COL1A1 and COL1A2 gDNA Testing

Genes

COL1A1, COL1A2

Test Guide

Over 95% of the forms of OI (lethal and non-lethal) result from a single dominant mutation in either COL1A1 or COL1A2, the two genes that encode the chains of type I procollagen.  The phenotype that results from the disease-causing variant is a consequence of the underlying mutation type and location in the alpha 1 or alpha 2 chain of type I procollagen.  Null mutations of COL1A1 result in OI type I and missense mutations in either COL1A1 or COL1A2 result in variable phenotypes within a spectrum of age of onset, stature and deformity.

For guidelines on the correct test to order and for pertinent references, consult the Osteogenesis Imperfecta Test Guide.

Methodology

Next Generation Sequencing:  Next generation DNA sequencing is performed to identify nucleotide variants in the coding portion of the genome. All nucleotides in the coding exons and their flanking splice junctions are sequenced to a read coverage of greater than 20X.  The sequence data are assembled and compared to the published genomic reference sequence.  Sanger sequencing is performed if necessary to ensure complete nucleotide coverage of the target sequence and to confirm all reported variants.  Human Genome Variation Society (HGVS) recommendations are followed for variant nomenclature and ACMGG/AMP variant interpretation guidelines are followed to assess variant pathogenicity, unless otherwise indicated.  The following online databases and in silico analysis tools are routinely used for variant investigation: ClinVar, NHLBI Exome Sequencing Project, 1000 Genomes, dbSNP, Exome Aggregation Consortium (ExAC), available loci specific variant databases, PolyPhen-2, SIFT, Provean, Mutation Taster and Human Splicing Finder.

Specimen Requirements

BLOOD IS PREFERRED.

BLOOD:
2 EDTA (purple top) tubes
Adults: 5-10cc
Children: 3-5cc
Infants: 2-3cc

Whole blood may be stored up to 5-7 days in the refrigerator before shipping.

DNA:
5µg DNA at a minimum concentration of ≥200 ng/µl

SALIVA:
Oragene Saliva samples are accepted

PRENATAL:
Amniocytes or Cultured CVS Cells: Two confluent T-25 flasks of cultured amniocytes or CVS cells, well-labeled as Prenatal Sample. Please call ahead to notify the CDL that a prenatal sample will be coming.

Special Instructions

Blood samples (or DNA) should be well labeled with patient’s full name and an identifying number.

Ship sample at room temperature with overnight delivery.

Clinical information outlining the indication for the requested tests and pertinent medical history and family history is a necessary component of testing. Please include a clinic note when available.

Radiographs are welcome for analysis by Laboratory Directors.

Related Tests

Dominant OI Panel

Reflex to Deletion/Duplication Studies: The Collagen Diagnostic Laboratory offers testing for copy number changes using a custom high-density targeted oligonucleotide array for these genes. The targeted regions have probe coverage in both the coding sequences and 10 kb upstream of the gene(s) of interest.

 

CPT Code & Cost

81408 x 2
$1600.00

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