Skeletal Dysplasia Panel, Sequencing and Deletion/Duplication

Use to assess for causative gene variant(s) in individuals with clinical features of a skeletal dysplasia

  • Use to assess for causative variant(s) in a fetus with clinical features of a skeletal dysplasia
  • May also be used as predictive testing in a fetus known to be at risk for a skeletal dysplasia based on family history
  • Recommended test for a known familial sequence variant previously identified in a family member
  • A copy of the family member’s test result documenting the known familial variant is required.

Skeletal dysplasias are a heterogeneous group of more than 400 disorders characterized by abnormal growth of cartilage or bone. Some skeletal dysplasias are detectable prenatally while others are not evident until after birth or in later childhood. Symptoms are dependent on the specific skeletal dysplasia and include the shortening of the bones of the arms and legs >3 standard deviations below the mean; head circumference >75th percentile, bone abnormalities (eg, bowed or fractured, irregular, thickened, or thin) undermineralization of bones, abnormal ribs and/or small chest circumference, and polydactyly.

When skeletal dysplasia is suspected prenatally, the fetal skeletal dysplasia panel is the recommended first-line test because providers correctly predict the accurate skeletal dysplasia diagnosis in only 40% of prenatal cases. When skeletal dysplasia is suspected postnatally, radiographs and medical genetic consultation are recommended. If a geneticist is confident in the clinical diagnosis, targeted testing for the specific disorder should be performed. If two or more diagnoses are being considered, the skeletal dysplasia panel is recommended.

Genetics

Genes

See Genes Tested table for genes included in this panel.

Prevalence

~1/5,000 births 

Etiology

Pathogenic variants in numerous genes with various inheritance patterns (see table below)

Test Interpretation

Methodology

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Clinical Sensitivity

  • Variable, dependent on specific skeletal dysplasia
  • Clinical sensitivity of the most common prenatally detected skeletal dysplasias:
    • Thanatophoric dysplasia, 99% 
    • COLA1/2-related osteogenesis imperfecta, >97% 
    • Achondroplasia, 99% 
    • Achondrogenesis type IB, >90% 
    • Campomelic dysplasia, ~92% 
    • Diastrophic dysplasia, >90% 

Analytic Sensitivity

For massively parallel sequencing:

Variant Class Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region Analytic Specificity (NPA)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc deletions

97.8 (90.3-99.8) [2 exons or larger]

62.5 (38.3-82.6) [Single exon]

>99.9

Exon-levelc duplications

83.3 (56.4-96.4) [3 exons or larger]

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; PPA, positive percent agreement; NPA, negative percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude diagnosis of a skeletal dysplasia.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplantation.
  • The following will not be evaluated:
    • Variants outside the coding regions and intron-exon boundaries of the targeted genes
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
    • EVC (NM_153717) 1 exon is not sequenced due to technical limitations of the assay
    • Deletions/duplications in the upstream regulatory region of SOX9
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by MPS
    • Large duplications less than 3 exons in size
    • Noncoding transcripts
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
    • Variants in the chr17:70,119,704-70,119,743 region of SOX9 exon 3
    • Low-level somatic variants
    • Single exon deletions/duplications in the following exons:
    • Gene Exon(s)

