Targeted pre-mRNA Splicing Analysis

Posted on by Dru Leistritz

It is now clear that missense and synonymous variants within exons and some intronic variants can affect pre-mRNA splicing.  While predictive programs can identify alterations in splice enhancers and suppressors and creation or deletion of recognition sequences, they are poor at determining if they are used.  In addition, it is difficult to determine the splice outcomes of variants that affect canonical splice acceptor and donor sites, which may affect assessments of the clinical outcomes.  Thus when genomic sequencing identifies a variant that may affect pre-mRNA splicing or a variant that is predicted to be pathogenic at the molecular level but the nature and abundance of abnormal mRNA splice products are unknown, it is important for clinical decision making and management to determine the effects through functional studies.  Because these studies are generally unavailable the CDL now offers mRNA splicing studies of genes that are included in our test menu and are expressed in dermal fibroblasts.

The sample requirement is two T25 flasks of near confluent dermal fibroblasts.  We do NOT accept skin biopsies.  Please inform our lab genetic counselor (Dru Leistritz, MS, CGC, phone: 206-543-5464, dru2@uw.edu) in advance before submitting cells for splicing studies.  The turnaround time will depend on the complexity of the splice outcome but should fall in the range of 3-5 weeks.

Stickler Syndrome Panel

Posted on by Dru Leistritz

The CDL offers a testing panel sequencing 6 genes associated with Stickler syndrome.  Pathogenic variants in the COL2A1, COL9A1, COL9A2, COL9A3, COL11A1 and COL11A2 genes, which code for type II, IX, and XII collagen, cause Stickler syndrome.

Stickler syndrome is a connective tissue disorder that may include ocular findings of myopia, cataract, and retinal detachment; hearing loss; midfacial underdevelopment and cleft palate; and mild spondylospiphyseal dysplasia and/or precocious arthritis.  The phenotype may be quite variable both within and between families.

Retinal Dystrophy Panel

Posted on by Dru Leistritz

The Retinal Dystrophy exome panel testing includes more than 200 genes that have been identified to be responsible for disorders in which retinal dystrophy is a noted feature:

Retinal Dystrophy Panel Gene List

Retinal Dystrophy exome panel testing is the most cost-efficient and precise approach to diagnostic testing as there is overlap between phenotypes and the lack of characteristic “other” features in many instances.   Study of the panel genes from the DNA of a single individual allows us to focus on variants reported as pathogenic in the past, on those with a very low population frequency, with nucleotide conservation across species and with likely pathogenic consequence. When variants of unknown significance are identified by panel testing, DNA is requested from first degree relatives to interrogate the significance of the variant. There is no charge for added studies used to aid in interpretation of a sequence change found in the index case.

Reflex to Exome Sequencing:  If a causative or potentially causative variant is not identified by this exome panel test it is possible to order a REFLEX clinical exome.   The full exome sequence will be analyzed as is done for our Clinical Exome Sequencing test using the data obtained from the exome panel test.  Submission of parental samples, and or other family members may be needed to assist in the interpretation of sequence variants. Order REFLEX to EXOME SEQUENCING.

C1S and C1R gDNA Testing

Posted on by Dru Leistritz

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.

Comprehensive EDS Panel

Posted on by Dru Leistritz

The Collagen Diagnostic Laboratory specializes in testing for Ehlers-Danlos Syndrome and offers the most comprehensive EDS testing available. The Comprehensive EDS Panel includes testing for 15 genes associated with Ehlers-Danlos Syndrome, including the recently described Periodontal form of EDS (EDS type VIII).   Panel genes: COL5A1, COL5A2, COL3A1, FLNA, PLOD1, COL1A1, COL1A2, ADAMTS2, C1S, C1R, ATP7A, CHST14, FKPB14, SLC39A13, and AEBP1.

