C1S and C1R gDNA Testing

Genes

C1R, C1S

Test Guide

The testing for EDS periodontal type (also known as EDS type VIII) includes genomic sequence analysis of C1S and C1R. Researchers in our group recently described pathogenic variants in these two genes as the underlying cause of EDS VIII. This autosomal dominant disorder is characterized by early-onset periodontitis and tooth loss.

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:
Single Gene, +/- array (del/dup):15 µg DNA at a minimum concentration of ≥200 ng/µl
Gene panels, +/- array (del/dup): 35 µg DNA at a minimum concentration of ≥200 ng/µl
Single site (known familial mutation or variant): 5 µg DNA

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.

CPT Code & Cost

81479
$1600.00

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