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Test Code WESMT Whole Exome and Mitochondrial Genome Sequencing, Varies


Ordering Guidance


The American College of Medical Genetics and Genomics (ACMG) recommends that whole exome sequencing be considered as a first-tier or second-tier test for patients with one or more congenital anomalies, or developmental delay or intellectual disability with onset prior to age 18 years.(1)

 

If a specific diagnosis is suspected, single gene testing or panel testing may be a more appropriate first-tier testing option.

 

This test is for affected patients (probands) only. For family member specimens being sent as comparators, order CMPRE / Family Member Comparator Specimen for Exome Sequencing, Varies. If this test is ordered on a family member comparator specimen, the test will be canceled and CMPRE will be performed as the appropriate test.

 

This test cannot support detection of deep intronic variants or trinucleotide repeat variants; variants in the mitochondrial genome are detected.

-For whole exome sequencing only, order WESDX / Whole Exome Sequencing for Hereditary Disorders, Varies.

-If mitochondrial genome testing only is needed, order MITOP / Mitochondrial Full Genome Analysis, Next-Generation Sequencing (NGS), Varies.

-If testing for variants in the mitochondrial genes encoded by the nuclear genome is desired, order MITON / Mitochondrial Nuclear Gene Panel, Next-Generation Sequencing (NGS), Varies.

 

This test is not appropriate for identification of somatic variants in solid tumors. If this testing is needed, order MCSTP / MayoComplete Solid Tumor Panel, Next-Generation Sequencing, Tumor.

 

This testing does not provide genotyping of patients for pharmacogenomic purposes. For an assessment for genes with strong drug-gene associations, order PGXQP / Focused Pharmacogenomics Panel, Varies.

 

Targeted testing for familial variants (also called site-specific or known variant testing) is available for variants identified by this test. See FMTT / Familial Variant, Targeted Testing, Varies.



Additional Testing Requirements


To order testing with comparator specimens, see the following steps:

1. Order this test on the patient (proband)

2. Order CMPRE / Family Member Comparator Specimen for Exome Sequencing, Varies on all family members being submitted as comparator specimens.

 a. When available, the patient's biological mother and biological father are the preferred family member comparators.

 b. If one or both of the patient's biological parents are not available for testing, specimens from other first-degree relatives (siblings or children) can be used as comparators. Contact the laboratory at 800-533-1710 for approval to send specimens from other relatives.

 c. The cost of analysis for family member comparator specimens is applied to the patient's (proband's) test. Family members will not be charged separately.

3. Collect patient (proband) and family member specimens. Label specimens with full name and birthdate. Do not label family members' specimens with the proband's name.

4. Complete the signature sections of the Informed Consent (required for New York State clients) portion of Whole Exome Sequencing: Ordering Checklist.

5. If the patient wishes to opt-out of receiving secondary findings or change the DNA storage selection, select the appropriate boxes in the Informed Consent section.

6. Attach clinic notes from specialists relevant to patient's clinical features, if available.

7. Attach pedigree information, if available.

8. Send paperwork to the laboratory along with the specimens. If not sent with the specimen, fax a copy of the paperwork to 507-284-1759, Attention: WES Genetic Counselors.

 

For more information see Whole Exome and Genome Sequencing Information and Test Ordering Guide.



Shipping Instructions


Specimen preferred to arrive within 96 hours of collection.



Necessary Information


Whole Exome Sequencing: Ordering Checklist is required. Fill out one form for the family and send with the specimens.



Specimen Required


Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. Call 800-533-1710 for instructions for testing patients who have received a bone marrow transplant.

 

Submit only 1 of the following specimens:

Specimen Type: Whole blood

Container/Tube:

Preferred: Lavender top (EDTA) or yellow top (ACD)

Acceptable: Any anticoagulant

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Specimen Stability Information: Ambient (preferred)/Refrigerated

Additional Information: If a cord blood specimen is received, MATCC / Maternal Cell Contamination, Molecular Analysis, Varies will be performed at an additional charge.

 

Specimen Type: Skin biopsy

Supplies: Fibroblast Biopsy Transport Media (T115)

Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin.

Specimen Volume: 4-mm punch

Specimen Stability Information: Refrigerated (preferred)/Ambient

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Cultured fibroblasts

Container/Tube: T-25 flask

Specimen Volume: 2 Flasks

Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy from another laboratory. Cultured cells from a prenatal specimen will not be accepted.

Specimen Stability Information: Ambient (preferred)/Refrigerated (<24 hours)

Additional Information: A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks is required to culture fibroblasts before genetic testing can occur.

 

Specimen Type: Blood spot

Supplies: Card-Blood Spot Collection (Filtration Paper) (T493)

Container/Tube:

Preferred: Collection card (Whatman Protein Saver 903 Paper)

Acceptable: PerkinElmer 226 (formerly Ahlstrom 226) filter paper or blood spot collection card

Specimen Volume: 5 Blood spots

Collection Instructions:

1. An alternative blood collection option for a patient older than 1 year is a fingerstick. For detailed instructions, see How to Collect Dried Blood Spot Samples.

