FAQs: Clinical Interpretation and Reporting

Answers for providers who have questions about clinical interpretation and reporting.

Accurate phenotypic information helps us provide the best possible interpretation of a patient’s genomic data. Our analysis platform for exome and genome sequencing specifically requires clinical input to run its phenotype-matching algorithm.
We also take additional information such as family history and/or prior testing results into account to further improve data interpretation and variant classification.

Orders placed in our online portal will result in the same portal for ease of use.
Orders that come in other formats can have results delivered via our resulting portal GeneResults or via secure email. The result return method is determined by the selection you choose on the requisition under-reporting information. 

Although we cannot guarantee a TAT quicker than what is posted we will accept and accommodate, to the best of our abilities, expedited requests. A request for expedited results can be made by emailing help@baylorgenetics.com or calling in at 1-800-411-4363.

Diagnostic testing:
A result may be any of the following:
Positive: A pathogenic or likely pathogenic variant or combination of variants was identified and determined to be clinically relevant with reference to the patient’s phenotype.
Indeterminate / Variants of uncertain significance (VUS): Genomic variants possibly related to the patient’s phenotype were detected, however, the clinical significance is unclear at this time. Further investigation may be needed.
Negative: No variants were identified that can explain the patient’s phenotype.
Of note, for trio exome and genome sequencing analysis, an additional table with de novo, biallelic and hemizygous variants in genes unrelated to the clinical phenotype, or genes with no currently known disease association is included.

Screening tests (reproductive carrier / hereditary cancer screening):
Positive: A pathogenic or likely pathogenic variant was detected. This may be indicative of carrier status for that particular disorder in the setting of reproductive carrier testing and/or hereditary susceptibility to cancer(s) depending on the gene and current risk associations.
Negative: No pathogenic or likely pathogenic variants were detected.
No variants of uncertain significance (VUS) are reported for screening tests.

Patients/parents have the choice to opt in or opt out for secondary findings (SF), as indicated on the Baylor Genetics exome and genome requisition/consent form. Secondary findings include pathogenic and likely pathogenic variants in a series of genes as recommended by the ACMG (currently SF v3.0, containing 73 genes). The recommended list of genes by ACMG is selected based on genetic disorders that include opportunistic screening to facilitate the identification and/or management of risks through established interventions aimed at preventing or significantly reducing morbidity and mortality.

For proband-only analyses only a report for the proband will be issued, including any variants that were identified related to the patient’s phenotype, and, when opt-in was chosen at consent, secondary finding variant(s).

For duo and trio analyses, a separate report for the parent will be issued, specifying whether secondary finding results were declined or requested, and if so, any secondary findings that were detected. The parental analysis for ACMG SF is performed independently of the proband data, i.e. the ACMG gene list is analyzed in the parental data regardless of any potential positive findings in the proband’s data.

All test results include information about the patient such as name and date of birth, how the test was performed, and the test results. Depending on the type of test you have, results may indicate a variant that is the cause of the disease or symptoms you or your child have. Some results may indicate a variant of unknown significance called a VUS, which may or may not be associated with a disease. It is also important to understand that genetic tests may have limitations in detecting specific types of variants, so it is best to consult with your physician about the testing you are undergoing.