J Pediatr Genet 2021; 10(04): 284-291
DOI: 10.1055/s-0040-1716400
Original Article

Whole-Exome Sequencing in Idiopathic Short Stature: Rare Mutations Affecting Growth

Shahab Noorian
1   Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
,
2   Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
,
Shahram Savad
3   Pars Genome Medical Genetics Clinic, Karaj, Iran
,
Benyamin Hakak-Zargar
4   Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
,
Tessa Voth
5   Department of Biomedical Physiology and Kinesiology, Faculty of Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
,
Koroush Kabir
6   Department of Community Medicine and Epidemiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
› Author Affiliations
Funding This project was funded through an award from Alborz University of Medical Sciences.

Abstract

Idiopathic short stature (ISS) is a common diagnosis of exclusion in patients with short stature (SS). In this article, we aimed to identify the genetic causes of SS in patients with ISS and investigate treatment options. Fourteen children with diagnosis of ISS were identified, and whole-exome sequencing (WES) was subsequently conducted on blood-derived DNA. Five patients were correctly diagnosed with ISS and four had rare mutations that have not been previously reported. Four patients had mutations known to cause SS and one had a mutation that was known not to affect height. WES can help identify rare mutations implicated in ISS.

Ethical Approval and Consent to Participate

This research was approved by the Alborz University of Medical Sciences research ethics committee. The purpose of this study was explained to the participant's parents/legal guardians in depth and written consent was obtained from them to use the data for research purposes. A separate informed written consent was obtained from all the patients' parents/legal guardians for publication purposes.


Availability of Data and Materials

The datasets used and/or analyzed during the current study are available from the corresponding author on request, with approval of the patients' legal guardians.


Authors' Contributions

N.M.K. and S.N. designed the study, clinical reviews, and performed the treatment of the patients. S.S. and B.H.Z performed genetic testing and analyzed genetic findings. K.K. designed the data collection instruments and performed data analysis. N.M.K. aided in the genetic study, drafted the initial manuscript, reviewed and revised the manuscript, enrolled the patients in the study, collected the data, and drafted the final manuscript. B.H.Z. and T.V. prepared, revised, and reviewed the final manuscript.


All authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work.




