In This Section      
 

SkeletalZoom

Genes:
See test page

Skeletal dysplasias and craniosynostoses

Genes: ALPL, ALX1, ALX3, ALX4, ASXL1, BMP4, CDC45, CYP26B1, DHODH, EFNB1, EFTUD2, ERF, ESCO2, FBN1, FGFR1, FGFR2, FGFR3, FREM1, GJA1, GLI3, IFT122, IFT140, IFT43, IHH, IL11RA, IMPAD1, IRX5, KRAS, MASP1, MEGF8, MSX2, P4HB, PEX7, PHF8, POLR1C, POLR1D, POR, RAB23, RECQL4, RSPRY1, RUNX2, SCARF2, SEC24D, SKI, SLC25A24, SMO, SOX9, TCF12, TCOF1, TGFBR1, TGFBR2, TMCO1, TWIST1, WDR19, WDR35, ZIC1

 

Osteogenesis imperfecta

Genes: BMP1, COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, CREB3L1, CRTAP, FKBP10, IFITM5, MBTPS2, P3H1, PPIB, SERPINF1, SERPINH1, SP7, SPARC, TENT5A, TMEM38B, WNT1

 

Connective Tissue

*Coming Soon*

Test Information

Test Method

DNA extraction (if applicable) and ultrasonic fragmentation; targeted capture of the coding regions and intron/exon boundaries of protein coding RefSeq genes using the Agilent Clinical Research Exome kit; next generation sequencing (NGS) on an Illumina HiSeq 2500 instrument; alignment to the human reference genome (GRCh37/hg19) using the Burrows-Wheeler Aligner (bwa); variant calling using GATK; Sanger sequencing to confirm low quality and/or complex indel variants related to the specified phenotype(s); Review of sequence data for the specified genes by multiple staff members; Variant classification following ACMG criteria (if applicable). Bioinformatic analysis was performed using DDL pipeline DDL.CRExome.v1.2018_04_18.

Clinical Utility

Discrimination between multiple heritable disorders involving the skeletal system; identification of causative mutations in complex cases that span multiple phenotypes; facilitation of targeted carrier or presymptomatic testing of relatives of proband and/or predictive prenatal testing

Clinical Sensitivity

The detection rate for the SkeletalZoom panel is undetermined at this point, due to ongoing research in the field.

Analytic Sensitivity

> 99% for single nucleotide and >92% for small insertion/deletion variants for the nucleotides evaluated. Lower limit of detection: Single nucleotide variants: 25% allele frequency (>96% sensitivity), Small insertion/deletion variants: 50% allele frequency (>94% sensitivity). This test is not validated to identify deletions/insertions of greater than 20bp, copy number changes, nucleotide repeat expansions, mitochondrial DNA variants or mosaicism. Disease-associated variants in regions that are not captured and/or sufficiently sequenced will not be detected by this assay.

Sample Requirements

3-6ml whole blood in EDTA (purple topped) tubes
Saliva collected in an appropriate collection device (Oragene®-DNA 500 or 600 device)
DNA extracted from fibroblast or lymphocyte cell line (must be extracted in a CLIA-certified laboratory)

Turn Around Time

6-8 weeks

Fee and CPT Codes

Exome Panel: $2915
CPT Code: 81479
*If you are a provider outside of Johns Hopkins we are only accepting institutional billing