COMPREHENSIVE EDS PANEL

CLASSIFICATIONCLINICAL FEATURESINHERITANCEGENE(S)AVAILABLE CLINICAL TESTING
Classical Type (EDS types I)Soft, velvety, hyperextensible skin; easy bruising; "cigarette paper" scarsDominantCOL5A1 and COL5A2Classical EDS
EDS Panel
Comprehensive EDS Panel
Classical type (EDS type II)Similar to EDS type I but less severe. Soft, hyperextensible skin; joint hypermobility; bruising; normal scar formationDominant (rare recessives)COL5A1 and COL5A2Classical EDS
Classical-like, 2 Joint and skin laxity, osteoporosis, osteoarthritis, abnormal scarring, joint dislocationsRecessiveAEBP1Comprehensive EDS Panel
Hypermobility Type (EDS type III) or Tenascin Deficient TypeMarked large and small joint hypermobility, joint pain, easy bruising, easy bleeding, normal scarsDominantTNXB (<5%)(Not available through CDL)
Vascular Type (EDS type IV)Thin, translucent skin with visible veins; marked bruising; skin and joints have normal extensibility; arterial, bowel and uterine ruptureDominantCOL3A1Vascular, type IV
Ocular-scoliotic (Kyphoscoliosis) Type (EDS type VI)Progressive kyphoscoliosis, joint hypermobility, smooth, hyperelastic and fragile skin, muscular hypotonia and scleral fragility and rupture of the globeRecessivePLOD1Ocular-scoliotic, type VI
Arthrochalasia Type (EDS type VIIA and VIIB)Congenital hip dislocation; very soft, fragile, bruisable skin, marked joint hypermobility, blue sclerae, small jaw, hypertrichosisDominantCOL1A1, COL1A2Arthrochalasia, type VII A/B (Exon 6 COL1A1/2 )
Dermatosparaxis Type (EDS type VIIC)Soft and very thin, fragile skin (tearing of the skin), stretchy skin, easy bruising, joint hypermobilityRecessiveADAMTS2Dermatosparaxis, Type VIIC
Cardiac-Valvular FormJoint hypermobility, skin hyperextensibility, cardiac valvular defectsRecessiveCOL1A2Comprehensive EDS Panel
Periodontal (EDS type VIII)Periodontitis, gingival recession, early tooth loss, easy bruising, skin hyperpigmentation, atrophic scars, joint hypermobility, thin skinDominantC1S, C1RPeridontal, Type VIII
Musculocontractural TypeCraniofacial dysmorphism, congenital contractures of thumbs and fingers, clubfeet, severe kyphoscoliosis, hypotonia, thin skin, easy bruising, atrophic scarring, joint hypermobilityRecessiveCHST14Comprehensive EDS Panel
EDS with progressive kyphoscoliosis, myopathy, and hearing lossSevere muscle hypotonia at birth, progressive scoliosis, joint hypermobility, elastic skin, myopathy, hearing lossRecessiveFKBP14FKBP14-Related EDS
Occipital horn (EDS type XI)Easy bruising, hyperelastic skin, hernias, bladder diverticula, joint hypermobility, varicosities, multiple skeletal abnormalitiesX-Linked RecessiveATP7AComprehensive EDS Panel
Periventricular heterotopia variant (PVNH4)Epilepsy, cardiac defects, joint hypermobilityX-Linked DominantFLNAComprehensive EDS Panel
Spondylocheirdysplastic formShort stature, blue sclerae, thin and hyperelastic skin, muscle atrophyRecessiveSLC39A13Comprehensive EDS Panel

Please consult the Ehlers-Danlos Syndrome Test Guide for more information.

Complex EDS-like Disorders

Posted on by Dru Leistritz

The Linkeropathies (also called Complex EDS-like disorders) are a group of disorders that result from inherited defects in the synthesis and modification of glycosaminoglycan. The CDL offers a 7 gene panel for autosomal recessive forms of Ehlers-Danlos Syndrome (EDS) that are associated with these defects. Disorders include: progeroid Ehlers-Danlos Syndrome (EDS) (B3GALT6), EDS with short stature and limb anomalies (B4GALT7), musculocontracural-type EDS (CHST14), EDS-like connective tissue disorder (B3GAT3), spondyloepiphyseal dysplasia (CHST3), Desbuquois dysplasia (XYLT1), and spondoocular syndrome (XYLT2). This panel is recommended for individuals with possible autosomal recessive conditions whose clinical features are similar to these disorders.

OI and Genetic Bone Disorders Panel

Posted on by Dru Leistritz

The Collagen Diagnostic Laboratory offers a comprehensive Osteogenesis Imperfecta (OI) and Genetic Bone Disorder panel of 42 genes.  The OI and Genetic Bone Disorders panel includes 4 genes associated with autosomal dominant forms of OI, COL1A1, COL1A2, IFITM5 and PLS3, and 13 genes associated with autosomal recessive forms of OI and hypophosphatasia, FKBP10, CRTAP, P3H1/LEPRE1, PPIB, SERPINH1, SP7/OSX, SERPINF1, PLOD2, ALPL, BMP1, TMEM38B, WNT1 and CREB3L1.  It also includes testing for hypophosphatasia, x-linked osteoporosis, bone mineralization disorders, and other skeletal dysplasias (see complete list on test requisition form).

