Insights from exome sequencing for endocrine disorders

Nature Reviews Endocrinology

Volumn 11, Issue 8, 2015, Pages 455-464

  De Bruin, Christiaan ^a   Dauber, Andrew ^a  

^a CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIOVASCULAR DISEASE; DYSLIPIDEMIA; ENDOCRINE DISEASE; ENDOCRINE TUMOR; ENDOCRINOLOGY; EXOME; FAMILIAL DISEASE; FAMILIAL GLUCOCORTICOID DEFICIENCY; GENE SEQUENCE; GROWTH DISORDER; HORMONE DEFICIENCY; HUMAN; HYPERCORTISOLISM; HYPOGONADISM; NEUROENDOCRINE TUMOR; NON INSULIN DEPENDENT DIABETES MELLITUS; OSTEOPOROSIS; PRIMARY HYPERALDOSTERONISM; PRIORITY JOURNAL; PUBERTY DISORDERS; RARE DISEASE; REVIEW; THYROID DYSGENESIS; WHOLE EXOME SEQUENCING; X CHROMOSOME LINKED DISORDER; GENETICS; HIGH THROUGHPUT SEQUENCING; SEQUENCE ANALYSIS; SEXUAL MATURATION;

ENDOCRINE SYSTEM DISEASES; EXOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS; SEXUAL MATURATION;

EID: 84937732630     PISSN: 17595029     EISSN: 17595037     Source Type: Journal    
DOI: 10.1038/nrendo.2015.72     Document Type: Review

References (104)

1. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001
2. Bamshad, M.J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755 (2011
3. Biesecker, L.G. & Green, R.C. Diagnostic clinical genome and exome sequencing. N. Engl. J. Med. 371, 1170 (2014
4. Biesecker, L.G., Shianna, K.V. & Mullikin, J.C. Exome sequencing: the expert view. Genome Biol. 12, 128 (2011
5. Ng, S.B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790-793 (2010
6. Dunkel, L. & Quinton, R. Transition in endocrinology: induction of puberty. Eur. J. Endocrinol. 170, R229-R239 (2014
7. Abreu, A.P. et al. Central precocious puberty caused by mutations in the imprinted gene MKRN3. N. Engl. J. Med. 368, 2467-2475 (2013
8. Macedo, D.B. et al. Central precocious puberty that appears to be sporadic caused by paternally inherited mutations in the imprinted gene makorin ring finger 3. J. Clin. Endocrinol. Metab. 99, E1097-E1103 (2014
9. Forni, P.E. & Wray, S. GnRH, anosmia and hypogonadotropic hypogonadism-where are we?. Front. Neuroendocrinol. 36C, 165-177 (2015
10. Kotan, L.D. et al. Mutations in FEZF1 cause Kallmann syndrome. Am. J. Hum. Genet. 95, 326-331 (2014
11. Eckler, M.J., McKenna, W.L., Taghvaei, S., McConnell, S.K. & Chen, B. Fezf1 and Fezf2 are required for olfactory development and sensory neuron identity. J. Comp. Neurol. 519, 1829-1846 (2011
12. Shi, C.H. et al. Ataxia and hypogonadism caused by the loss of ubiquitin ligase activity of the U box protein CHIP. Hum. Mol. Genet. 23, 1013-1024 (2014
13. Synofzik, M. et al. PNPLA6 mutations cause Boucher-Neuhauser and Gordon Holmes syndromes as part of a broad neurodegenerative spectrum. Brain 137, 69-77 (2014
14. Topaloglu, A.K. et al. Loss of function mutations in PNPLA6 encoding neuropathy target esterase underlie pubertal failure and neurological deficits in Gordon Holmes syndrome. J. Clin. Endocrinol. Metab. 99, E2067-E2075 (2014
15. Margolin, D.H. et al. Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination. N. Engl. J. Med. 368, 1992-2003 (2013
16. Zangen, D. et al. XX ovarian dysgenesis is caused by a PSMC3IP/HOP2 mutation that abolishes coactivation of estrogen-driven transcription. Am. J. Hum. Genet. 89, 572-579 (2011
17. Caburet, S. et al. Mutant cohesin in premature ovarian failure. N. Engl. J. Med. 370, 943-949 (2014
18. Kasippillai, T. et al. Mutations in eIF4ENIF1 are associated with primary ovarian insufficiency. J. Clin. Endocrinol. Metab. 98, E1534-E1539 (2013
19. De Vries, L. et al. Exome sequencing reveals SYCE1 mutation associated with autosomal recessive primary ovarian insufficiency. J. Clin. Endocrinol. Metab. 99, E2129-E2132 (2014
20. Meimaridou, E. et al. Familial glucocorticoid deficiency: new genes and mechanisms. Mol. Cell. Endocrinol. 371, 195-200 (2013
21. Meimaridou, E. et al. Mutations in NNT encoding nicotinamide nucleotide transhydrogenase cause familial glucocorticoid deficiency. Nat. Genet. 44, 740-742 (2012
22. Prasad, R. et al. Thioredoxin reductase 2 (TXNRD2) mutation associated with familial glucocorticoid deficiency (FGD). J. Clin. Endocrinol. Metab. 99, E1556-E1563 (2014
23. Hughes, C.R. et al. MCM4 mutation causes adrenal failure, short stature, and natural killer cell deficiency in humans. J. Clin. Invest. 122, 814-820 (2012
24. Meimaridou, E. et al. ACTH resistance: genes and mechanisms. Endocr. Dev. 24, 57-66 (2013
25. Masai, H., You, Z. & Arai, K. Control of DNA replication: regulation and activation of eukaryotic replicative helicase, MCM. IUBMB Life 57, 323-335 (2005
26. Sun, Y. et al. Loss-of-function mutations in IGSF1 cause an X linked syndrome of central hypothyroidism and testicular enlargement. Nat. Genet. 44, 1375-1381 (2012
27. Joustra, S.D. et al. The IGSF1 deficiency syndrome: characteristics of male and female patients. J. Clin. Endocrinol. Metab. 98, 4942-4952 (2013
28. Joustra, S.D. et al. IGSF1 deficiency syndrome: a newly uncovered endocrinopathy. Rare Dis. 1, e24883 (2013
29. Mazzarella, R., Pengue, G., Jones, J., Jones, C. & Schlessinger, D. Cloning and expression of an immunoglobulin superfamily gene (IGSF1) in Xq25. Genomics 48, 157-162 (1998
30. Kuhnen, P. et al. Identification of PENDRIN (SLC26A4) mutations in patients with congenital hypothyroidism and "apparent" thyroid dysgenesis. J. Clin. Endocrinol. Metab. 99, E169-E176 (2014
31. Manolio, T.A. Genome-wide association studies and assessment of the risk of disease. N. Engl. J. Med. 363, 166-176 (2010
32. SIGMA Type 2 Diabetes Consortium. Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population. JAMA 311, 2305-2314 (2014
33. Lange, L.A. et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am. J. Hum. Genet. 94, 233-245 (2014
34. Rosenthal, E.A. et al. Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia. Am. J. Hum. Genet. 93, 1035-1045 (2013
