FAQs: Testing and Technical Specification

Sample types vary by test requisition. Visit our test catalog to find validated sample types and requested volumes for the test you intend to order. This information is also listed on our test requisition. If you are considering using an unvalidated sample type or substantially lower volume, please contact us by calling 1.800.411.4363 or by filling out our contact form.

Unless the study is being done specifically to monitor for results related to the transfusion, blood is not an acceptable specimen type for these individuals, as results may represent the donor rather than the patient. Saliva and buccal swab specimens may be considered however studies show these specimens may also represent the donor rather than the patient.
For patients with recent blood transfusions, we prefer to receive either a pre-transfusion blood specimen or DNA extracted from a pre-transfusion specimen if available. Otherwise, wait at least 2 weeks after a packed cell/platelet transfusion and at least 4 weeks after a whole blood transfusion for a repeat blood draw for all molecular studies, other than mitochondrial DNA studies. For mitochondrial DNA studies, please wait approximately 6 weeks after the transfusion. If this is not possible, please see the listing of alternate specimen types by searching under the desired test code here on our website.

Unless the study is being done specifically to monitor for results related to the transplant, blood is not an acceptable specimen type for these individuals as results may represent the donor rather than the patient. Saliva and buccal swab specimens would not be ideal as studies show these can also represent the donor rather than the patient.
For patients with bone marrow transplants or allogeneic peripheral blood stem cell transplants, we prefer to receive either a pre-transplant blood specimen or DNA obtained from a pre-transplant specimen if available. If this is not possible, please see the listing of alternate specimen types by searching under the desired test code here on our website. We will, however, accept a blood specimen from a patient who has received an autologous peripheral blood stem cell transplant.

Our minimum requirements are dependent on the sample type and testing methodology, which can be found in our test catalog. To request exceptions for unvalidated sample types or minimal volumes, please contact us by calling 1.800.411.4363 or filling out our contact form.

In general, we prefer to extract specimens in the Baylor Genetics Lab to maximize the likelihood of meeting our quality metrics. However, for certain tests, extracted DNA from a validated specimen type may be sent when the originating specimen is an appropriate sample type for a test. The origin of the extracted DNA should be noted on the requisition. Please note Global MAPS®, biochemical/enzymatic analyses, FISH analysis, and chromosome analysis cannot be performed on extracted DNA. In addition, prenatal testing on extracted DNA needs to be discussed with one of our genetic counselors prior to sending the sample.
The following parameters must be met for extracted DNA for sequence and NGS analysis, Southern blots, microarrays, and MLPA testing:

Extracted in a CLIA-certified laboratory

20 ug at 0.5 – 1.0 ug/ul concentration

260/280 ratio: between 1.75 and 2.00

260/230 ratio: greater than 1.70

Prenatal tests and the accepted specimen types can be found here on our website.

Place the small room temperature ice pack in the freezer for return shipping upon receipt. Thaw media tube and use immediately or refrigerate for up to 1 week. Media that has arrived thawed should be stored in the refrigerator and used within 7 days.  

GeneAware is a reproductive carrier screen from Baylor Genetics. It assesses carrier status for many hereditary genetic disorders caused by pathogenic/likely pathogenic variants to identify potential risks of having a child with a genetic condition. 

We offer some of the most comprehensive mtDNA testing available, including NGS analysis of each of the mtDNA genome and select nuclear genes associated with mitochondrial disease, numerous mitochondrial NGS panels targeted to various mitochondrial phenotypes and underlying etiology, a variety of metabolic panels by phenotype and underlying etiology, as well as electron transport chain and mtDNA copy number analysis. Further information regarding our various testing options can be found, here.

PreSeekTM is a non-invasive prenatal screening tool to assess fetal risk for some of the most common autosomal dominant disorders observed in pregnancy. Patients carrying a singleton pregnancy at 9 weeks gestation or greater are eligible for PreSeekTM. In addition, pregnancies conceived via egg and/or sperm donors and/or utilizing a surrogate gestation carrier are also eligible. A maternal blood specimen via EDTA tube is required for analysis. While PreSeekTM can also be utilized to assess risk for one of the genes assessed on the panel, we are unable to provide an informative result for a fetal status of a maternally-inherited variant at this time.

