Comprehensive Short Stature Syndrome Panel

Last modified: Jun 12, 2018

Summary

  • Is a 75 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of short stature and associated disorders.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

75

Test code

MA2101

CPT codes

SEQ 81404
SEQ 81405
SEQ 81406
DEL/DUP 81479

Summary

The Blueprint Genetics Comprehensive Short Stature Syndrome Panel (test code MA2101):

  • Is a 75 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Comprehensive Short Stature Syndrome Panel

ICD-10 Disease
Q87.1 Short stature and associated syndromes

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

The clinical phenotypes of the disorders covered by this panel range in the severity of growth retardation and microcephaly, as well as in the degree of developmental delay, but there can be significant clinical overlap among syndromes. In addition to the disorders covered by the sub-panels, this comprehensive panel covers several other diseases associated with short stature, such as growth delay due to insulin-like growth factor I resistance or IGF1 deficiency (mutations in IGF1R and IGF1), hypothyroidism due to deficient transcription factors involved in pituitary development or function (HESX1, LHX3, LHX4, POU1F1 and PROP1), Rubinstein-Taybi syndrome (CREBBP and EP300), Cornelia de Lange syndrome (NIPBL, RAD21, SMC3, HDAC8 and SMC1A) and different forms of disproportionate short stature. Disproportionate short stature can manifest itself as short-limbed dwarfism or short-trunk dwarfism. Achondroplasia (autosomal dominant, mutations is FGFR3) is the most common form of disproportionate growth retardation, its estimated incidence is at about 1/25,000 live births worldwide. Identification of rare monogenic causes of short stature is critical since the genetic diagnosis may alert the clinician to other medical comorbidities for which the patient is at risk. For example, a male patient with 3-M syndrome will need to be monitored for the development of hypogonadism. Based on genetic studies in children with severe short stature of unknown etiology it has been suggested that monogenic causes of short stature are underdiagnosed in the pediatric endocrine clinic. Factors that increase the likelihood for a monogenic cause of short stature are severe GH deficiency, multiple pituitary hormone deficiency, unequivocal GH insensitivity, small for gestational age without catch-up growth, additional congenital anomalies or dysmorphic features, associated intellectual disability, microcephaly and height below −3 SD.

Genes in the Comprehensive Short Stature Syndrome Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ACTB* Baraitser-Winter syndrome AD 46 54
ACTG1* Deafness, Baraitser-Winter syndrome AD 25 43
ATR Cutaneous telangiectasia and cancer syndrome, Seckel syndrome AD/AR 8 18
B3GAT3* Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects AR 5 13
BCS1L Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1 AR 33 37
BRAF* LEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndrome AD 135 65
CBL Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia AD 23 38
CCDC8 Three M syndrome 3 AR 2 3
CDC6 Meier-Gorlin syndrome (Ear-patella-short stature syndrome) AR 2 2
CDC45 Meier-Gorlin syndrome 7 AR 10 19
CDT1 Meier-Gorlin syndrome (Ear-patella-short stature syndrome) AR 6 11
CENPJ Seckel syndrome, Microcephaly AR 32 9
CEP63 Seckel syndrome AR 7 2
CEP152# Seckel syndrome, Microcephaly AR 19 20
CREBBP Rubinstein-Taybi syndrome AD 156 348
CUL7 3-M syndrome, Yakut short stature syndrome AR 26 80
DHCR7 Smith-Lemli-Opitz syndrome AR 67 216
EP300 Rubinstein-Taybi syndrome AD 57 91
FGD1 Aarskog-Scott syndrome, Mental retardation, syndromic XL 26 49
FGFR3 Lacrimoauriculodentodigital syndrome, Muenke syndrome, Crouzon syndrome with acanthosis nigricans, Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome, Achondroplasia, Hypochondroplasia, Thanatophoric dysplasia type 1, Thanatophoric dysplasia type 2, SADDAN AD/AR 53 72
GH1* Isolated growth hormone deficiency, Kowarski syndrome AD/AR 25 86
GHR Growth hormone insensitivity syndrome (Laron syndrome) AD/AR 35 109
GHRHR Isolated growth hormone deficiency AR 13 43
GLI2 Culler-Jones syndrome AD 26 76
GNAS McCune-Albright syndrome, Progressive osseous heteroplasia, Pseudohypoparathyroidism, Albright hereditary osteodystrophy AD 62 265
HDAC8 Cornelia de Lange syndrome XL 33 44
HESX1 Septooptic dysplasia, Pituitary hormone deficiency, combined AR/AD 14 26
HRAS Costello syndrome, Congenital myopathy with excess of muscle spindles AD 41 29
IGF1 Insulin-like growth factor I deficiency AR 4 8
IGF1R Insulin-like growth factor I, resistance AD/AR 12 61
IGFALS Insulin-like growth factor-binding protein, acid-labile subunit, deficiency AR 5 33
INSR Hyperinsulinemic hypoglycemia, familial, Rabson-Mendenhall syndrome, Donohoe syndrome AD/AR 44 183
IRS1 Diabetes mellitus, noninsulin-dependent AD/AR 3 16
KRAS* Noonan syndrome, Cardiofaciocutaneous syndrome AD 61 34
LARP7 Alazami syndrome AR 16 6
LHX3 Pituitary hormone deficiency, combined AR 9 16
LHX4 Pituitary hormone deficiency, combined AD 10 23
LZTR1 Schwannomatosis, Noonan syndrome AD 27 64
MAP2K1 Cardiofaciocutaneous syndrome AD 45 21
MAP2K2 Cardiofaciocutaneous syndrome AD 21 35
NIPBL Cornelia de Lange syndrome AD 290 419
NOTCH2* Alagille syndrome, Hajdu-Cheney syndrome AD 35 63
NRAS Noonan syndrome AD 31 14
OBSL1 3-M syndrome AR 13 33
ORC1 Meier-Gorlin syndrome (Ear-patella-short stature syndrome) AR 9 9
ORC4 Meier-Gorlin syndrome (Ear-patella-short stature syndrome) AR 22 6
ORC6 Meier-Gorlin syndrome (Ear-patella-short stature syndrome) AR 7 6
OTX2 Microphthalmia, syndromic, Pituitary hormone deficiency, combined, Retinal dystrophy, early-onset, and pituitary dysfunction AD 21 68
PCNT Microcephalic osteodysplastic primordial dwarfism AR 48 84
PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly AD 23 96
POC1A Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT syndrome) AR 4 8
POU1F1 Pituitary hormone deficiency, combined AR 19 41
PROP1 Pituitary hormone deficiency, combined AR 27 37
PTPN11 Noonan syndrome, Metachondromatosis AD 128 139
RAD21* Cornelia de Lange syndrome 4 AD 9 11
RAF1 LEOPARD syndrome, Noonan syndrome, Dilated cardiomyopathy (DCM) AD 44 48
RASA2# Noonan syndrome AD 1 3
RBBP8 Seckel syndrome, Jawad syndrome AR 6 6
RIT1 Noonan syndrome AD 20 25
RNU4ATAC Roifman syndrome, Microcephalic osteodysplastic primordial dwarfism type 1, Microcephalic osteodysplastic primordial dwarfism type 3 AR 15 21
RRAS Noonan-syndrome like phenotype AD/AR 2
RTTN Microcephaly, short stature, and polymicrogyria with or without seizures AR 13 10
SHOC2 Noonan-like syndrome with loose anagen hair AD 2 4
SHOX* Leri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Short stature XL/PAR 25 426
SMC1A Cornelia de Lange syndrome XL 56 87
SMC3 Cornelia de Lange syndrome AD 21 20
SOS1 Noonan syndrome AD 45 67
SOX2* Microphthalmia, syndromic AD 31 100
SOX3 Panhypopituitarism XL 4 25
SRCAP Floating-Harbor syndrome AD 13 40
STAT5B* Growth hormone insensitivity with immunodeficiency AR 8 10
TBX3 Ulnar-Mammary syndrome AD 6 20
TBX19 Adrenocorticotropic hormone deficiency AR 8 27
TRIM37 Mulibrey nanism AR 19 21
XRCC4 Short stature, microcephaly, and endocrine dysfunction AR 9 11

