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Test Code
5117
Test Name
Skeletal Dysplasia Core NGS Panel
CPT Codes
81479
Expected Turnaround Time
Typically 2 to 4 weeks from receipt of a sample in the laboratory. All cases involving ongoing pregnancies will be expedited.
Clinical Utility
Genetic analysis to provide a molecular diagnosis of this disorder. Recommended for individuals with a personal and/or family history of this disorder to ensure appropriate treatment and establish recurrence risk for family members.
Specimen and Container Info

Non-Prenatal Specimens


Preferred/Alternate

Specimen Type

Containers

Volume

Preferred Specimen Type

Whole Blood

Lavender Top (EDTA)

3 mL

Alternate Specimen Type

Genomic DNA

1.5 mL Tube

3 µg (at a concentration of at least 30 ng/µl), preferably in TE solution.

Alternate Specimen Type

Fibroblasts

T-25 Flasks

2 confluent T-25 flasks, filled to capacity

Alternate Specimen Type

Saliva (Whole blood is recommended for CNV)

DNA Self-Collection Kit or Oragene Saliva Collection Kit for Young Children

Follow kit instructions (www.dnagenotek.com)


Prenatal Specimens

Either specimen type below is acceptable.


Specimen Type

Containers

Volume

Cultured cells

T-25 Flasks

2 confluent T-25 flasks derived from amnio or CVS samples.

Genomic DNA

1.5 mL Tube

3 µg (at a concentration of at least 30 ng/µl), preferably in TE solution.


NOTE: For specimens from outside of North America, the preferred specimen type is Genomic DNA. HNL Genomics does not recommend shipping whole blood or cultured cells from any location other than the United States, Canada, or Mexico.
Transport Instructions
  • Transport at room temperature within 24 hours.
  • If the specimen cannot be transported to the lab within 24 hours, refrigerate for up to 72 hours.
  • Do not freeze or expose to extreme temperatures, refrigerate for up to 72 hours if cannot be transported to lab within 24 hours. 
Stability Requirements

Room Temperature

24 hours

Refrigerated

72 hours
Causes for Rejection
  • Improperly labeled specimen (minimum of two patient identifiers)
  • Inappropriate specimen type
  • Incomplete or incorrect test request form
  • Insufficient volume
  • Specimen has leaked in transit
  • Specimen without a test order
Methodology
Next Generation Sequencing and Copy Number Variation Analysis
Performing Location
Genomics - Snowdrift
Description

Genomics offers three options for skeletal dysplasia testing. The core skeletal dysplasia panel is designed to detect mutations in genes responsible for lethal or severe skeletal dysplasias that occur with a high incidence. The extended skeletal dysplasia panel contains genes linked to disorders that are also phenotypically severe but occur less frequently. These two panels may also be ordered as a single combined panel (Skeletal dysplasia core & extended NGS panel). The Skeletal dysplasia core and extended panel may also be combined with the Skeletal ciliopathy NGS panel.

The genes constituting these panels have been selected with input from several clinical geneticists with expertise in the skeletal dysplasia field.

The Skeletal dysplasia core NGS panel consists of ten genes: ALPL, COL1A1, COL1A2, COL2A1, FGFR3, INPPL1, NKX3-2, SLC26A2, SOX9, TRIP11.


Gene

Disorder

MIM

Inheritance

ALPL

Hypophosphatasia, adult

Hypophosphatasia, childhood

Hypophosphatasia, infantile

146300

241510

241500

AD / AR

COL1A1

Osteogenesis imperfecta, type I (OI1)

Osteogenesis imperfecta, type II (OI2)

Osteogenesis imperfecta, type III (OI3)

Osteogenesis imperfecta, type IV (OI4)

166200

166210

259420

166220

AD

COL1A2

Osteogenesis imperfecta, type II (OI2)

Osteogenesis imperfecta, type III (OI3)

Osteogenesis imperfecta, type IV (OI4)

166210

259420

166220

AD

COL2A1

Achondrogenesis, type II (ACG2) and Hypochondrogenesis

Platyspondylic skeletal dysplasia, Torrance type (PLSTD)

Spondyloepiphyseal dysplasia congenita (SEDC)

200610

151210

183900

AD

FGFR3

Achondroplasia (ACH)

Hypochondroplasia (HCH)

Thanatophoric dysplasia, type I (TD1)

Thanatophoric dysplasia, type II (TD2)

100800

146000

187600

187601

AD

INPPL1

Opsismodysplasia (OPSMD)

258480

AR

NKX3-2

Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD)

613330

AR

SLC26A2

Achondrogenesis, type IB (ACG1B)

Atelosteogenesis, type II (AO2)

Diastrophic dysplasia (DTD)

600972

256050

222600

AR

SOX9

Campomelic dysplasia

114290

AD

TRIP11

Achondrogenesis, type IA (ACG1A)

200600

AR
Testing Schedule
Monday-Friday
Genes
ALPL, COL1A2, FGFR3, NKX3-2, SOX9, COL1A1, COL2A1, TRIP11, SLC26A2, INPPL1
MIM
241500, 166210, 183900, 100800, 241510, 258480, 151210, 187601, 146300, 114290, 187600, 616482, 222600, 256050, 200600, 166220, 259420, 146000, 200610, 613330, 166200, 600972
Disease Group
Skeletal Disorders
The American Medical Association (AMA) Current Procedural Terminology (CPT) codes published by HNL Lab Medicine are guidelines and are intended for informational purposes only. CPT coding is the exclusive responsibility of the billing entity. View the Terms.
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