A list of discontinued tests can be found here. If you are looking for a comparable alternative, please reach out to our Customer Experience Specialists at 1.800.411.4363 or fill out our contact form. Please include the canceled test you are looking to compare, and we will be happy to suggest an alternative if available (or if appropriate).

Whole Exome Sequencing (WES) reanalysis is available via test code 1900. Additional information such as turnaround time and release to new physicians may also be found at that link. The first reanalysis is free of charge, further reanalysis will be subject to a $300 fee.
Other analyses such as array do not currently offer reanalysis, however specific questions may be emailed to [email protected].

Requests for current variant classification or re-curation may be submitted through our contact form. Please include the patient’s name and date of birth, or the Baylor Genetics lab and family numbers, along with gene(s) and variant(s) of interest. Please limit requests to no more than 5 variants and include any pertinent new information or publications you would like the lab to consider.

Yes. Please fill out the Patient Request for Release of Clinical Reports and/or Raw Data form by clicking here and submit it to [email protected] 

Yes, most of our consents are available in English, Arabic, French, and Spanish. Click here to access our consent forms page. We will accept physician verification if consenting was done in a language other than English, Arabic, French, and Spanish.

Yes, specimen collection kits may be requested during the online ordering process or separately by placing a supply request on our website.

Each specimen should be accompanied by a complete and appropriate requisition. Please be sure that the patient’s name, date of birth, sample type, and sample date of the collection match what is listed on the requisition.  

Baylor Genetics can provide a collection kit and help find local options for your patient to select from for a blood draw. Patients who need assistance finding a blood draw location can call our client services team at 1-800-411-4363. 

Baylor Genetics’ saliva kits come with collection instructions enclosed. Instructions can also be found here.

The Baylor Genetics Buccal Swab collection kit will have collection instructions enclosed. You may also reference this youtube video for further instructions.

Baylor Genetics collection kits come with a return mailer to ship specimens back to Baylor Genetics. If you do not have a re-mailer you may call our customer support team at 1-800-411-4363 and they can assist in getting you a shipping label.  

Baylor genetics will pay for domestic sample shipping. Due to customs regulations, Baylor Genetics cannot cover shipping costs for samples coming from outside of the US.  

Baylor Genetics follows the FedEx Holiday schedule. If FedEx is open and delivering packages a Baylor Genetics employee will be on-site to receive specimens.
Our laboratory is open to accept deliveries on Saturday, 8 am – 5 pm CST, provided the courier service is also operating that day. If you would like your sample to arrive at our lab on a Saturday, please mark your package for Saturday delivery. Note, we are unable to accept deliveries on Sunday.

Sample stability is dependent upon the tube type:

EDTA blood should arrive at Baylor Genetics within 72 hours of collection
ACD blood should arrive at Baylor Genetics within 36 hours of collection.
Blood in a Strek tube must arrive at Baylor Genetics no more than 5 days after collection.

Whole blood of any kind should arrive ambient and never be frozen or heated.

Please call our customer support team at 1-800-411-4363 or send us an email with your query at [email protected]. We will respond to the same as soon as possible. We are working on transitioning our tests to the new website and may experience some delays in seeing some of our older tests on the website.

If a sample fails, you will receive a cancellation memorandum with the appropriate next steps listed. If you have questions regarding the reason for failure or the next steps, please feel free to reach out at [email protected] or 1-800-411-4363.

Testing failures can occur for many reasons such as sample quality and DNA yield. Your test cancellation memo should list the specific reason for the test failure as well as the next steps. If you have further questions, please reach out to our team at 1-800-411-4363 or [email protected].

Post-mortem specimens can be accepted in some cases for certain test codes. Please reach out to our team at [email protected] to confirm the sample type and volume required and the appropriate test code.

Yes. Tests not currently available in the online portal can still be ordered using a paper test requisition provided in the online test menu. We are in the process of adding additional tests to the portal, so check back frequently for updates. If you cannot find the test you need, please, please contact the client services team at 1-800-411-4363 or via email at [email protected].

Variant confirmation is dependent on the genomic location of that variant. Variants in regions with high sequence homology and known pseudogenes, low-coverage regions, skewed allele fractions, and mosaic variants will undergo confirmation.

SNV confirmation for NGS-based testing is performed by Sanger sequencing. Various methods for CNV confirmation are available, including PCR-based testing, multiplex ligation-dependent probe amplification, etc.

