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FeedbackMassively Parallel Sequencing
Massively Parallel Sequencing
- 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
If a familial sequence variant has been previously identified, targeted sequencing for that variant may be appropriate; refer to the Laboratory Test Directory for additional information.
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
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:
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
-
3746832
Orioli IM, Castilla EE, Barbosa-Neto JG. The birth prevalence rates for the skeletal dysplasias. J Med Genet. 1986;23(4):328-332.
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11241532
Chen CP, Chern SR, Shih JC, et al. Prenatal diagnosis and genetic analysis of type I and type II thanatophoric dysplasia. Prenat Diagn. 2001;21(2):89-95.
-
21829228
van Dijk FS, Byers PH, Dalgleish R, et al. EMQN best practice guidelines for the laboratory diagnosis of osteogenesis imperfecta. Eur J Hum Genet. 2012;20(1):11-19.
-
7847369
Bellus GA, Hefferon TW, de Luna RIOrtiz, et al. Achondroplasia is defined by recurrent G380R mutations of FGFR3. Am J Hum Genet. 1995;56(2):368-373.
-
11241838
Rossi A, Superti-Furga A. Mutations in the diastrophic dysplasia sulfate transporter (DTDST) gene (SLC26A2): 22 novel mutations, mutation review, associated skeletal phenotypes, and diagnostic relevance. Hum Mutat. 2001;17(3):159-171.
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10213041
Olney PN, Kean LS, Graham D, et al. Campomelic syndrome and deletion of SOX9. Am J Med Genet. 1999;84(1):20-24.
Use to assess for causative gene variant(s) in individuals with clinical features of a skeletal dysplasia.