aggressive behavior in Drosophila melanogaster. Genetics 182: 889–897.

66. ZegginiE (2011) Next-generation association studies for complex traits. Nat Genet 43: 287–288.

67. PanoutsopoulouK, TachmazidouI, ZegginiE (2013) In search of low-frequency and rare variants affecting complex traits. Hum Mol Genet 22: R16–21.

68. StraussKA, PuffenbergerEG (2009) Genetics, medicine, and the Plain people. Annu Rev Genomics Hum Genet 10: 513–536.

69. KuhnertF, MancusoMR, ShamlooA, WangHT, ChoksiV, et al. (2010) Essential regulation of CNS angiogenesis by the orphan G protein-coupled receptor GPR124. Science 330: 985–989.

70. CullenM, ElzarradMK, SeamanS, ZudaireE, StevensJ, et al. (2011) GPR124, an orphan G protein-coupled receptor, is required for CNS-specific vascularization and establishment of the blood-brain barrier. Proc Natl Acad Sci U S A 108: 5759–5764.

71. WulffH, CastleNA, PardoLA (2009) Voltage-gated potassium channels as therapeutic targets. Nat Rev Drug Discov 8: 982–1001.

72. KuoPH, ChuangLC, LiuJR, LiuCM, HuangMC, et al. (2014) Identification of novel loci for bipolar I disorder in a multi-stage genome-wide association study. Prog Neuropsychopharmacol Biol Psychiatry

73. Benkert AR, Puffenberger EG, Markx S, Paul SM, Jinks RN, et al. (2013) A novel variant in the HERG3 voltage-gated potassium ion channel gene (KCHN7) is associated with bipolar spectrum disorder among the Old Order Amish. (Abstract #55) Presented at the 63rd Annual Meeting of The American Society of Human Genetics, Boston, MA.

74. KernerB, RaoAR, ChristensenB, DandekarS, YourshawM, et al. (2013) Rare Genomic Variants Link Bipolar Disorder with Anxiety Disorders to CREB-Regulated Intracellular Signaling Pathways. Front Psychiatry 4: 154.

75. CruceanuC, AmbalavananA, SpiegelmanD, GauthierJ, LafreniereRG, et al. (2013) Family-based exome-sequencing approach identifies rare susceptibility variants for lithium-responsive bipolar disorder. Genome 56: 634–640.

76. CongdonE, PoldrackRA, FreimerNB (2010) Neurocognitive phenotypes and genetic dissection of disorders of brain and behavior. Neuron 68: 218–230.

77. StefanssonH, Meyer-LindenbergA, SteinbergS, MagnusdottirB, MorgenK, et al. (2013) CNVs conferring risk of autism or schizophrenia affect cognition in controls. Nature 505: 361–366.

78. StyrkarsdottirU, ThorleifssonG, SulemP, GudbjartssonDF, SigurdssonA, et al. (2013) Nonsense mutation in the LGR4 gene is associated with several human diseases and other traits. Nature 497: 517–520.

79. AgarwalaV, FlannickJ, SunyaevS, AltshulerD (2013) Evaluating empirical bounds on complex disease genetic architecture. Nat Genet 45: 1418–1427.

80. EgelandJA, SussexJN, EndicottJ, HostetterAM, OffordDR, et al. (1990) The impact of diagnoses on genetic linkage study for bipolar affective disorders among the Amish. Psychiatric Genetics 1: 5–18.

81. EndicottJ, LothJE (1988) Schedule for Affective Disorders and Schizophrenia Lifetime Version, Third Edition. New York State Psychiatric Institute 1–46.

82. EndicottJ, SpitzerRL (1978) A diagnostic interview: the schedule for affective disorders and schizophrenia. Arch Gen Psychiatry 35: 837–844.

83. CarnevaliP, BaccashJ, HalpernAL, NazarenkoI, NilsenGB, et al. (2012) Computational techniques for human genome resequencing using mated gapped reads. J Comput Biol 19: 279–292.

84. LiuX, JianX, BoerwinkleE (2013) dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat 34: E2393–2402.

85. DiskinSJ, LiM, HouC, YangS, GlessnerJ, et al. (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 36: e126.

86. SmithEN, KollerDL, PanganibanC, SzelingerS, ZhangP, et al. (2011) Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes. PLoS Genet 7: e1002134.

87. HowieBN, DonnellyP, MarchiniJ (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5: e1000529.

88. LajonchereCM (2010) Changing the landscape of autism research: the autism genetic resource exchange. Neuron 68: 187–191.

89. CheungCY, ThompsonEA, WijsmanEM (2013) GIGI: an approach to effective imputation of dense genotypes on large pedigrees. Am J Hum Genet 92: 504–516.

90. MatiseTC, ChenF, ChenW, De La VegaFM, HansenM, et al. (2007) A second-generation combined linkage physical map of the human genome. Genome Res 17: 1783–1786.

91. BacanuSA (2005) Robust estimation of critical values for genome scans to detect linkage. Genet Epidemiol 28: 24–32.

92. MyersAJ, GibbsJR, WebsterJA, RohrerK, ZhaoA, et al. (2007) A survey of genetic human cortical gene expression. Nat Genet 39: 1494–1499.