Genetic Analysis of Short Stature

A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

BACKGROUND

Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a "large" number of genes with "small" effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size.

METHODS

The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs.

RESULTS

GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67-66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~ 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~ 65.67-66.31 Mb).

CONCLUSIONS

To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

[How do Affected Children and Adolescents Experience their Short Stature, and what is the Point of View of their Parents?]

How do Affected Children and Adolescents Experience their Short Stature, and what is the Point of View of their Parents? Despite a large number of publications on the psychosocial situation of short statured children and their parents only a few qualitative studies focus on the perspective of the affected families. Within the European QoLISSY study ("Quality of Life in Short Stature Youth") an instrument to assess the health related quality of life of short statured children was developed. The aim of this project was to examine the self-perceived quality of life of the children themselves in comparison to their parents' perspective. During the development of the QoLISSY instrument, focus groups were conducted as a first step of this study. A total of 23 short statured children and 31 parents participated and discussed their experiences in separate groups with trained moderators. The discussions were analyzed qualitatively und results were used to generate a first list of items for the questionnaire to be developed. While parents focused on socio-emotional problems, children talked much more about their growth hormone treatment and problems in their social environment. In comparison to other studies children rated their quality of life worse than their parents. Not only medical treatment but also a psychological and socio-emotional intervention seems to be indicated.

A Track Record on SHOX: From Basic Research to Complex Models and Therapy

SHOX deficiency is the most frequent genetic growth disorder associated with isolated and syndromic forms of short stature. Caused by mutations in the homeobox gene SHOX, its varied clinical manifestations include isolated short stature, Léri-Weill dyschondrosteosis, and Langer mesomelic dysplasia. In addition, SHOX deficiency contributes to the skeletal features in Turner syndrome. Causative SHOX mutations have allowed downstream pathology to be linked to defined molecular lesions. Expression levels of SHOX are tightly regulated, and almost half of the pathogenic mutations have affected enhancers. Clinical severity of SHOX deficiency varies between genders and ranges from normal stature to profound mesomelic skeletal dysplasia. Treatment options for children with SHOX deficiency are available. Two decades of research support the concept of SHOX as a transcription factor that integrates diverse aspects of bone development, growth plate biology, and apoptosis. Due to its absence in mouse, the animal models of choice have become chicken and zebrafish. These models, therefore, together with micromass cultures and primary cell lines, have been used to address SHOX function. Pathway and network analyses have identified interactors, target genes, and regulators. Here, we summarize recent data and give insight into the critical molecular and cellular functions of SHOX in the etiopathogenesis of short stature and limb development.

Radiological Features in Patients with Short Stature Homeobox-Containing (SHOX) Gene Deficiency and Turner Syndrome before and after 2 Years of GH Treatment

BACKGROUND/AIMS

The short stature homeobox-containing (SHOX) gene is one of many genes that regulate longitudinal growth. The SHOX deficiency (SHOX-D) phenotype, caused by intragenic or regulatory region defects, ranges from normal stature to mesomelic skeletal dysplasia. We investigated differences in radiological anomalies between patients with SHOX-D and Turner syndrome (TS) and the effect of 2 years of growth hormone (GH) treatment on these anomalies.

METHODS

Left hand/wrist, forearm and lower leg radiographs were assessed at baseline and after 2 years in children with genetically confirmed SHOX-D (GH-treated and untreated groups) and TS (GH-treated) in a randomised, controlled, multinational study.

RESULTS

Radiological anomalies of hand, wrist and forearm were common in SHOX-D and TS. Radial bowing appeared more prevalent in SHOX-D, while lower leg anomalies were more common in TS. There were no significant differences in radiological findings between GH-treated and untreated patients with SHOX-D after 2 years.

CONCLUSION

GH treatment had no systematic effect on skeletal findings in SHOX-D, based on limited radiological differences between the GH-treated and untreated groups at 2 years. Bone age radiographs allow assessment of radiological signs indicating a potential diagnosis of SHOX-D and may lead to earlier genetic confirmation and initiation of GH therapy.

MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature

The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.

