Blueprint Genetics

FAQs

Billing

What is an insurance Benefit Investigation (BI)?

Blueprint Genetics will contact the patient’s insurance provider and verify that the insurance is current and active. Coverage for clinical diagnostic genetic testing services can vary significantly across insurance providers and plans. The purpose of the insurance Benefit Investigation (BI) is to determine the in-network and out-of-network coverage including deductibles, co-pays, co-insurances, out-of-pocket maximums, exclusions, and requirements such as prior authorization (PA) or pre-certification.

What happens after a benefit investigation?

If a patient’s financial responsibility is less than $100, Blueprint Genetics will simply move forward with testing. Whenever a patient’s out-of-pocket costs exceed $100, a billing specialist will contact the patient in a timely manner (within 72 hours) to minimize delays in testing.

What am I financially responsible for if I have commercial insurance?

Patients are responsible for co-pays, co-insurance, and any unmet deductible as determined by their insurance provider. Blueprint Genetics has a generous Financial Assistance Program (FAP) that can reduce a patient’s financial responsibility based on need and family income level.

What if I cannot afford the cost of genetic testing?

Many patients and families experience economic challenges associated with their clinical situation. In certain situations, patients may qualify for a reduction in their out-of-pocket expense. Eligibility for our financial assistance program (FAP) is based on need and requires that patients supply information on family size and income.

Will my insurance pay for the testing?

Coverage for testing can depend on various factors including your medical condition, family history, and what kind of testing has been ordered as well as your insurance plan’s determination of medical necessity. The billing specialists at Blueprint Genetics work closely with insurance benefit providers to collect the maximum allowable reimbursement under each unique plan.

Are you in-network or contracted with my insurance plan?

Blueprint Genetics works with all commercial insurances and every patient with active benefits can access our diagnostic testing service. We are in the process of contracting with a number of plans but at this time we would most likely file a claim with your plan as an out-of-network service provider.

What happens if my insurance plan denies the claim?

If a claim for reimbursement is denied, or the amount of reimbursement is insufficient, Blueprint Genetics will file an appeal with the insurance provider whenever allowed. We will also assist patients if the appeal for medical review must be initiated by the patient or policy holder. Patients are responsible for any unmet deductible, co-pays, and co-insurance even if the insurance plan denies the claim and all subsequent appeals.

Will you process prior-authorizations?

Blueprint Genetics’ billing specialists will process insurance prior authorizations (PA) on behalf of the patient whenever allowed, and will assist clinicians with submitting letters of medical necessity (LOMN) and supporting clinical documents.

Can you tell me exactly how much I am responsible for?

Under our commercial insurance billing policy patients are responsible for any unmet deductible, co-pay, or co-insurance up to the full amount of the test. In some cases, the insurance company may only approve a portion of the billed amount (allowable), and in those situations the patient is responsible for any unmet deductible, co-pay, or co-insurance up to the allowable amount.

Do you balance bill patients?

Patient financial responsibility (also known as out-of-pocket or OOP) is limited to unmet deductible, co-pays, and co-insurance. Blueprint Genetics will make every effort to obtain the maximum amount of reimbursement from insurance benefits providers which may include patient participation in the appeal process. Under our commercial insurance billing policy, the financial responsibility (OOP) for each patient will be communicated up-front so patients can make informed decisions about testing.

What if I am not satisfied with my options under the financial assistance program (FAP)?

Blueprint Genetics is committed to increasing accessibility for all patients to our diagnostic testing services. If a situation arises where we cannot provide an acceptable billing solution, there is no obligation to proceed with testing. In the rare case that a patient decides not to move forward with testing, we will obtain approval from the ordering physician and cancel the test.

When am I responsible for paying my portion (OOP)?

Patients who choose to participate in our self-pay option under the Blueprint Genetics financial assistance program (FAP) are expected to make some kind of payment before testing is started. When Blueprint Genetics bills a patient’s insurance for our services we usually finish the testing and report our results before the claims process is completed. Patients are sent a statement from Blueprint Genetics which includes their final determination of financial responsibility (OOP) once the claims and appeals process has been exhausted. In certain situations, the patient financial responsibility (OOP) can be less than the original amount of unmet deductible, co-pay, and co-insurance communicated to the patient.