35. Pagliarini, D.J. et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell 134, 112-123 (2008
36. Musunuru, K. et al. Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia. N. Engl. J. Med. 363, 2220-2227 (2010
37. Koishi, R. et al. Angptl3 regulates lipid metabolism in mice. Nat. Genet. 30, 151-157 (2002
38. Abifadel, M. et al. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat. Genet. 34, 154-156 (2003
39. Cohen, J. et al. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat. Genet. 37, 161-165 (2005
40. Farnier, M. PCSK9: From discovery to therapeutic applications. Arch. Cardiovasc. Dis. 107, 58-66 (2014
41. Albrechtsen, A. et al. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia 56, 298-310 (2013
42. Lohmueller, K.E. et al. Whole-exome sequencing of 2, 000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am. J. Hum. Genet. 93, 1072-1086 (2013
43. Steinthorsdottir, V. et al. Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes. Nat. Genet. 46, 294-298 (2014
44. Kushner, J.A. et al. Cyclins D2 and D1 are essential for postnatal pancreatic β-cell growth. Mol. Cell Biol. 25, 3752-3762 (2005
45. Maestro, M.A. et al. Distinct roles of HNF1β, HNF1a, and HNF4a in regulating pancreas development, β-cell function and growth. Endocr. Dev. 12, 33-45 (2007
46. Wood, A.R. et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46, 1173-1186 (2014
47. Chan, Y. et al. Common variants show predicted polygenic effects on height in the tails of the distribution, except in extremely short individuals. PLoS Genet. 7, e1002439 (2011
48. Nilsson, O. et al. Short stature, accelerated bone maturation, and early growth cessation due to heterozygous aggrecan mutations. J. Clin. Endocrinol. Metab. 99, E1510-E1518 (2014
49. Van Dijk, F.S. et al. PLS3 mutations in X linked osteoporosis with fractures. N. Engl. J. Med. 369, 1529-1536 (2013
50. Laine, C.M. et al. A novel splice-mutation in PLS3 causes X linked early-onset low-turnover osteoporosis. J. Bone Miner. Res. 30, 510-518 (2014
51. Thomas, F., Desmedt, C., Aftimos, P. & Awada, A. Impact of tumor sequencing on the use of anticancer drugs. Curr. Opin. Oncol. 26, 347-356 (2014
52. Sahakitrungruang, T. et al. Germline and somatic DICER1 mutations in a pituitary blastoma causing infantile onset Cushing disease. J. Clin. Endocrinol. Metab. 99, E1487-E1492 (2014
53. Goh, G. et al. Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors. Nat. Genet. 46, 613-617 (2014
54. Sato, Y. et al. Recurrent somatic mutations underlie corticotropin-independent Cushing's syndrome. Science 344, 917-920 (2014
55. Cao, Y. et al. Activating hotspot L205R mutation in PRKACA and adrenal Cushing's syndrome. Science 344, 913-917 (2014
56. Beuschlein, F. et al. Constitutive activation of PKA catalytic subunit in adrenal Cushing's syndrome. N. Engl. J. Med. 370, 1019-1028 (2014
57. Assie, G. et al. Integrated genomic characterization of adrenocortical carcinoma. Nat. Genet. 46, 607-612 (2014
58. Assie, G. et al. ARMC5 mutations in macronodular adrenal hyperplasia with Cushing's syndrome. N. Engl. J. Med. 369, 2105-2114 (2013
59. Gagliardi, L. et al. ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia. J. Clin. Endocrinol. Metab. 99, E1784-E1792 (2014
60. Tissier, F. et al. Mutations of β-catenin in adrenocortical tumors: activation of the Wnt signaling pathway is a frequent event in both benign and malignant adrenocortical tumors. Cancer Res. 65, 7622-7627 (2005
61. Fagugli, R.M. & Taglioni, C. Changes in the perceived epidemiology of primary hyperaldosteronism. Int. J. Hypertens. 2011, 162804 (2011
62. Al-Salameh, A., Cohen, R. & Desailloud, R. Overview of the genetic determinants of primary aldosteronism. Appl. Clin. Genet. 7, 67-79 (2014
63. Conn, J.W. & Louis, L.H. Primary aldosteronism: a new clinical entity. Trans. Assoc. Am. Physicians 68, 215-231 (1955
64. Choi, M. et al. K+ channel mutations in adrenal aldosterone-producing adenomas and hereditary hypertension. Science 331, 768-772 (2011
65. Monticone, S. et al. A Novel Y152C KCNJ5 mutation responsible for familial hyperaldosteronism type III. J. Clin. Endocrinol. Metab. 98, E1861-E1865 (2013
66. Beuschlein, F. et al. Somatic mutations in ATP1A1 and ATP2B3 lead to aldosterone-producing adenomas and secondary hypertension. Nat. Genet. 45, 440-444 (2013
67. Azizan, E.A. et al. Somatic mutations in ATP1A1 and CACNA1D underlie a common subtype of adrenal hypertension. Nat. Genet. 45, 1055-1060 (2013
68. Newey, P.J. et al. Whole-exome sequencing studies of nonhereditary (sporadic) parathyroid adenomas. J. Clin. Endocrinol. Metab. 97, E1995-E2005 (2012
69. Cromer, M.K. et al. Identification of somatic mutations in parathyroid tumors using whole-exome sequencing. J. Clin. Endocrinol. Metab. 97, E1774-E1781 (2012
70. Newey, P.J. et al. Whole-exome sequencing studies of nonfunctioning pituitary adenomas. J. Clin. Endocrinol. Metab. 98, E796-E800 (2013