[Living with achondroplasia- how do young persons with disproportional short stature rate their quality of life and which factors are associated with quality of life?]

OBJECTIVE

Presently, little is known aqout the quality of life (QoL) as well as the strengths and difficulties of young people with achondroplasia. This study describes these patient-reported indicators and identifies possible correlates.

METHOD

At the invitation of a patient organization, a total of 89 short-statured patients aged 8 to 28 years and their parents participated in this study. QoL was assessed cross-sectionally with both generic and disease-specific instruments and the Strengths and Difficulties Questionnaire (SDQ) as a brief behavioral screening. In addition to descriptive analyses, patient data were compared with a reference population. Hierarchical regression analyses reflecting sociodemographic, clinical, and psychological variables were conducted to identify correlates of QoL.

RESULTS

QoL and the strengths and difficulties of young patients with achondroplasia did not differ substantially from a healthy norm sample. However, the participants reported more behavioral problems and limitations in their physical and social QoL compared to patients with another short stature diagnosis. Strengths and difficulties, height-related beliefs, and social support correlated significantly with QoL. Adding psychological variables to the regression model increased the proportion of variance explained in QoL.

CONCLUSIONS

Young persons with achondroplasia did not differ in their QoL and strengths and difficulties from healthy controls. Characteristics such as height appear less important for the self-perceived QoL than are strengths and difficulties and protective psychosocia~factors.

Clinical dilemmas in evaluating the short child

Concerns about a child's growth are one of the most common topics parents voice during general pediatric office visits and are a leading cause for referral to a pediatric endocrinologist. There are a variety of conditions that lead to short stature in children; however, in the absence of true pathology, idiopathic short stature and constitutional delay are the most frequent causes. This article reviews the general approach to evaluating the short child and clinical signs that should prompt further evaluation and referral. We also address the unique psychological issues that these children face and approaches to counseling families with a child with idiopathic short stature.

Validation of the Flemish version of the Quality of Life in Short Stature Youth (QoLISSY) questionnaire

OBJECTIVES

The Quality of Life in Short Stature Youth (QoLISSY) questionnaire was recently developed in five European countries to assess health-related quality of life in children and adolescents with idiopathic short stature or growth hormone deficiency from child and parent perspectives. In addition to the existing French version, a Flemish version is needed for use of QoLISSY in the Flemish speaking part of Belgium.

METHODS

Children (8-18 years) and their parents recruited from two Belgian paediatric endocrinology clinics completed the QoLISSY in a cross-sectional study. Cronbach's Alpha and test-retest reliability was assessed. Validity was examined by correlation with the generic KIDSCREEN questionnaire as well as by group comparisons according to diagnostic and treatment status.

RESULTS

The QoLISSY scales had an acceptable internal consistency with Cronbach's Alpha ranging from 0·80 to 0·94 (child version) and from 0·77 to 0·92 (parent version). Test-retest reliability correlation coefficients ranged from r = 0·75 to 0·89 in the child version and from r = 0·58 to 0·85 in the parent version. Moderate correlations with the generic KIDSCREEN questionnaire suggested construct validity. Differences between child groups according to child age, underlying diagnosis, and degree of height deficit were found. Correlations with the European QoLISSY were significant for all scales.

DISCUSSION

The Flemish QoLISSY instrument is a psychometrically sound, reliable, and valid short stature specific questionnaire measuring health-related quality of life. It is expected to be of great use in upcoming clinical research on growth disorders and growth hormone treatment in Belgium and Europe.

Genetic evaluation of short stature

After a proper medical history, growth analysis and physical examination of a short child, followed by radiological and laboratory screening, the clinician may decide to perform genetic testing. We propose several clinical algorithms that can be used to establish the diagnosis. GH1 and GHRHR should be tested in children with severe isolated growth hormone deficiency and a positive family history. A multiple pituitary dysfunction can be caused by defects in several genes, of which PROP1 and POU1F1 are most common. GH resistance can be caused by genetic defects in GHR, STAT5B, IGF1, IGFALS, which all have their specific clinical and biochemical characteristics. IGF-I resistance is seen in heterozygous defects of the IGF1R. If besides short stature additional abnormalities are present, these should be matched with known dysmorphic syndromes. If no obvious candidate gene can be determined, a whole genome approach can be taken to check for deletions, duplications and/or uniparental disomies.