What payment methods can I use?

Bank transfers, credit cards, PayPal, or checks are all accepted forms of payment.

Does Blueprint Genetics accept Medicare or State Medicaid?

Blueprint Genetics does not accept Medicare or State Medicaid plans at this time. Patients with government insurance plans can take advantage of our discounted self-pay price. For more information contact Blueprint Genetics billing support at billing.us@blueprintgenetics.com.

Does Blueprint Genetics accept Tricare, CHAMPUS, or other Military Insurance plans?

Blueprint Genetics does not process claims for Tricare or CHAMPUS plans at this time, however patients with military insurance plans can take advantage of our discounted self-pay price. For more information contact Blueprint Genetics billing support at billing.us@blueprintgenetics.com.

What happens if my insurance company sends me a payment instead of Blueprint Genetics?

It is the patient’s responsibility to forward Blueprint Genetics the entire payment within 10 days of receipt.

Certifications and Important Numbers

Is Blueprint Genetics an accredited diagnostic laboratory?

Yes. Blueprint Genetics is accredited by both Finnish Accreditation Service (FINAS) in accordance with SFS-EN ISO 15189:2013 and College of American Pathologists (CAP).

  • FINAS / SFS-EN ISO 15189:2013: #T292, please see the flexible scope here.
  • CAP: #9257331

Is Blueprint Genetic CLIA certified?

Yes. We have certification from the U.S. Department of Health and Human Services’ Centers for Medicare and Medicaid Services (CMS) under the Clinical Laboratory Improvement Amendments (CLIA) of 1988 for high complexity genetic testing. CLIA certification and separate state certifications allows us to operate in several states or districts in the USA.

Are your tests FDA-approved?

Our tests are developed and validated in-house and the FDA has determined that such clearance or approval is not necessary.

Important numbers

  • NPI (National Provider Identifier): 1497133573
  • EIN/Tax ID: 371768269

Please contact our Quality Management Team in any questions regarding laboratory quality and regulatory compliance (e.g certifications) in qm.office@blueprintgenetics.com

Are your tests CE marked?

Yes. All Blueprint Genetics’ panel tests are CE marked, general IVD devices. General devices include all IVD devices other than those covered by Annex II and IVDs for self-testing. This means that Blueprint Genetics self-declares conformity with the relevant Essential Requirements of the Directive 98/79/EC and ensures the devices fulfil the applicable obligations described in Annex III. These devices do not require the involvement of a notified body.

Clinical Genetics Support

Clinical Genetics Support

Blueprint Genetics offers Clinical Genetics Support for situations requiring specialized expertise in genetic diagnostics.

These situations include:

  • questions on challenging biological samples and shipment strategies
  • discussions on selecting an optimal diagnostic tool for your patient
  • questions concerning the clinical statement and discussions on variant classification
  • assistance in genetic counseling of your patient and the family
  • other requests that require tailoring of our service to your clinical needs.

Our mission is to improve our services and our Clinical Genetics Support team is happy to discuss strategies that can lead to better service and improved quality of diagnostics.

When contacting us, you will have a chance to discuss your issue with our Clinical Team consisting of physicians, geneticists or genetic counselors. You may send your requests via email genetics.support@blueprintgenetics.com and we will respond to you within 24 hours or contact you by phone if requested. You may also call our Customer Support in North America at (650) 452-9340 or in Europe at +358 40 2511 372 which will direct your call to our Clinical Team.

Our Customer Support can also assist you with all other practical issues such as billing, sample collection kits, ordering options or to evaluate the status of your patient’s analysis.

Connecting Clinicians

What is Connecting Clinicians?

Connecting Clinicians is feature that is built into our Nucleus online portal. The feature provides healthcare professionals the opportunity to share between them clinical information about their patients who have the same Variant of Uncertain Significance (VUS) or Likely Pathogenic (LP) variant in a given gene.

Watch a video introduction to Connecting Clinicians or read more about the service:
From phenotype to diagnosis: Blueprint Genetics launches an open digital platform to connect clinicians based on matching rare variants.

 

What information is shared in the initial connection?

Only the variant information and your contact information can be seen by the other user; no patient details are shared. Connections are created only between users that have agreed to be part of the Connecting Clinicians program.

