Mosaicism Disorders

Mosaicism disorders can lead to a range of clinical manifestations and often require specialized genetic testing methods for accurate diagnosis. WUSM clinical genomics service offers Mosaicism Disorders NGS panels, which are advanced genetic tests that utilize high-throughput sequencing technologies to provide assessment of genetic conditions that arise from the presence of post-zygotic genetic alterations during early embryonic development or later during somatic cell division. WUSM Mosaicism Disorders NGS panels can detect single nucleotide variants (SNVs) and small insertions or deletions (indels) at a low-level variant allele fraction, which may be missed by traditional genetic testing methods, aiding in the diagnosis and management of mosaic disorders, such as somatic overgrowth, vascular anomalies, nevus, inborn errors of immunity, and cortical malformation and epilepsy.

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Indications for Testing

Some example indications for testing include:

• Congenital, lipomatous, overgrowth, vascular malformations, epidermal nevi and scoliosis/skeletal/spinal anomalies (CLOVES)
• Curry-Jones Syndrome
• Epidermal nevi and seborrheic keratoses
• Klippel-Trenaunay syndrome (KTS)
• Macrocephaly–capillary malformation (M-CM)
• Maffucci Syndrome
• McCune Albright Syndrome
• Megalencephaly-polymicrogyria-polydactyly-hydrocephalus (MPPH)
• Ollier Disease
• Proteus syndrome
• Schimmelpenning-Feuerstein-Mims

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Test Order Options

Standard Panel Analysis – Panels with set gene content. If a clinician orders a hard coded panel, where the gene content has been set – ONLY the genes in that set panel will be analyzed and reported. These include all orderable Mosaicism Disorder panels except for the PIK3CA-Related Overgrowth Spectrum panel and Custom panels.

Focused vs. Comprehensive Analysis – Clinicians ordering the PIK3CA-Related Overgrowth Spectrum panel or a Custom panel may choose between a focused or comprehensive panel option. Since many of these DoSM share phenotypes related to overgrowth, vascular malformations, and/or skin lesions, we have found that with certain phenotypes, reflexive reanalysis of an expanded set of genes known to be driving DoSM improves the diagnostic yield for compelling cases with initially negative findings. Based on this experience, we
believe that client-driven decisions at the time of ordering will result in a faster and more efficient diagnostic outcome. Our revised requisition now contains selectable options for either a focused or comprehensive analysis for PIK3CA and custom orders. Selection of a focused analysis will result in the evaluation of ONLY the gene(s) included in the ordered subset. A negative result will trigger reporting of a negative finding (no pathogenic or likely pathogenic variants) or inconclusive finding (variants of unknown significance). Selection of comprehensive analysis includes an initial evaluation of the focused gene(s) only, and if a pathogenic or likely pathogenic (P/LP) variant is identified, the analysis ends and a report is generated. However, if no P/LP variants are initially identified from the ordered subset, then a comprehensive analysis automatically occurs, and any P/LP variants identified from our comprehensive list of 75 DoSM-associated genes is reported. If no P/LP variants are identified after comprehensive analysis, we generate a report with negative or inconclusive findings.

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Available Tests and Gene Lists

Gene lists are below. Please note that the PIK3CA-Related Overgrowth Spectrum and custom test order options have a focused or a comprehensive option.

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Testing Methodology

All tests are performed using targeted hybridization capture coupled with next-generation sequencing (NGS) in our CAP accredited/CLIA certified clinical genomics labs for deep, comprehensive coverage of all coding exons of ordered genes.

Types of variation detected include single nucleotide variants (SNVs) small insertions and deletions (indels).

This test is routinely performed using formalin fixed paraffin embedded (FFPE) or fresh tissues and is able to detect alterations down to 1% allele fraction in affected tissues. A buccal swab may be considered in certain circumstances if affected tissue is not available, however sensitivity may be significantly limited. Please contact us prior to submitting buccal swabs for primary analysis.

Peripheral blood will be accepted as the primary specimen for the Inborn Errors of Immunity panel. It can also be accepted in other extenuating circumstances, please call the laboratory to discuss.

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Results and Interpretation

DNA sequence data are analyzed by a clinically validated bioinformatics pipeline to identify and annotate genetic variants associated with mosaicism disorders.

Variants are interpreted by a board-certified clinical genomicists in the context of the patient’s disease. Those that are most likely to account for the observed clinical phenotype based on evidence from the medical literature are highlighted.

Results are returned to the ordering physician in a concise report.

The turnaround time for NGS testing on the primary tissue is 3 weeks from the time a specimen arrives. For cases where the VAF of the identified variant is not informative, Sanger sequencing on a comparator specimen may be recommended and those results take an additional 4 weeks.

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Specimen Requirements

Primary specimen for all panels except the Inborn Errors of Immunity panel is tissue from the affected area. 

Acceptable materials for submission include disease involved tissue in the form of a formalin fixed paraffin embedded (FFPE) tissue block or fresh tissue in transport or tissue culture media.

Tissue fixation protocols must be compatible with molecular testing; EDTA decalcification is acceptable, acid decalcification is not.

For cases where the VAF of the identified variant is not informative, Sanger sequencing on a comparator specimen may be recommended. In this instance, 2-5 mL of peripheral blood in a lavender-top EDTA tube will be requested for comparative study.

Kits for testing are available upon request.

***Already extracted DNA can be accepted only with laboratory approval. The isolation of nucleic acids for clinical testing must have occurred in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS.

Request specimen kit  »

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Clinical Utility

While many genetic disorders are caused by inherited DNA variants (germline), it is increasingly apparent that many rare disorders arise through genetic changes that occur during embryonic and fetal development in a subset of cells; so called somatic variants that are distributed according to the embryological segmental pattern.

Such is the case in disorders associated with somatic variation in the PI3K/AKT/mTOR pathway, a critical regulatory pathway for cellular proliferation, mobility and survival.

The phenotypic consequences of such somatic variation include fibroadipose overgrowth, vascular malformations, epidermal nevi, skeletal abnormalities, and megalencephaly, among other clinical findings. Somatic variation within the PI3K/AKT/mTOR pathway has been described in individuals diagnosed with M-CM, CLOVES, HMEG and Proteus syndrome, among others.

McCune-Albright is rare disorder characterized by a triad of clinical features including fibrous dysplasia, café au lait spots, and precocious puberty. Somatic variation within the GNAS gene, which encodes the stimulatory alpha subunit for a guanine nucleotide binding protein (G protein), results in the observed clinical features associated with McCune-Albright due to constitutive activation of adenylate cyclase.

Due to the somatic nature of these disorders testing is strongly recommended from affected tissue.

Next-generation sequencing provides clinicians with a powerful tool to manage patients with these diagnostically challenging disorders.