Ann Pediatr Endocrinol Metab.  2017 Jun;22(2):90-94. 10.6065/apem.2017.22.2.90.

Next generation sequencing and array-based comparative genomic hybridization for molecular diagnosis of pediatric endocrine disorders

Affiliations
  • 1Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan. fukami-m@ncchd.go.jp

Abstract

Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders. Array CGH is currently used as the standard procedure for molecular cytogenetic analysis. Array CGH can detect various submicroscopic genomic rearrangements involving exons or enhancers of disease-associated genes. This review introduces some examples of the use of NGS and array CGH for the molecular diagnosis of pediatric endocrine disorders.

Keyword

Next-generation sequencer; Mutation; Comparative genomic hybridization; DNA Copy-number variations; Diagnosis

MeSH Terms

Comparative Genomic Hybridization*
Cytogenetic Analysis
Diagnosis*
Exome
Exons
Mass Screening

Figure

  • Fig. 1 Representative results of next generation sequencing. Each gray bar denotes a 100-bp DNA fragment obtained from a patient's sample. Substituted nucleotides are highlighted by colored letters. This patient carries a heterozygous A to C substitution (the blue box). All other substitutions in this figure are likely to be sequence errors.

  • Fig. 2 Representative results of array-based comparative genomic hybridization. Submicroscopic deletion identified in a patient with 46,XY disorders of sex development is shown. This deletion likely encompasses a cis-acting enhancer(s) of SOX914). The deletion was shared by the patient's mother. The black, red, and green dots denote signals indicative of the normal, the increased (>+0.5) and the decreased (<−1.0) copy-numbers, respectively. Green arrows depict deleted regions. Genomic positions refer to the Human Genome (hg19, build 37).