As a default, your name, title, hospital/institution, email address, and phone number (if provided) can be seen once both have decided to accept the connection. You will be given the same contact information about the connected user. You may, or may not, choose to communicate with users connected with you. Nucleus only provides the contact information of the other user and does not host the conversations.

How are the connections made?

This service is available to anyone with a Nucleus account and for any VUS or LP variant, even if it was not identified at Blueprint Genetics.

The submission of the VUS or LP variant to the Connecting Clinicians service is done automatically if the variant was identified by Blueprint Genetics. Alternatively, users can manually upload VUS or LP variant information into the Find connections tab under Connecting Clinicians if the variant was identified at a different laboratory.

A connection between users is generated if there is:

  • a perfect match found in the database (the exact same genetic variant was reported in another patient or submitted manually by another user)
  • an approximate match found in the database (the genetic variant suggested is not further than 2 nucleotides away).

When a variant match is made, Connecting Clinicians creates a pending connection. You will receive a notification when a new connection is available. If both of the users agree to be connected for that particular variant, the connection will be confirmed, and the users will be able to see each other’s contact information. No patient information is shared by Blueprint Genetics. If you do not want to discuss clinical details with the connected user for a particular case/variant, you can choose not to accept the connection and it will be removed from the pending connections list.

 

Can I delete a connection?

If you wish to delete a connection, please contact Customer Support at support.us@blueprintgenetics.com.

Can I disable Connecting Clinicians?

While the Connecting Clinicians feature cannot be fully disabled, contact information is only shared when you accept a suggested connection. You may disable notification emails, which include Connecting Clinician emails. You can change the email preferences under Profile settings.

Forms

Further Testing

What is the procedure for adding on further testing to a sample already at Blueprint Genetics?

An additional test can be added on to a sample already at Blueprint Genetics by making a new order in our system and notifying this exception in the referral. In this case, write the ID number of the previous purchase on the new referral.

I would like to order another test on a patient who was tested previously. Do I need to submit another sample?

No. Generally, we obtain enough DNA from one sample to allow completion of another test. A second sample is not usually necessary and in case of any exceptions the referring physician will be promptly informed.

Invoicing

What payment methods can I use?

You can use either bank transfer or Credit Card (Mastercard/Visa).

Can I set up an institutional billing account?

Yes. Generally an account is set to each department of the hospital. Simply provide the contact information (name, phone and fax numbers, email/physical address) to which we can mail an invoice.

What is the global billing policy of Blueprint Genetics?

Blueprint Genetics provides clinical genetic diagnostics throughout the globe with significant variability in healthcare systems and billing policies. In principle, Blueprint Genetics invoices the payer or customer when the analysis is complete. Exceptions with this policy may occur. Blueprint Genetics offers diagnostic services only when ordered by a healthcare professional. Blueprint Genetics may have different pricing and service models in different territories. Our philosophy is full transparency in pricing.
 

Nucleus

What is Nucleus?

Nucleus is Blueprint Genetics’ online ordering and networking portal. Through Nucleus, users can order genetic testing, track the test’s progress, and review the results. There is also a built-in feature that enables clinicians to connect based on matching rare variants.

 

How do I create a Nucleus account?

Healthcare professionals can create their own Nucleus account for themselves by clicking on the “Request an account” link at nucleus.blueprintgenetics.com. You will receive an email to confirm your account. Once you have confirmed your email address, you can start placing orders immediately. The ability to share orders with colleagues within the same hospital will activate within a few days.

Do I have to pay for a Nucleus account?

No, there is no cost associated with having a Nucleus account.

How do I place an order in Nucleus?

To place an order in Nucleus, log in at nucleus.blueprintgenetics.com and Choose Orders page. Click the New test button. Select, fill and submit the form of the desired test. Nucleus provides a guided way to order and ensures that all necessary fields are filled out. To complete your order, send us the patient sample and the informed consent for testing.

See our webinar: Nucleus – Faster and easier access to ordering genetic testing for your patient to get started with using Nucleus.

Is Nucleus secure? Can I safely attach patient information to my online order in Nucleus?

Nucleus has several safeguards in place to ensure that the information entered and stored in Nucleus is secured. Outside access is controlled; only specific and authenticated users are authorized to access the site and in an end-to-end encrypted manner. A number of mechanisms have been implemented for monitoring and protecting against outside attacks seeking to compromise the Nucleus system or data. We conduct periodic third-party security penetration testing to ensure adequate level of security.