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
BCS1L Chr2:219524871 c.-147A>G NM_004328.4
CUL7 Chr6:43010511 c.3897+29G>A NM_001168370.1
EP300 Chr22:41537040 c.1879-12A>G NM_001429.3
GH1 Chr17:61995349 c.291+28G>A NM_000515.3 rs863223306
GHR Chr5:42689204 c.287+83G>T NM_001242399.2
GHR Chr5:42700896 c.639+792A>G NM_001242399.2
GHRHR Chr7:31003560 c.-124A>C NM_000823.3
GNAS Chr20:57478716 c.2242-11A>G NM_080425.2
LZTR1 Chr22:21340117 c.264-13G>A NM_006767.3 rs587777176
NIPBL Chr5:36953718 c.-79-2A>G NM_133433.3
NIPBL Chr5:36877266 c.-94C>T NM_133433.3
NIPBL Chr5:37022138 c.5329-15A>G NM_133433.3 rs587783968
PITX2 Chr4:111539855 c.412-11A>G NM_000325.5
PROP1 Chr5:177420059 c.343-11C>G NM_006261.4
PTPN11 Chr12:112915602 c.934-59T>A NM_002834.3
RBBP8 Chr18:20581745 c.2287+53T>G NM_002894.2
SHOX ChrX:585124 c.-645_-644insGTT NM_000451.3
TRIM37 Chr17:57106096 c.1949-12A>G NM_015294.3
XRCC4 Chr5:82400728 c.-10-1G>T NM_022406.2 rs869320678

Added and removed genes from the panel

Genes added Genes removed
ACTB
ACTG1
B3GAT3
BCS1L
BRAF
CBL
CCDC8
CDC45
GNAS
HDAC8
HRAS
LARP7
LZTR1
MAP2K1
MAP2K2
NRAS
POC1A
RAD21
RASA2
RIT1
RRAS
RTTN
SHOC2
SMC3
SRCAP
TRIM37
XRCC4
AKT1
BMP2
BMP4
BMPR1A
EYA1
FGF3
FOXL2
NR5A1
PTCH1
SHH
SIX3
TGIF1
ZIC2

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: CEP152 (26), RASA2 (3, 6, 17, 19, 20). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics comprehensive short stature syndrome panel covers classical genes associated with 3-M syndrome, Seckel syndrome, Meier-Gorlin syndrome (Ear-patella-short stature syndrome), Jawad syndrome, Short stature and associated syndromes, microcephalic primordial dwarfism disorders (MOPD) and Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.