Reference

1. Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet. 2007; 39(7 Suppl):S48–S54. PMID: 17597782.
Article
2. Buonocore F, Achermann JC. Human sex development: targeted technologies to improve diagnosis. Genome Biol. 2016; 17:257. PMID: 27978845.
Article
3. Eggers S, Sadedin S, van den Bergen JA, Robevska G, Ohnesorg T, Hewitt J, et al. Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort. Genome Biol. 2016; 17:243. PMID: 27899157.
Article
4. Burke W. Genetic testing. N Engl J Med. 2002; 347:1867–1875. PMID: 12466512.
Article
5. Katsanis SH, Katsanis N. Molecular genetic testing and the future of clinical genomics. Nat Rev Genet. 2013; 14:415–426. PMID: 23681062.
Article
6. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008; 18:1638–1642. PMID: 18775913.
Article
7. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008; 26:1135–1145. PMID: 18846087.
Article
8. Metzker ML. Sequencing technologies: the next generation. Nat Rev Genet. 2010; 11:31–46. PMID: 19997069.
9. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998; 20:207–211. PMID: 9771718.
Article
10. Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, Choy CO, et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet. 2003; 73:1261–1270. PMID: 14628292.
Article
11. Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006; 7:85–97. PMID: 16418744.
Article
12. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010; 86:749–764. PMID: 20466091.
Article
13. Izumi Y, Suzuki E, Kanzaki S, Yatsuga S, Kinjo S, Igarashi M, et al. Genome-wide copy number analysis and systematic mutation screening in 58 patients with hypogonadotropic hypogonadism. Fertil Steril. 2014; 102:1130–1136.e3. PMID: 25064402.
Article
14. Katoh-Fukui Y, Igarashi M, Nagasaki K, Horikawa R, Nagai T, Tsuchiya T, et al. Testicular dysgenesis/regression without campomelic dysplasia in patients carrying missense mutations and upstream deletion of SOX9. Mol Genet Genomic Med. 2015; 3:550–557. PMID: 26740947.
15. Kon M, Suzuki E, Dung VC, Hasegawa Y, Mitsui T, Muroya K, et al. Molecular basis of non-syndromic hypospadias: systematic mutation screening and genome-wide copy-number analysis of 62 patients. Hum Reprod. 2015; 30:499–506. PMID: 25605705.
Article
16. Fukami M, Suzuki E, Izumi Y, Torii T, Narumi S, Igarashi M, et al. Paradoxical gain-of-function mutant of the G-protein-coupled receptor PROKR2 promotes early puberty. J Cell Mol Med. 2017; 3. 24. [Epub]. DOI: 10.1111/jcmm.13146.
17. Alatzoglou KS, Kelberman D, Cowell CT, Palmer R, Arnhold IJ, Melo ME, et al. Increased transactivation associated with SOX3 polyalanine tract deletion in a patient with hypopituitarism. J Clin Endocrinol Metab. 2011; 96:E685–E690. PMID: 21289259.
Article
18. Kim HG, Ahn JW, Kurth I, Ullmann R, Kim HT, Kulharya A, et al. WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. Am J Hum Genet. 2010; 87:465–479. PMID: 20887964.
Article
19. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011; 12:745–755. PMID: 21946919.
Article
20. Abreu AP, Dauber A, Macedo DB, Noel SD, Brito VN, Gill JC, et al. Central precocious puberty caused by mutations in the imprinted gene MKRN3. N Engl J Med. 2013; 368:2467–2475. PMID: 23738509.
Article
21. Settas N, Dacou-Voutetakis C, Karantza M, Kanaka-Gantenbein C, Chrousos GP, Voutetakis A. Central precocious puberty in a girl and early puberty in her brother caused by a novel mutation in the MKRN3 gene. J Clin Endocrinol Metab. 2014; 99:E647–E651. PMID: 24438377.
Article
22. Shin YL. An update on the genetic causes of central precocious puberty. Ann Pediatr Endocrinol Metab. 2016; 21:66–69. PMID: 27462581.
Article
23. Christoforidis A, Skordis N, Fanis P, Dimitriadou M, Sevastidou M, Phelan MM, et al. A novel MKRN3 nonsense mutation causing familial central precocious puberty. Endocrine. 2017; 56:446–449. PMID: 28132164.
Article
24. Bashamboo A, Donohoue PA, Vilain E, Rojo S, Calvel P, Seneviratne SN, et al. A recurrent p.Arg92Trp variant in steroidogenic factor-1 (NR5A1) can act as a molecular switch in human sex development. Hum Mol Genet. 2016; 25:3446–3453. PMID: 27378692.
Article
25. Baetens D, Stoop H, Peelman F, Todeschini AL, Rosseel T, Coppieters F, et al. NR5A1 is a novel disease gene for 46,XX testicular and ovotesticular disorders of sex development. Genet Med. 2017; 19:367–376. PMID: 27490115.
Article
26. Igarashi M, Takasawa K, Hakoda A, Kanno J, Takada S, Miyado M, et al. Identical NR5A1 missense mutations in two unrelated 46,XX individuals with testicular tissues. Hum Mutat. 2017; 38:39–42. PMID: 27610946.