You can safely attach patient information with your order in Nucleus. We strongly recommend (and encourage!) that you provide as much clinical information as possible with each order. This might include a pedigree, consultation letter and/or reports of investigations (including normal results). Where possible, please upload any documents with identifying information directly to Nucleus; do not send them by email.

How do I change my password?

Log in to Nucleus, click on your username on the top right corner, then select “Profile settings”. Choose “Change password”. Type in your old and new password, and select “Save”.

Two-Factor Authentication

We highly recommend using the two-factor authenticator feature.  Two-factor authentication can be enabled through your own profile settings.

My account has been inactivated. Why did this happen and how do I reactivate it?

For data security reasons, your Nucleus account password must be changed once a year. You will receive an email reminder 30 days and 7 days before the password is due to be changed. Your account will be inactivated if you do not change your password within the given time frame. Your account can be re-activated by contacting our Customer Support at support.us@blueprintgenetics.com.

How do I share the results with my colleague?

Genetic test results can be shared with colleagues within the same institution through Nucleus. You can choose which of your colleagues you wish to share results with by selecting them from a list of Nucleus users within your clinic/hospital/network on page 6, second last page, of Nucleus order form. The colleagues with whom you are sharing results will receive an email, notifying them of the shared order. They will also receive a notification email when the results are ready. No patient information is shared in these notification emails.

Please note that users who have registered for a Nucleus account with an email account not affiliated with an institution/network or company (e.g. gmail, Hotmail, Yahoo) are not able to share results for security reasons.

I received an email notifying me that results have been shared with me. How do I review them?

Any orders shared with you can be seen by switching to the “Shared with me” tab above your own list of orders.

Can I make changes to my order after submitting it?

Once an order is submitted, field entries cannot be modified. If you wish to make any changes, please contact our Customer Support.

How do I add additional information to an order after it has been submitted?

Once your order is submitted, it can be viewed by logging into Nucleus and clicking on “View”. You will have access to a new free text field called “Comments”. Additional information such as clinical notes can be added here. Any other changes to the order must be done by contacting our Customer Support team.

What other features are built in to Nucleus?

Connecting Clinicians is a feature which enables clinicians to connect based on matching variants, with the same likely pathogenic (LP) or variant of uncertain significance (VUS). Click here for more information.

Ordering

How to order?

The easiest way to order is via our online portal, Nucleus. This expedites the ordering and analysis as it ensures that we have all the necessary information to begin the test. Any genetic test can also be ordered by completing a paper requisition form.  Please visit How to order for more information about the ordering process.

Who can order genetic tests from Blueprint Genetics?

Our genetic tests can only be ordered by healthcare professionals. If you are a patient interested in genetic testing, please discuss your options with a local healthcare professional or a genetic counselor: National Society of Genetic Counseling.

What should I consider prior to ordering a genetic test for my patient?

Prior to ordering the genetic test, we recommend that the healthcare professional discusses the following with their patient:

  • The purpose of the test
  • The possible test results (positive, negative and results of uncertain significance), what these mean and their implications
  • Possible incidental findings and their implications
  • That test results may reveal information about a patient family members’ health and/or family relationships.

If you do not feel comfortable discussing the above with your patient, we recommend that you refer your patient to a genetic counselor. A list of genetic counselors (by region and area of expertise) can be found at www.nsgc.org.

If you are unsure about which test to order for your patient, please review the different genetic tests we have available for your patient by clicking on the Diagnostic Tests link in the website top menu bar. Each page includes a short description of the test, a list of genes and regions covered, test performance and potential limitations. You can also visit What to order.

If your patient’s phenotype is unclear and/or you are still unsure about which test to order, you can contact our Clinical Genetics Support team for further assistance. Please do not include any patient identifying information in your email. We aim to respond to all emails within one business day.

What different testing options are available?

Whole Exome Sequencing

Whole Exome Sequencing (WES) is our most comprehensive test option. WES is the analysis of the protein coding regions of all ~20,000 genes of the human genome (known as the exome) using next generation sequencing technologies.