2. Let blood dry on the filter paper at ambient temperature in a horizontal position for a minimum of 3 hours.

3. Do not expose specimen to heat or direct sunlight.

4. Do not stack wet specimens.

5. Keep specimen dry.

Specimen Stability Information: Ambient (preferred)/Refrigerated

Additional Information:

1. Due to lower concentration of DNA yielded from blood spot, it is possible that additional specimen may be required to complete testing.

2. For collection instructions, see Blood Spot Collection Instructions.

3. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777).

4. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800).


Forms

1. Whole Exome Sequencing: Ordering Checklist is required.

2. New York Clients-Informed consent is required, included in the above form. Document on the request form or electronic order that a copy is on file.

3. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Neurology Specialty Testing Client Test Request (T732)

-Biochemical Genetics Test Request (T798)

Useful For

Serving as a first-tier test to identify a molecular and/or mitochondrial diagnosis in patients with suspected genetic disorders, which can allow for:

-Better understanding of the natural history/prognosis

-Targeted management (anticipatory guidance, management changes, specific therapies)

-Predictive testing of at-risk family members

-Testing and exclusion of disease in siblings or other relatives

-Recurrence risk assessment

 

Serving as a second-tier test for patients in whom previous genetic testing was negative.

 

Providing a potentially cost-effective alternative to establishing a molecular diagnosis compared to performing multiple independent molecular assays.

Genetics Test Information

This test provides results from both whole exome sequencing and mitochondrial genome sequencing.

 

Whole exome sequencing utilizes next-generation sequencing (NGS) to detect single nucleotide and copy number variants within the protein-coding regions of approximately 20,000 genes. See Method Description for additional details.

 

Mitochondrial genome sequencing includes amplification of the entire mitochondrial genome by long-range polymerase chain reaction followed by sequencing on the NGS platform to evaluate for variants within the mitochondrial genome.

 

Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, recurrence risk assessment, familial screening, and genetic counseling.

 

It is highly recommended that samples are submitted from the patient (proband), the patient's biological mother, and the patient's biological father (trio analysis). However, testing for singletons (patient only), duos (patient and one relative to be used as a comparator), and nontraditional trios (patient and 2 relatives to be used as comparators) will also be accepted if the patient’s biological mother and biological father are not available for testing.

 

Additional first-tier testing may be considered/recommended. For more information, see the Ordering Guidance section.

Profile Information

Test ID Reporting Name Available Separately Always Performed
WESDX Whole Exome Sequencing Yes Yes
MITOP Mitochondrial Full Genome Analysis Yes Yes

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
MATCC Maternal Cell Contamination, B Yes No
G226 Number of Comparators for WESDX No, (Bill Only) No
CULFB Fibroblast Culture for Genetic Test Yes No

Testing Algorithm

This test is a single order that performs whole exome sequencing and mitochondrial full genome analysis concurrently, with independently reported results. When this test is resulted, the component tests, WESDX and MITOP, are billed separately.

 

If a cord blood specimen is received, maternal cell contamination testing will be added and performed at an additional charge.

 

For skin biopsy or cultured fibroblast specimens, fibroblast culture testing will be performed at an additional charge. If viable cells are not obtained, the client will be notified.

Reporting Name

Exome and Mitochondrial Genome

Specimen Type

Varies

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Frozen 
  Refrigerated 

Reject Due To

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.  

Reference Values

An interpretive report will be provided.

Day(s) Performed

Varies

Report Available

84 days

Specimen Retention Time

Whole blood: 2 weeks (if available); Extracted DNA: 3 months; Blood spots, cultured fibroblasts, skin biopsy, cord blood: 1 month

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

81415-Patient only

81415, 81416-Patient and one family member comparator sample (duo) (as appropriate)

81415, 81416 x 2-Patient and two family member comparator samples (trio or non-traditional trio) (as appropriate)

81415, 81416 x 3-Patient and three family member comparator samples (quad) (as appropriate)

81460-Whole Mitochondrial Genome

81465-Whole Mitochondrial Genome Large Deletion Analysis

88233-Tissue culture, skin, solid tissue biopsy (if appropriate)

88240-Cryopreservation (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
WESMT Exome and Mitochondrial Genome 86205-2

 

Result ID Test Result Name Result LOINC Value
55281 Result Summary 50397-9
616410 Interpretation 69047-9
616411 Specimen 31208-2
55282 Result 82939-0
55283 Interpretation 69047-9
616412 Source 31208-2
616413 Released By 18771-6
55284 Additional Information 48767-8
55285 Specimen 31208-2
55286 Source 31208-2
55287 Released By 18771-6