Article
27. Miyado M, Inui M, Igarashi M, Katoh-Fukui Y, Takasawa K, Hakoda A, et al. The p.R92W variant of NR5A1/Nr5a1 induces testicular development of 46,XX gonads in humans, but not in mice: phenotypic comparison of human patients and mutation-induced mice. Biol Sex Differ. 2016; 7:56. PMID: 27833742.
Article
28. Beckmann JS, Estivill X, Antonarakis SE. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet. 2007; 8:639–646. PMID: 17637735.
Article
29. Igarashi M, Dung VC, Suzuki E, Ida S, Nakacho M, Nakabayashi K, et al. Cryptic genomic rearrangements in three patients with 46,XY disorders of sex development. PLoS One. 2013; 8:e68194. PMID: 23861871.
Article
30. Fukami M, Naiki Y, Muroya K, Hamajima T, Soneda S, Horikawa R, et al. Rare pseudoautosomal copy-number variations involving SHOX and/or its flanking regions in individuals with and without short stature. J Hum Genet. 2015; 60:553–556. PMID: 26040210.
Article
31. Fukami M, Seki A, Ogata T. SHOX haploinsufficiency as a cause of syndromic and nonsyndromic short stature. Mol Syndromol. 2016; 7:3–11. PMID: 27194967.
32. Shima H, Tanaka T, Kamimaki T, Dateki S, Muroya K, Horikawa R, et al. Systematic molecular analyses of SHOX in Japanese patients with idiopathic short stature and Leri-Weill dyschondrosteosis. J Hum Genet. 2016; 61:585–591. PMID: 26984564.
Article
33. Benito-Sanz S, Barroso E, Heine-Suñer D, Hisado-Oliva A, Romanelli V, Rosell J, et al. Clinical and molecular evaluation of SHOX/PAR1 duplications in Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS). J Clin Endocrinol Metab. 2011; 96:E404–E412. PMID: 21147883.
34. Benito-Sanz S, Royo JL, Barroso E, Paumard-Hernández B, Barreda-Bonis AC, Liu P, et al. Identification of the first recurrent PAR1 deletion in Léri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer. J Med Genet. 2012; 49:442–450. PMID: 22791839.
Article
35. Fukami M, Kato F, Tajima T, Yokoya S, Ogata T. Transactivation function of an approximately 800-bp evolutionarily conserved sequence at the SHOX 3' region: implication for the downstream enhancer. Am J Hum Genet. 2006; 78:167–170. PMID: 16385461.
Article
36. Fukami M, Shozu M, Soneda S, Kato F, Inagaki A, Takagi H, et al. Aromatase excess syndrome: identification of cryptic duplications and deletions leading to gain of function of CYP19A1 and assessment of phenotypic determinants. J Clin Endocrinol Metab. 2011; 96:E1035–E1043. PMID: 21470988.
37. Fukami M, Tsuchiya T, Vollbach H, Brown KA, Abe S, Ohtsu S, et al. Genomic basis of aromatase excess syndrome: recombination- and replication-mediated rearrangements leading to CYP19A1 overexpression. J Clin Endocrinol Metab. 2013; 98:E2013–E2021. PMID: 24064691.
Article
38. Fukami M, Miyado M, Nagasaki K, Shozu M, Ogata T. Aromatase excess syndrome: a rare autosomal dominant disorder leading to pre- or peri-pubertal onset gynecomastia. Pediatr Endocrinol Rev. 2014; 11:298–305. PMID: 24716396.
39. Shihara D, Miyado M, Nakabayashi K, Shozu M, Ogata T, Nagasaki K, et al. Aromatase excess syndrome in a family with upstream deletion of CYP19A1. Clin Endocrinol (Oxf). 2014; 81:314–316. PMID: 24102311.
Article
40. Vasli N, Böhm J, Le Gras S, Muller J, Pizot C, Jost B, et al. Next generation sequencing for molecular diagnosis of neuromuscular diseases. Acta Neuropathol. 2012; 124:273–283. PMID: 22526018.
Article
41. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013; 15:565–574. PMID: 23788249.
42. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015; 17:405–424. PMID: 25741868.
43. Matthijs G, Souche E, Alders M, Corveleyn A, Eck S, Feenstra I, et al. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet. 2016; 24:2–5. PMID: 26508566.
Article
44. Wapner RJ, Martin CL, Levy B, Ballif BC, Eng CM, Zachary JM, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012; 367:2175–2184. PMID: 23215555.
45. Benn P, Cuckle H, Pergament E. Non-invasive prenatal testing for aneuploidy: current status and future prospects. Ultrasound Obstet Gynecol. 2013; 42:15–33. PMID: 23765643.
46. Marrs T, Flohr C. The role of skin and gut microbiota in the development of atopic eczema. Br J Dermatol. 2016; 175(Suppl 2):13–18.
47. Ma L, Xie Y, Han Z, Giesy JP, Zhang X. Responses of earthworms and microbial communities in their guts to Triclosan. Chemosphere. 2017; 168:1194–1202. PMID: 27810239.
Full Text Links
  • APEM
Actions
Cited
CITED
export Copy
Close
Share
  • Twitter
  • Facebook
Similar articles
Copyright © 2024 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr