Ordering a targeted variant test

HNL Genomics (CTGT) performs targeted variant analysis for any gene on our test menu. The targeted variant may have been originally identified by our laboratory or by an outside laboratory. Targeted variant analysis is available for all standard specimen types, including prenatal specimens.

Specimens

Our standard specimen requirements (whole blood, isolated DNA, prenatal specimens, fibroblasts, saliva) also apply to targeted variant tests. Please clearly label the specimen container with at least two patient identifiers (for example, patient name and date of birth). HNL Genomics (CTGT) cannot accept specimens that do not have two patient identifiers.

Requisition form

HNL Genomics (CTGT) provides a separate requisition form for targeted variant tests. To order a target variant test, complete the Targeted Variant Test Requisition Form, including payment information, and send the completed form with the specimen toHNL Genomics (CTGT). If the variant was identified at HNL Genomics (CTGT), please include the HNL Genomics (CTGT) identification number or the name and date of birth of the patient in whom the variant was previously identified. If the variant was identified by an outside laboratory, please submit the report issued by the laboratory that previously identified the variant. If the report is not available, please include the nucleotide change and amino acid change for the variant and, if possible, the cDNA reference sequence number used by the outside laboratory.

Turnaround time

Targeted variant testing is performed by Sanger sequencing. Our standard turnaround time for Sanger sequencing, approximately 1-2 weeks from receipt of the specimen in the laboratory, also applies to targeted variant analysis.

Positive control

In most cases, HNL Genomics (CTGT) does not require a positive control to be provided for targeted variant testing.

Billing

HNL Genomics (CTGT) standard billing requirements apply to targeted variant tests.


Test Code Tests Price CPT Code
1387 One mutation $200 81403
1388 Two mutations $400 81403x2
2027 Three mutations $600 81403x3
Targeted variant testing may be performed at no cost when a variant of uncertain significance (VUS) is identified in a patient, as described below.

Variant of Uncertain Significance (VUS) Resolution

At HNL Genomics (CTGT), we are committed to working with health care providers and patients to provide follow up genetic testing for patients that are found to have variants of uncertain significance.

When variants of uncertain significance are identified by HNL Genomics (CTGT) sequencing tests, testing additional family members will be offered at no cost if there is a high likelihood that testing will provide evidence to assist in variant reclassification. In these cases, the patient’s report will clearly state that testing at no cost for two family members is being offered. Some family members are more informative than others for variant resolution; therefore, recommendations for which family members to test are listed below.

  • For autosomal dominant disorders with no family history of the disorder, testing of both parents is recommended.
  • For autosomal dominant disorders with a family history of the disorder, testing of two affected family members (preferably an affected parent and one other affected family member) is recommended.
  • For autosomal recessive disorders where two variants of uncertain significance or one VUS and one pathogenic/likely pathogenic variant are identified, testing of both parents is recommended.

If the recommended individuals are not available for testing, other family members will be tested. For guidance on selection of the most informative family members, we suggest contacting our Client Services team at 484-244-2900 or secure form.

Testing at no cost will only be performed if the relationship to the original patient is clearly stated and the clinical history indicating if the family members are affected or unaffected is provided. Additionally, testing at no cost will only be performed if the family member’s samples are received within six months of the date the original patient’s report was issued.

Please note that follow up testing may not result in an immediate reclassification of the VUS.

How to Order VUS Resolution

Complete the Targeted Variant Test Requisition Form and send the completed form with the specimen to HNL Genomics (CTGT).

  • Include the HNL Genomics (CTGT) case number or the name and date of birth (DOB) of the original patient tested at HNL Genomics (CTGT)
  • Include clinical history clearly indicating if the family members being tested are affected or unaffected
  • Note the relationship of the family member being tested to the original patient

If this information is not provided, testing of the family members will be placed on hold until the information is received.

Testing takes approximately 1-2 weeks from the time the sample and all required information are received.

Patients that do not qualify

If testing to resolve a VUS is not offered at no cost on the patient’s report, it is unlikely that testing of additional family members will assist in variant reclassification. For these cases, family members can still be tested but they will be charged the regular rate for a targeted variant test, $200 per variant.

The American Medical Association (AMA) Current Procedural Terminology (CPT) codes published by HNL Lab Medicine are guidelines and are intended for informational purposes only. CPT coding is the exclusive responsibility of the billing entity. HNL Lab Medicine strongly recommends confirmation of CPT codes with third-party payors and/or the AMA. We assume no responsibility for billing errors due to reliance upon CPT codes provided by HNL Lab Medicine.

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