      COL1A2

      (NM_000089) 3

      EVC

      (NM_153717) 1

      EVC

      (NM_001306090) 1

      EVC

      (NM_001306092) 1

      FGFR1

      (NM_001354367) 18

      FGFR1

      (NM_001354369) 18

      FGFR1

      (NM_001354370) 17

      DYM

      (NM_001353212) 14

      DYM

      (NM_001353213) 14

      DYM

      (NM_001353214) 14

      DYM

      (NM_001353215) 14

      DYM

      (NM_001374428) 15

      DYM

      (NM_001374429) 14

      DYM

      (NM_001374430) 14, 18

      DYM

      (NM_001374431) 14

      DYM

      (NM_001374432) 13

      DYM

      (NM_001374433) 17

      DYM

      (NM_001374441) 9

      NEK1

      (NM_001374422) 17

      NEK1

      (NM_001374423)16

      POR

      (NM_001382655) 3

Genes Tested

Gene MIM Number Disorder Inheritance

AGPS

603051

Rhizomelic chondrodysplasia punctata, type 3

AR

ALPL

171760

Hypophosphatasia, adult

Odontohypophosphatasia

AD, AR

Hypophosphatasia, infantile

Hypophosphatasia, childhood

AR

ARSL

300180

Chondrodysplasia punctata, XL

XL

CANT1

613165

Desbuquois dysplasia 1

Epiphyseal dysplasia, multiple, 7

AR

CCN6 603400 Progressive pseudorheumatoid dysplasia AR
CILK1 612325

Endocrine-cerebro-osteodysplasia

Epilepsy, juvenile myoclonic, susceptibility to, 10
AR, AD

COL1A1

120150

Caffey disease

Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 1

Ehlers-Danlos syndrome, arthrochalasia type, 1

Osteogenesis imperfecta, types I, II, III, and IV

AD

COL1A2

120160

Combined osteogenesis imperfecta and Ehlers-Danlos syndrome 2

Osteogenesis imperfecta, types II, III, and IV

Osteoporosis, postmenopausal

AD

Ehlers-Danlos syndrome, cardiac valvular type

AR

COL2A1

120140

Achondrogenesis, type II or hypochondrogenesis

Avascular necrosis of the femoral head

Czech dysplasia

Kniest dysplasia

Legg-Calve-Perthes disease

Osteoarthritis with mild chondrodysplasia

Platyspondylic lethal skeletal dysplasia, Torrance type

SMED Strudwick type

Spondyloepiphyseal dysplasia

Spondyloepiphyseal dysplasia, Stanescu type

Stickler syndrome, type 1

Stickler syndrome, type 1 nonsyndrome ocular

AD

COL10A1 120110 Metaphyseal chondrodysplasia, Schmid type AD
COL11A1 120280

Marshall syndrome

Stickler syndrome, type II

Otospondylomegaepiphyseal dysplasia, autosomal dominant

AD
Fibrochondrogenesis 2 AD, AR

Fibrochondrogenesis 1

Otospondylomegaepiphyseal dysplasia, autosomal recessive

AR

COMP

600310

Carpal tunnel syndrome 2

Epiphyseal dysplasia, multiple, 1

Pseudoachondroplasia

AD

CRTAP

605497

Osteogenesis imperfecta, type VII

AR

DDR2

 

191311

 

Warburg-Cinotti syndrome AD

Spondylometaepiphyseal dysplasia, short limb-hand type

AR

DLL3

602768

Spondylocostal dysostosis 1, AR

AR

DYM 607461

Dyggve-Melchior-Clausen disease

Smith-McCort dysplasia

AR

DYNC2H1

603297

Short-rib thoracic dysplasia 3 with or without polydactyly

AR, Digenic

EBP

300205

Chondrodysplasia punctata 2, X-linked dominant

MEND syndrome

XL

EVC

604831

Ellis-van Creveld syndrome

AR

EVC2 607261 Weyers acrofacial dysostosis AD

Ellis-van Creveld syndrome

AR

FGFR1

136350

Hartsfield syndrome

Hypogonadotropic hypogonadism 2 with or without anosmia

Jackson-Weiss syndrome

Osteoglophonic dysplasia​

Pfeiffer syndrome

Trigonocephaly 1

AD

FGFR2

176943

Antley-Bixler syndrome without genital anomalies or disordered steroidogenesis

Apert syndrome

Beare-Stevenson cutis gyrata syndrome

Bent bone dysplasia syndrome

Craniofacial-skeletal-dermatologic dysplasia

Craniosynostosis, nonspecific

Crouzon syndrome

Jackson-Weiss syndrome

Lacrimoauriculodentodigital (LADD) syndrome

Pfeiffer syndrome

Saethre-Chotzen syndrome

Scaphocephaly and Axenfeld-Rieger anomaly

Scaphocephaly, maxillary retrusion, and mental retardation

AD

FGFR3

134934

Achondroplasia

Achondroplasia, severe, with developmental delay and acanthosis nigricans (SADDAN)