Most variants detected by any of the NGS-based tests do not undergo confirmation, except for regions with high sequence homology and known pseudogenes, low-coverage regions, skewed allele fractions, and mosaic variants.

Three different microarrays are used for postnatal CMA testing. All of them are custom-designed Agilent oligonucleotide arrays. They have different numbers of targeted genes. Genes not well covered in one array may be covered well in another array. Please check with Baylor Genetics’ client services team to select the array with the best coverage for genes of interest. Below is the comparison of the three arrays:

Our WGS is built on HG-38.

Variant classification is based on various types of evidence:
• Population data: the frequency of a variant in healthy population databases (such as gnomAD) – considering the penetrance and phenotype associated with the gene of interest.
• Clinical evidence: publications describing this variant detected in affected individuals (including segregation info), internal database evidence, etc.
• Theoretical & functional evidence: variant type & location in the gene in relation to the gene’s disease-mechanism, in silico predictions, functional studies such as RNA-sequencing, cell line experiments, biochemical data, etc.

Our internal database can provide us both with variant frequency information, and phenotype information of previously tested affected individuals. This can help either to rule out a variant or give it a higher pathogenicity ranking.

Cell culture is the process where the laboratory incubates cells under controlled conditions to provide sufficient material for testing. Once cultures grow to a sufficient volume, molecular or cytogenetic testing can be performed. Cell culture on average takes about 2 weeks before it is ready to be used for genetic testing, however, this is highly dependent on the specimen size, quality, and cell growth.

Yes. Our prenatal team at Baylor Genetics meets weekly to discuss the status of all culture samples. Any slow growth or lack of growth is noted at this time and someone from our team will reach out to provide this information as well as any delays that may be a result.

The success of a saliva sample is highly dependent on the quality of sample collection. On average we see about a 4% failure rate for saliva samples in our clinical tests.

Muscle is a mitochondria-rich tissue and has high energy demand. Therefore, a muscle biopsy provides an optimal opportunity to detect possible abnormalities in the function of mitochondria. Recent advances in the techniques of molecular diagnostics, such as Next-Generation Sequencing (NGS), have made it possible to offer a more minimally invasive option for those with suspected mitochondrial disease. The diagnosis of mitochondrial disease is complex because of its clinical and genetic heterogeneity and often requires the integration of biochemical, histological, and molecular testing. If you are suspicious of a mitochondrial disorder and would like to discuss which might be the most appropriate sample for your patient, please contact our laboratory and ask to speak to one of our genetic counselors. You can reach our team at 1-800-411-4363 or by email at [email protected].

If the original testing identified a variant of unknown significance (VUS), testing for at-risk family members can be offered free of charge. Qualification for free testing is dependent on the situation and should be discussed prior to sending the sample. 

Search for the specific test in our test menu and scroll to the ‘technical information’ section toward the bottom of the page. The test methodology will be listed for you there.

You can find relevant publications and resources for our tests on our website. Click on the links below or visit the website. Relevant publications for tests are listed under the “The Papers” section.
• https://www.baylorgenetics.com/whole-genome-sequencing/
• https://www.baylorgenetics.com/whole-exome-sequencing/
• https://www.baylorgenetics.com/cma/
• https://www.baylorgenetics.com/global-maps/
• https://www.baylorgenetics.com/mitochondrial/
• https://www.baylorgenetics.com/preseek/
• https://www.baylorgenetics.com/geneaware/

You can find a comparison chart for our different iterations of Whole Exome, here. This chart will illustrate which tests require parental samples.
A similar chart for our Whole Genome offerings can be found here.

Our sample reports are provided upon request. If you need a sample report, please email [email protected] and provide the test code for the sample report needed.

Whole exome sequencing primarily includes analysis of single nucleotide variant (SNV) in coding regions, extending into the exon-intron junction regions. In addition, copy number variant (CNV) analysis is included for homozygous/hemizygous deletions and duplications, and heterozygous CNV equaling or larger than 3 exons. Repeat expansions, mitochondrial DNA variants, and balanced chromosomal rearrangements cannot be detected.

Baylor Genetics does offer reanalysis on both WES and WGS. You can request a reanalysis by submitting our exome reanalysis requisition or genome reanalysis requisition to [email protected] in addition to any new patient information that may assist in the interpretation.