ACMG practice guideline: genetic evaluation of short stature

Short stature is a common indication for genetic evaluation. The differential diagnosis is broad and includes both pathologic causes of short stature and nonpathologic causes. The purpose of genetic evaluation for short stature is to provide accurate diagnosis for medical management and to provide prognosis and recurrence risk counseling for the patient and family. There is no evidence-based data to guide the geneticist in an efficient, cost-effective approach to the evaluation of a patient with short stature. This guideline provides a rubric for the evaluation of short stature evaluation and summarizes common diagnoses and clinical testing available.

Idiopathic short stature: definition, epidemiology, and diagnostic evaluation

Idiopathic short stature is a condition in which the height of the individual is more than 2 SD below the corresponding mean height for a given age, sex and population, in whom no identifiable disorder is present. It can be subcategorized into familial and non-familial ISS, and according to pubertal delay. It should be differentiated from dysmorphic syndromes, skeletal dysplasias, short stature secondary to a small birth size (small for gestational age, SGA), and systemic and endocrine diseases. ISS is the diagnostic group that remains after excluding known conditions in short children.

SHOX at a glance: from gene to protein

The Short Stature Homeobox-containing Gene SHOX was identified as the genetic cause of the short stature phenotype in patients with Turner Syndrome and in certain patients with idiopathic short stature. Shortly after, SHOX mutations were also associated with the growth failure and skeletal deformities seen in patients with Léri - Weill dyschondrosteosis and Langer mesomelic dysplasia. Today it is estimated that SHOX mutations occur with an incidence of roughly 1:1,000 in newborns, making mutations of this gene one of the most common genetic defects leading to growth failure in humans. This review summarises the involvement of SHOX in several short stature syndromes and describes recent advances in our understanding of SHOX functions and regulation. We also discuss the current evidence in the literature that points to a role of this protein in growth and bone development. These studies have improved our knowledge of the SHOX gene and protein functions, and have given insight into the etiopathogenesis of short stature. However, the exact role of SHOX in bone development still remains elusive and poses the next major challenge for researchers in this field.

Genotypes and phenotypes in children with short stature: clinical indicators of SHOX haploinsufficiency

BACKGROUND

Short stature affects approximately 2% of children, representing one of the more frequent disorders for which clinical attention is sought during childhood. Despite assumed genetic heterogeneity, mutations or deletions of the short stature homeobox-containing gene (SHOX) are found quite frequently in subjects with short stature. Haploinsufficiency of the SHOX gene causes short stature with highly variable clinical severity, ranging from isolated short stature without dysmorphic features to Léri-Weill syndrome, and with no functional copy of the SHOX gene, Langer syndrome.

METHODS

To characterise the clinical and molecular spectrum of SHOX deficiency in childhood we assessed the association between genotype and phenotype in a large cohort of children of short stature from 14 countries.

RESULTS

Screening of 1608 unrelated individuals with sporadic or familial short stature revealed SHOX mutations or deletions in 68 individuals (4.2%): complete deletions in 48 (70.6%), partial deletions in 4 (5.9%) and point mutations in 16 individuals (23.5%). Although mean height standard deviation score (SDS) was not different between participants of short stature with or without identified SHOX gene defects (-2.6 vs -2.6), detailed examination revealed that certain bone deformities and dysmorphic signs, such as short forearm and lower leg, cubitus valgus, Madelung deformity, high-arched palate and muscular hypertrophy, differed markedly between participants with or without SHOX gene defects (p<0.001). Phenotypic data were also compared for 33 children with Turner syndrome in whom haploinsufficiency of SHOX is thought to be responsible for the height deficit.

CONCLUSION

A phenotype scoring system was developed that could assist in identifying the most appropriate subjects for SHOX testing. This study offers a detailed genotype-phenotype analysis in a large cohort of children of short stature, and provides quantitative clinical guidelines for testing of the SHOX gene.