This panel may be done in a tiered manner, with the dominant genes tested first and the remaining genes only tested if the dominant genes were normal (please indicate this on the test requisition form).  Over 95% of OI phenotypes result from a single dominant mutation in either COL1A1 or COL1A2, the two genes that encode the chains of type I procollagen, so this test is always recommended as a first step in testing individuals with a clinical diagnosis of OI.

When considering recessive forms of OI or other bone disorders, consultation with the laboratory genetic counselors or laboratory director is recommended as clinical and family history and x-ray review may be needed.  Occasionally new candidate genes for recessive form of OI will be included as part of the panel; there is no additional charge for testing of these genes.

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

Maternal Cell Contamination (MCC) Studies

Posted on by Dru Leistritz

Maternal Cell Contamination studies are available for prenatal samples through the Collagen Diagnostic Laboratory.

The CDL offers targeted mutation analysis for a known familial mutation on prenatal samples (all genes) and full sequencing of the Osteogenesis Imperfecta genes (Dominant and Recessive) in pregnancies.

We ask that you notify one of the genetic counselors in advance (Sam Bailey or Dru Leistritz, 206-543-5464) before sending a prenatal sample.  The turnaround time for prenatal testing (including MCC studies) is 5-7 days for known mutations and approximately 2 weeks for full sequencing.

Ectopia Lentis Panel

Posted on by Dru Leistritz

The CDL offers a 5 gene panel for genes associated with ectopia lentis. Pathogenic variants in ADAMTS10, ADAMTS17, ADAMTSL4, FBN1, and CBS have been identified in individuals with ectopia lentis. This panel is recommended for individuals with possible autosomal dominant or autosomal recessive ectopia lentis.

Ectopia lentis is the displacement of the eye’s crystalline lens, a clear structure at the front of the eye that focuses light. Vision problems are common in these individuals and may include nearsightedness (myopia), irregular curvature of the lens (astigmatism), clouding (cataracts), or increased pressure within the eyes (glaucoma). Ectopia lentis occurs in approximately 1 in 15,600 individuals and usually occurs as part of a broader, systemic condition such as Marfan Syndrome or Homocystinuria.

Cutis Laxa Panel

Posted on by Dru Leistritz

The CDL offers a 13 gene panel for genes associated with cutis laxa. Pathogenic variants in ALDH18A1, ATP6V0A2, ATP6V1A, ATP6V1E1, ATP7A, EFEMP2, ELN, FBLN5, GORAB, LTBP4, PYCR1, RIN2, and SLC2A10 have been identified in individuals with cutis laxa. This panel is recommended for individuals with possible autosomal dominant, autosomal recessive, and X-linked forms of cutis laxa.

Cutis laxa is a rare connective tissue disorder characterized by loose, hanging skin that is inelastic. Affected individuals have skin that hangs in loose folds, often causing the face and body to have a droopy appearance. In severe cases, the internal organs such as the lungs, heart, intestines, or arteries may also be affected.

FKBP14 gDNA Testing

Posted on by Dru Leistritz

FKBP14-related Ehlers-Danlos syndrome is characterized by severe muscle hypotonia at birth, progressive scoliosis, joint hypermobility, hyperelastic skin, myopathy, sensorineural hearing impairment, and normal pyridinoline excretion in urine. The disorder shares many features with the kyphoscoliotic form of EDS (EDS type VI) and Ullrich congenital muscular dystrophy.  It is autosomal recessive.

PLS3 gDNA Testing

Posted on by Dru Leistritz

PLS3 mutations have recently been identified in about 4% of male individuals with the clinical diagnosis of osteogenesis imperfecta type I or juvenile idiopathic osteoporosis AND normal sequence analysis of the type I procollagen genes (COL1A1 and COL1A2).  Most of the known mutations (van Dijk et al. 2013, Fahiminiya et al. 2014, CDL unpublished data) create premature termination codons and, probably, mRNA instability that results in absence of the PLS3 protein.  Women who were reported to be PLS3 mutation carriers did not have a history of fractures.  PLS3 encodes plastin 3, which is an actin-bundling protein that is highly expressed in the mechanosensing dendrites of osteocyte.  Mechanosensing appears to be critical for the conversion of mechanical to intracellular biochemical signals so that the bone architecture can adapt to the constantly changing mechanical demands.

PLOD1 gDNA Testing

Posted on by Dru Leistritz

The kyphoscoliotic type of Ehlers-Danlos Syndrome, EDS type VI, is characterized by severe muscular hypotonia, kyphoscoliosis at birth, joint laxity, scleral fragility, and rupture of the ocular globe.  EDS type VI is an autosomal recessive disorder caused by mutations in PLOD1.