Publication History

Received: 18 May 2020

Accepted: 26 July 2020

Article published online:
18 September 2020

© 2020. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 
  • References

  • 1 Pedicelli S, Peschiaroli E, Violi E, Cianfarani S. Controversies in the definition and treatment of idiopathic short stature (ISS). J Clin Res Pediatr Endocrinol 2009; 1 (03) 105-115
  • 2 Bryant J, Baxter L, Cave CB, Milne R. Recombinant growth hormone for idiopathic short stature in children and adolescents. Cochrane Database Syst Rev 2007; (03) CD004440
  • 3 Seaver LH, Irons M. American College of Medical Genetics Professional Practice and Guidelines Committee. ACMG practice guideline: genetic evaluation of short stature. Genet Med 2009; 11 (06) 465-470
  • 4 Wit JM, Clayton PE, Rogol AD, Savage MO, Saenger PH, Cohen P. Idiopathic short stature: definition, epidemiology, and diagnostic evaluation. Growth Horm IGF Res 2008; 18 (02) 89-110
  • 5 Sisley S, Trujillo MV, Khoury J, Backeljauw P. Low incidence of pathology detection and high cost of screening in the evaluation of asymptomatic short children. J Pediatr 2013; 163 (04) 1045-1051
  • 6 Lifshitz F, Moses N. Nutritional dwarfing: growth, dieting, and fear of obesity. J Am Coll Nutr 1988; 7 (05) 367-376
  • 7 Forchielli ML, McColl R, Walker WA, Lo C. Children with congenital heart disease: a nutrition challenge. Nutr Rev 1994; 52 (10) 348-353
  • 8 Rosenfeld RG, Albertsson-Wikland K, Cassorla F. et al. Diagnostic controversy: the diagnosis of childhood growth hormone deficiency revisited. J Clin Endocrinol Metab 1995; 80 (05) 1532-1540
  • 9 Rappold G, Blum WF, Shavrikova EP. et al. Genotypes and phenotypes in children with short stature: clinical indicators of SHOX haploinsufficiency. J Med Genet 2007; 44 (05) 306-313
  • 10 Kruszka P, Porras AR, Addissie YA. et al. Noonan syndrome in diverse populations. Am J Med Genet A 2017; 173 (09) 2323-2334
  • 11 Eggermann T, Gonzalez D, Spengler S, Arslan-Kirchner M, Binder G, Schönherr N. Broad clinical spectrum in Silver-Russell syndrome and consequences for genetic testing in growth retardation. Pediatrics 2009; 123 (05) e929-e931
  • 12 Dauber A, Rosenfeld RG, Hirschhorn JN. Genetic evaluation of short stature. J Clin Endocrinol Metab 2014; 99 (09) 3080-3092
  • 13 Wit JM, Ranke MB, Kelnar CJJ. The ESPE classification of paediatric endocrine diagnoses-Foreword. Horm Res 2007; 68 (02) 1-120
  • 14 Lindsay R, Feldkamp M, Harris D, Robertson J, Rallison M. Utah Growth Study: growth standards and the prevalence of growth hormone deficiency. J Pediatr 1994; 125 (01) 29-35
  • 15 Chernausek SD. Whole exome sequencing in short stature: finding needles in the haystack. Horm Res Paediatr 2014; 82 (01) 1-2
  • 16 Savage MO, Bang P. The variability of responses to growth hormone therapy in children with short stature. Indian J Endocrinol Metab 2012; 16 (Suppl. 02) S178-S184
  • 17 Vassart G, Costagliola S. G protein-coupled receptors: mutations and endocrine diseases. Nat Rev Endocrinol 2011; 7 (06) 362-372
  • 18 Yin Y, Li Y, Zhang W. The growth hormone secretagogue receptor: its intracellular signaling and regulation. Int J Mol Sci 2014; 15 (03) 4837-4855
  • 19 Pantel J, Legendre M, Nivot S. et al. Recessive isolated growth hormone deficiency and mutations in the ghrelin receptor. J Clin Endocrinol Metab 2009; 94 (11) 4334-4341
  • 20 van Berkel Y, Ludwig M, van Wijk JAE, Bökenkamp A. Proteinuria in Dent disease: a review of the literature. Pediatr Nephrol 2017; 32 (10) 1851-1859
  • 21 Yanagida H, Ikeoka M, Kuwajima H. et al. A boy with Japanese Dent's disease exhibiting abnormal calcium metabolism and osseous disorder of the spine: defective megalin expression at the brushborder of renal proximal tubules. Clin Nephrol 2004; 62 (04) 306-312
  • 22 Lieske JC, Milliner DS, Beara-Lasic L, Harris P, Cogal A, Abrash E. Dent disease. In: Adam MP, Ardinger HH, Pagon RA. et al., eds. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 2017
  • 23 Li F, Yue Z, Xu T. et al. Dent disease in Chinese children and findings from heterozygous mothers: phenotypic heterogeneity, fetal growth, and 10 novel mutations. J Pediatr 2016; 174: 204-210.e1
  • 24 Newman WG, Friedman TB, Conway GS, Demain LA. Perrault syndrome. In: Adam MP, Ardinger HH, Pagon RA. et al., eds. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 2018
  • 25 Nishi Y, Hamamoto K, Kajiyama M, Kawamura I. The Perrault syndrome: clinical report and review. Am J Med Genet 1988; 31 (03) 623-629
  • 26 Weegerink NJ, Schraders M, Oostrik J. et al. Genotype-phenotype correlation in DFNB8/10 families with TMPRSS3 mutations. J Assoc Res Otolaryngol 2011; 12 (06) 753-766