Crouzon syndrome with acanthosis nigricans

Hypochondroplasia

Lacrimoauriculodentodigital (LADD) syndrome

Muenke syndrome

Thanatophoric dysplasia, type I

Thanatophoric dysplasia, type II

AD

Captodactyly, tall stature, and hearing loss syndrome (CATSHL) AD, AR

FKBP10

607063

Bruck syndrome 1

Osteogenesis imperfecta, type XI

AR

FLNA

300017

Cardiac valvular dysplasia, X-linked

Frontometaphyseal dysplasia 1

Heterotopia, periventricular, 1

Intestinal pseudoobstruction, neuronal

Melnick-Needles syndrome

Otopalatodigital syndrome, type I

Otopalatodigital syndrome, type II

Terminal osseous dysplasia

XL

FLNB

603381

Atelosteogenesis, type I

Atelosteogenesis, type III

Boomerang dysplasia

Larsen syndrome

AD

Spondylocarpotarsal synostosis syndrome

AR

GDF5 601146

Brachydactyly, type A2

Brachydactyly, type C

Multiple synostoses syndrome 2

Symphalangism, proximal 1B
AD
Brachydactyly, type A1, C AD, AR

Acromesomelic dysplasia 2A

Acromesomelic dysplasia 2B

AR

GNPAT

602744

Rhizomelic chondrodysplasia punctata, type 2

AR

HSPG2

142461

Dyssegmental dysplasia, Silverman-Handmaker type

Schwartz-Jampel syndrome, type 1

AR

IFT80

611177

Short-rib thoracic dysplasia 2 with or without polydactyly

AR

INPPL1 600829 Opsismodysplasia AR

LBR

600024

Greenberg dysplasia

AR

Pelger-Huet anomaly AD

LIFR

151443

Stuve-Wiedemann syndrome/Schwartz-Jampel type 2 syndrome

AR

NEK1

604588

Short-rib thoracic dysplasia 6 with or without polydactyly

AR, Digenic

Amyotrophic lateral sclerosis, susceptibility to, 24 AD
NPR2 108961 Acromesomelic dysplasia 1, Maroteaux type AR

Epiphyseal chondrodysplasia, Miura type

Short stature with nonspecific skeletal abnormalities
AD

P3H1

610339

Osteogenesis imperfecta, type VIII

AR

PCNT

605925

Microcephalic osteodysplastic primordial dwarfism, type II

AR

PEX7

601757

Peroxisome biogenesis disorder 9B

Rhizomelic chondrodysplasia punctata, type 1

AR

POR

124015

Antley-Bixler syndrome with genital anomalies and disordered steroidogenesis

AR

PPIB

123841

Osteogenesis imperfecta, type IX

AR

PTH1R

168468

Metaphyseal chondrodysplasia, Murk Jansen type

Failure of tooth eruption, primary

AD

Chondrodysplasia, Blomstrand type

Eiken Syndrome

AR

RUNX2

600211

Cleidocranial dysplasia

Cleidocranial dysplasia, forme fruste, dental anomalies only

Cleidocranial dysplasia, forme fruste, with brachydactyly

Metaphyseal dysplasia with maxillary hypoplasia with or without brachydacyly

AD

SERPINH1

600943

Osteogenesis imperfecta, type X

AR

SLC26A2

606718

Achondrogenesis, type IB

Atelosteogenesis, type II

De la Chapelle dysplasia

Diastrophic dysplasia

Diastrophic dysplasia, broad bone-platyspondylic variant

Epiphyseal dysplasia multiple, 4

AR

SLC35D1

610804

Schneckenbecken dysplasia

AR

SMACRCAL1 606622 Schimke immunoosseous dysplasia AR

SOX9

608160

Campomelic dysplasia

Campomelic dysplasia

Campomelic dysplasia with autosomal sex reversal

AD

TRIP11

604505

Achondrogenesis, type IA

Odontochondrodysplasia 1

AR

TRPV4

605427

Brachyolmia type 3

Digital arthropathy-brachydactyly, familial

Hereditary motor and sensory neuropathy, type IIc

Metatropic dysplasia

Neuronopathy, distal hereditary motor, type VIII

Parastremmatic, dwarfism

Scapuloperoneal spinal muscular atrophy

SED, Maroteaux type

Spondylometaphyseal dysplasia, Kozlowski type

AD

TTC21B 612014 Nephronophthisis 12 AR, AD

Short-rib thoracic dysplasia 4 with or without polydactyly

AR

WDR19

608151

Nephronophthisis 13

Senior-Loken syndrome 8

AR

WDR35

613602

Short-rib thoracic dysplasia 7 with or without polydactyly

Cranioectodermal dysplasia 2

AR

AD, autosomal dominant; AR, autosomal recessive; XL, X-linked

References

Additional Resources