71. Cao, M. et al. Analysis of the inheritance pattern of a Chinese family with phaeochromocytomas through whole exome sequencing. Gene 526, 164-169 (2013
72. Cao, Y. et al. Whole exome sequencing of insulinoma reveals recurrent T372R mutations in YY1. Nat. Commun. 4, 2810 (2013
73. Foulkes, W.D., Priest, J.R. & Duchaine, T.F. DICER1: mutations, microRNAs and mechanisms. Nat. Rev. Cancer 14, 662-72 (2014
74. Guo, M.H. et al. Whole exome sequencing to identify genetic causes of short stature. Horm. Res. Paediatr. 82, 44-52 (2014
75. Unger, S. et al. FAM111A mutations result in hypoparathyroidism and impaired skeletal development. Am. J. Hum. Genet. 92, 990-995 (2013
76. Biesecker, L.G. & Green, R.C. Diagnostic clinical genome and exome sequencing. N. Engl. J. Med. 370, 2418-2425 (2014
77. 1000 Genomes Project [online], http: //1000genomes.org (2014
78. NHLBI Exome Sequencing Project. Exome variant server [online], http: //evs.gs.washington.edu (2015
79. Exome Aggregation Consortium ExAC Browser (Beta) [online], http: //exac.broadinstitute.org (2015
80. Wang, G.T., Peng, B. & Leal, S.M. Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. Am. J. Hum. Genet. 94, 770-783 (2014
81. Flannick, J. et al. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nat. Genet. 45, 1380-1385 (2013
82. Green, R.C. et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet. Med. 15, 565-574 (2013
83. Smith, L.A., Douglas, J., Braxton, A.A. & Kramer, K. Reporting incidental findings in clinical whole exome sequencing: incorporation of the 2013 ACMG recommendations into current practices of genetic counseling. J. Genet. Couns. http: //dx.doi.org/10.1007/s10897-014-9794-4.
84. Yang, Y. et al. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. N. Engl. J. Med. 369, 1502-1511 (2013
85. Yang, Y. et al. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 312, 1870-1879 (2014
86. Lee, H. et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 312, 1880-1887 (2014
87. Baxter, R.M. et al. Exome sequencing for the diagnosis of 46, XY disorders of sex development. J. Clin. Endocrinol. Metab. 100, E333-E344 (2014
88. Waldman, L.A. & Chia, D.J. Towards identification of molecular mechanisms of short stature. Int. J. Pediatr. Endocrinol. 2013, 19 (2013
89. Dauber, A., Rosenfeld, R.G. & Hirschhorn, J.N. Genetic evaluation of short stature. J. Clin. Endocrinol. Metab. 99, 3080-3092 (2014
90. Samuels, M.E. et al. Bioinactive ACTH causing glucocorticoid deficiency. J. Clin. Endocrinol. Metab. 98, 736-742 (2013
91. Tegtmeyer, L.C. et al. Multiple phenotypes in phosphoglucomutase 1 deficiency. N. Engl. J. Med. 370, 533-542 (2014
92. Webb, E.A. et al. ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies. Brain 136, 3096-3105 (2013
93. Dauber, A. et al. Genetic defect in CYP24A1, the vitamin D 24-hydroxylase gene, in a patient with severe infantile hypercalcemia. J. Clin. Endocrinol. Metab. 97, E268-E274 (2012
94. Dauber, A. et al. Novel microcephalic primordial dwarfism disorder associated with variants in the centrosomal protein ninein. J. Clin. Endocrinol. Metab. 97, E2140-E2151 (2012
95. Hanson, D. et al. Exome sequencing identifies CCDC8 mutations in 3 M syndrome, suggesting that CCDC8 contributes in a pathway with CUL7 and OBSL1 to control human growth. Am. J. Hum. Genet. 89, 148-153 (2011
96. Nilsson, O. et al. Short stature, accelerated bone maturation, and early growth cessation due to heterozygous aggrecan mutations. J. Clin. Endocrinol. Metab. 99, E1510-E1518 (2014
97. Kerns, S.L. et al. A novel variant in CDKN1C is associated with intrauterine growth restriction, short stature, and early-Adulthood onset diabetes. J. Clin. Endocrinol. Metab. 99, E2117-E2122 (2014
98. Al-Maawali, A. et al. Prenatal growth restriction, retinal dystrophy, diabetes insipidus and white matter disease: expanding the spectrum of PRPS1-related disorders. Eur. J. Hum. Genet. 23, 310-316 (2015
99. Bashamboo, A. et al. Mutations in the FOG2/ZFPM2 gene are associated with anomalies of human testis determination. Hum. Mol. Genet. 23, 3657-3665 (2014
100. Stitziel, N.O. et al. Exome sequencing and directed clinical phenotyping diagnose cholesterol ester storage disease presenting as autosomal recessive hypercholesterolemia. Arterioscler. Thromb. Vasc. Biol. 33, 2909-2914 (2013
101. Gillis, D. et al. TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. J. Med. Genet. 51, 581-586 (2014
102. Peloso, G.M. et al. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56, 000 whites and blacks. Am. J. Hum. Genet. 94, 223-232 (2014
103. Moltke, I. et al. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature 512, 190-193 (2014
104. Du, M. et al. Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans. Hum. Mol. Genet. 23, 6607-6615 (2014