  • 27 Carpena NT, Lee MY. Genetic hearing loss and gene therapy. Genomics Inform 2018; 16 (04) e20
  • 28 Prinos P, Costa T, Sommer A, Kilpatrick MW, Tsipouras P. A common FGFR3 gene mutation in hypochondroplasia. Hum Mol Genet 1995; 4 (11) 2097-2101
  • 29 Walker BA, Murdoch JL, McKusick VA, Langer LO, Beals RK. Hypochondroplasia. Am J Dis Child 1971; 122 (02) 95-104
  • 30 Elder GH, Roberts AG. Uroporphyrinogen decarboxylase. J Bioenerg Biomembr 1995; 27 (02) 207-214
  • 31 Kushner JP, Barbuto AJ, Lee GR. An inherited enzymatic defect in porphyria cutanea tarda: decreased uroporphyrinogen decarboxylase activity. J Clin Invest 1976; 58 (05) 1089-1097
  • 32 de Verneuil H, Beaumont C, Deybach JC, Nordmann Y, Sfar Z, Kastally R. Enzymatic and immunological studies of uroporphyrinogen decarboxylase in familial porphyria cutanea tarda and hepatoerythropoietic porphyria. Am J Hum Genet 1984; 36 (03) 613-622
  • 33 Cantatore-Francis JL, Cohen-Pfeffer J, Balwani M. et al. Hepatoerythropoietic porphyria misdiagnosed as child abuse: cutaneous, arthritic, and hematologic manifestations in siblings with a novel UROD mutation. Arch Dermatol 2010; 146 (05) 529-533
  • 34 Horner ME, Alikhan A, Tintle S, Tortorelli S, Davis DMR, Hand JL. Cutaneous porphyrias part I: epidemiology, pathogenesis, presentation, diagnosis, and histopathology. Int J Dermatol 2013; 52 (12) 1464-1480
  • 35 Fujimoto A, Brazil JL. Hepatoerythropoietic porphyria in a woman with short stature and deformed hands. Am J Med Genet 1992; 44 (04) 496-499
  • 36 Monnier N, Romero NB, Lerale J. et al. An autosomal dominant congenital myopathy with cores and rods is associated with a neomutation in the RYR1 gene encoding the skeletal muscle ryanodine receptor. Hum Mol Genet 2000; 9 (18) 2599-2608
  • 37 Zullo A, Klingler W, De Sarno C. et al. Functional characterization of ryanodine receptor (RYR1) sequence variants using a metabolic assay in immortalized B-lymphocytes. Hum Mutat 2009; 30 (04) E575-E590
  • 38 Phillips MS, Fujii J, Khanna VK. et al. The structural organization of the human skeletal muscle ryanodine receptor (RYR1) gene. Genomics 1996; 34 (01) 24-41
  • 39 Urwyler A, Deufel T, McCarthy T, West S. European Malignant Hyperthermia Group. Guidelines for molecular genetic detection of susceptibility to malignant hyperthermia. Br J Anaesth 2001; 86 (02) 283-287
  • 40 Robinson R, Carpenter D, Shaw MA, Halsall J, Hopkins P. Mutations in RYR1 in malignant hyperthermia and central core disease. Hum Mutat 2006; 27 (10) 977-989
  • 41 Dowling JJ, Lillis S, Amburgey K. et al. King-Denborough syndrome with and without mutations in the skeletal muscle ryanodine receptor (RYR1) gene. Neuromuscul Disord 2011; 21 (06) 420-427
  • 42 Stewart CR, Kahler SG, Gilchrist JM. Congenital myopathy with cleft palate and increased susceptibility to malignant hyperthermia: King syndrome?. Pediatr Neurol 1988; 4 (06) 371-374
  • 43 Tobin JR, Jason DR, Challa VR, Nelson TE, Sambuughin N. Malignant hyperthermia and apparent heat stroke. JAMA 2001; 286 (02) 168-169
  • 44 Caputo V, Cianetti L, Niceta M. et al. A restricted spectrum of mutations in the SMAD4 tumor-suppressor gene underlies Myhre syndrome. Am J Hum Genet 2012; 90 (01) 161-169
  • 45 Schutte M. DPC4/SMAD4 gene alterations in human cancer, and their functional implications. Ann Oncol 1999; 10 (Suppl. 04) 56-59
  • 46 de Caestecker MP, Hemmati P, Larisch-Bloch S, Ajmera R, Roberts AB, Lechleider RJ. Characterization of functional domains within Smad4/DPC4. J Biol Chem 1997; 272 (21) 13690-13696
  • 47 Michot C, Le Goff C, Mahaut C. et al. Myhre and LAPS syndromes: clinical and molecular review of 32 patients. Eur J Hum Genet 2014; 22 (11) 1272-1277
  • 48 McGowan R, Gulati R, McHenry P. et al. Clinical features and respiratory complications in Myhre syndrome. Eur J Med Genet 2011; 54 (06) e553-e559
  • 49 Briggs MD, Chapman KL. Pseudoachondroplasia and multiple epiphyseal dysplasia: mutation review, molecular interactions, and genotype to phenotype correlations. Hum Mutat 2002; 19 (05) 465-478
  • 50 Bönnemann CG, Cox GF, Shapiro F. et al. A mutation in the alpha 3 chain of type IX collagen causes autosomal dominant multiple epiphyseal dysplasia with mild myopathy. Proc Natl Acad Sci U S A 2000; 97 (03) 1212-1217
  • 51 Chapman KL, Mortier GR, Chapman K, Loughlin J, Grant ME, Briggs MD. Mutations in the region encoding the von Willebrand factor A domain of matrilin-3 are associated with multiple epiphyseal dysplasia. Nat Genet 2001; 28 (04) 393-396
  • 52 Brennan M-L, Schrijver I. Cystic fibrosis: A review of associated phenotypes, use of molecular diagnostic approaches, genetic characteristics, progress, and dilemma. J Mol Diagn 2016; 18 (01) 3-14