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HelpTest Code LAB3689 Stickler Syndrome Panel
Additional Codes
StickSeq CNV
Clinical System Name
Stickler Syndrome Sequencing + CNV
Synonyms
Stickler Syndrome
COL2A1
COL11A2
COL11A1
COL9A1
COL9A2
COL9A3
Description
This is an NGS panel that includes sequencing and CNV anslysis of 12 genes: BMP4, COL11A1, COL11A2, COL2A1, COL9A1, COL9A2, COL9A3, GZF1, LOXL3, LRP2, PLOD3, VCAN.
This will detect Stickler I, II and III.
Sample Requirements
Specimen: Whole Blood
Container(s): Lavender/EDTA or Yellow/ACD
Preferred Vol: 3.0 - 5.0 mL
Minimum Vol: 1.0 mL for small infants
Specimen: DNA
Container(s): Sterile Plastic Tube
Preferred Vol: 5 µg -10 µg of purified DNA at a concentration of at least 100 ng/μL
Alternative Specimen (e.g. saliva or buccal): Alternate Specimen Collection Kits for Genetic Testing
Processing Instructions
Reject due to:
Spin: N
Aliquot: N
Temp: 2 - 8 C
Storage Location: Do not spin. Affix large Epic label(s) to tube(s) and store in CPA refrigerator, Send Outs rack.
Off-site Collection: Send whole blood refrigerated.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole Blood | Room Temp | 3 d |
| Refrigerated | 7 d | |
| Frozen | Unacceptable | |
| Extracted DNA | Room Temp | 3 - 4 d |
| Refrigerated | 1 y | |
| Frozen | Indefinitely |
Availability
| STAT | TAT |
|---|---|
| N | 3 - 4 w |
Performing Laboratory
PreventionGenetics
3800 S. Business Park Ave.
Marshfield, WI 54449
Phone Number: (715) 387-0484
Department
Department: Send Outs/Genetic
Phone Number: (206) 987-2563
Methodology
NextGen Sequencing: As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.
In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.
Copy Number Variant Analysis: The PGxome test detects most larger deletions and duplications including intragenic CNVs and large cytogenetic events; however aberrations in a small percentage of regions may not be accurately detected due to sequence paralogy (e.g., pseudogenes, segmental duplications), sequence properties, deletion/duplication size (e.g., 1-3 exons vs. 4 or more exons), and inadequate coverage. In general, sensitivity for single, double, or triple exon CNVs is ~70% and for CNVs of four exon size or larger is >95%, but may vary from gene-to-gene based on exon size, depth of coverage, and characteristics of the region.
Reference Range
Interpretive report is provided.
Clinical Utility
Stickler syndrome is a connective tissue disorder that can include ocular findings of myopia, cataract, and retinal detachment; hearing loss that is both conductive and sensorineural; midfacial underdevelopment and cleft palate (either alone or as part of the Robin sequence); and mild spondyloepiphyseal dysplasia and/or precocious arthritis. Variable phenotypic expression of Stickler syndrome occurs both within and among families; interfamilial variability is in part explained by locus and allelic heterogeneity.
Stickler syndrome (STL) is a multisystem disorder with ocular, skeletal, orofacial, and auditory defects, affecting approximately 1:7,500-1:9,000 individuals. Key features include myopia, cataract, retinal detachment, hearing loss (both conductive and sensorineural), midfacial underdevelopment, cleft palate, and mild skeletal abnormalities such as spondyloepiphyseal dysplasia and early-onset arthritis. STL is genetically heterogeneous, with both autosomal dominant (AD) and autosomal recessive (AR) inheritance patterns. Major genes involved include COL2A1, COL11A1, and COL11A2 for AD forms, and COL9A1, COL9A2, and COL9A3 for AR forms. Molecular diagnosis is complex due to overlapping clinical features with other skeletal disorders and the extensive genetic heterogeneity. Comprehensive genetic testing covering all known STL-associated genes is recommended for accurate diagnosis.
Causative variants in COL2A1 and COL11A1 account for 80-90% and 10-20% of variants identified in autosomal dominant STL syndrome, respectively; causative variants in COL11A2 account for rare dominant cases. Causative variants in COL9A1, COL9A2, COL9A3, LOXL3 and LRP2 have been found only in a few families affected with autosomal recessive inheritance of STL syndrome (Robin et al. 2011; Schrauwen et al. 2014; Alzahrani et al. 2015). Causative variants in the VCAN gene were identified in ten out of twelve families diagnosed with autosomal dominant VCAN-related vitreoretinopathy (Kloeckener-Gruissem and Amstutz 2016).
In addition to STL, causative variants in these genes also cause other skeletal dysplasia disorders. These skeletal disorders have overlapping clinical features with Stickler syndrome, which cause difficulties in reaching a correct clinical diagnosis. Molecular diagnosis of the skeletal dysplasia subtypes is also complex because extensive genetic heterogeneity exists for each disorder (Warman et al. 2011). Considering the clinical and genetic heterogeneity, a molecular testing approach that interrogates all known Stickler syndrome genes is highly recommended. See individual gene test descriptions for information on molecular biology of gene products.
Send Out Instructions
| Reference Test Name: | Stickler Syndrome Panel |
| Reference Lab Test Code: | 10271 |
| Instructions: | Ship whole blood via FedEx Priority Overnight at ambient temperature. PreventionGenetics accepts Saturday delivery. |