Baylor Genetics offers various single gene tests (Sanger sequencing or NGS-based). Once you have decided on the desired test code you will print out and complete the requisition linked on the test’s webpage, draw the specified sample, and ship it to Baylor Genetics. If you need testing or shipping supplies those can be ordered here.

Thaw media tube and use immediately or refrigerate for up to 1 week. Media that arrives thawed should be used within 7 days

Kits are shipped the same day if the request is received before 2 pm CST. All orders received after 2 pm CST will be shipped the following business day. Unless specified on the kit order, all kits will be sent via FedEx Ground Shipping (3-4 business days depending on destination location).

Yes, we provide testing materials and shipping and customs costs for the kits. We do not provide a return label or shipping and customs costs for the sample’s return to Baylor Genetics.

You may add testing to an existing sample by completing our Test Revision Authorization form and submitting that to [email protected]. Our team will add additional testing if there is sufficient sample volume to complete testing.
Please read the “important reminders” section at the top of the form to ensure all necessary actions are taken.

You may email [email protected] with the Baylor Genetics Lab#, DRL, and the test code you want to add. Our team will investigate and let you know if there is enough remaining sample for the requested test code.

Please email Baylor Genetics Lab# and DRL to [email protected] along with the variant of interest and our curation team will review and provide updates.

We highly recommend using our requisitions to ensure all needed information is obtained and prevent any associated testing delays. If you are having trouble locating the appropriate requisition on our website, you may call our team at 1-800-411-4363 and they will assist you.

GeneResults does not limit the number of delegates allowed. Please be sure to email our team at [email protected] if you assign delegates yourself so that we can ensure the delegates get their account verified and password set.

If written informed consent is not attainable from the patient, oral consent is acceptable. The clinician or Genetic counselor who received oral consent would note oral consent was obtained and can sign on behalf of the patient.

We typically offer raw data in bam, bai, vcf or fastqs files. However, if another file type is needed, please indicate the file type requested in the request form and our team will attempt to accommodate the request.

All kits (excluding saliva kits contain):
• Parafilm
• Specimen labels
• Plastic biohazard bag
• Clinical pak
• Prepaid airbill (domestic shipping only)
• Instructions
• Sample requisition

Yes, if you are a new client looking to send testing to Baylor Genetics, please reach out to our team at 1-800-411-4363 or [email protected] so we can establish your account. Once your account is established, we can accept samples.

The turnaround time for Rapid Whole Exome Sequencing (WES) depends on the sample type. It starts at 5 days for blood samples and 6 days for other samples such as buccal swabs.

The turnaround time for the comprehensive mitochondrial genome analysis and other mitochondrial sequencing tests is dependent on sample type. It varies from 14-28 days for sample types such as blood and purified DNA to 28-56 days for sample types such as liver, skeletal muscle, and fresh frozen tissue.

The turnaround time for Prenatal CMA tests depends on whether cell culture is required. The turnaround time ranges from 7-10 days but may be extended to 3-4 weeks if culturing is required, depending on culture growth. Baylor Genetics will make every attempt to report on direct specimens including the use of whole genome amplification (WGA).
Other points to consider are:
• The requirement of WGA may increase turnaround time by 1-2 days
• The requirement of parental CMA may increase the turnaround time by 3 – 4 days

Pathogenic events of short tandem repeats in NOTCH2NLC, ATN1, DIP2B, ATXN2, ATXN8OS, PABPN1, ATXN3, JPH3, TCF4, CACNA1A, DMPK, GLS, NOP56, CSTB, ATXN10, ATXN7, CNBP, HTT, RFC1, PHOX2B, PPP2R2B, ATXN1, TBP, C9orf72, FXN, AR, FMR1, and AFF2 will be reported, with descriptions of disease association and variant details.

The sensitivity of detection is reduced for borderline or incomplete penetrance alleles. Additionally, the number of repeats could be approximate due to the limitation of sequencing and/or confirmatory methods.

Confirmation testing will be ordered for reportable TNR variants, as needed. For critical cases, a preliminary report will be issued, and an updated report will follow with confirmation testing results.

Yes.

We submit new variants and reclassified variants to ClinVar yearly.

Sample retention is dependent on sample type:
• Whole Blood – All tests – 3 months
• Saliva– 3 months
• Buccal swabs – 3 months
To inquire about an old specimen please reach out to our team at 1-800-411-4363 or [email protected].
*All leftover specimens from New York State will be destroyed within 60 days. *