WES is most suitable for individuals with:

  • A complex, non-specific genetic disorder with multiple differential diagnoses
  • A genetically heterogeneous disorder where stepwise testing of genes significantly increases costs
  • A suspected genetic disorder where a specific genetic test is not available
  • Previous genetic testing that has not been diagnostic

Our Whole Exome Family includes high-quality Whole Exome sequence and CNV analysis of an index patient and parents (trio) or other family members. The trio approach used in the Whole Exome Family test increases the diagnostic yield by improving the variant filtering and readily enabling the detection of de novo variants, which are the cause of many severe, early onset diseases.

Panels

A panel is a genetic test that contains a subset of genes related to a specific phenotype or diagnosis. Some panels contain fewer genes and are most appropriate when a specific diagnosis is suspected. Some panels are much larger (e.g. over 100 genes) and are most appropriate for patients with complex phenotypes or multiple differential diagnoses.

Healthcare professionals can customize our panels by adding up to 20 genes and/or removing as many genes as desired at no additional cost. This is called a Flex panel.

Single Gene Testing
This test involves the sequence and CNV analysis of a single gene. It is most appropriate in situations where the patient’s diagnosis is most likely caused by a variant in a specific gene, or if you would like to perform carrier testing for reproductive planning.

Family Extension Service
You can extend your patient’s diagnostic evaluation to cover familial mutation testing for up to 5 first-degree family members.

  • Available for up to 5 first-degree family members whose testing is ordered and samples are received within 12 months from the original index patient’s report date
  • Family member testing is available for ‘likely pathogenic’ and ‘pathogenic’ variants only
  • Blueprint Genetics recommends genetic counselling for all individuals undergoing genetic testing

Read more about the service here.

Family Member Testing

The Family Member Testing (FMT) service provides targeted testing to the relatives of patients previously tested at Blueprint Genetics and in whom a variant has been identified.

Family Member Testing can be used for:

  • Diagnostic testing in affected family members
  • Predictive testing in unaffected family members
  • Carrier testing in the case of autosomal recessive (AR) and X-linked disorders
  • Segregation of variants of uncertain significance (VUS) where appropriate
  • Confirmation of research results

FMT takes approximately 3-4 weeks from the time the sample and all required information is received. Read more about FMT here.

VUS Clarification Service

Blueprint Genetics provides a free-of charge service that is available to patients tested at Blueprint Genetics and found to have a variant of uncertain significance (VUS) that could potentially be reclassified to likely pathogenic on the basis of family member testing. Read more about the service here.

What different types of analysis are available for WES and Panels?

There are three different types of analysis to choose from for panels and WES:

1) Plus Analysis is a combination of both sequencing and deletion/duplication (CNV) analysis. Plus Analysis has the highest overall diagnostic yield, as large deletions and duplications cannot be detected using sequence analysis alone, and is the most commonly ordered analysis. In addition, Plus Analysis can decrease the time it takes to make a diagnosis.

2) Sequence analysis is used to detect single nucleotide variants and small insertions / deletions, up to 50-200 base pairs in size. This does not include deletion/duplication (CNV) analysis.

3) Del/Dup (CNV) analysis is a targeted analysis used to detect larger disease-causing deletions or duplications (typically one exon or larger) and does not include sequence analysis.

For single genes and FVT you don’t need to separately choose an analysis type. Our Single Gene tests are automatically done as a Plus.

My patient had an inconclusive / negative test result and I would like to order more testing. How do I do this?

Consider using another panel or expanding to Whole Exome Sequencing. If your patient’s previous genetic testing (panel, single gene test) is inconclusive or there is a diagnostic finding that doesn’t explain the whole phenotype, you can provide your patient with the most comprehensive genetic test with Expand to Exome.

For WES orders, Blueprint Genetics also provides a re-evaluation service that revisits reported VUS and LP variants from a previous WES order. A more extensive WES Re-analysis will be available later in 2019, for WES orders placed after November 27th, 2017. This more extensive re-analysis includes fully new bioinformatics and a full interpretation. The goal is to potentially find new clinically relevant variants, for example in light of new phenotypic information from the patient. Read more about re-evaluation and re-analysis here.

Prenatal testing

What are the ordering healthcare provider responsibilities when requesting prenatal testing?

By ordering a prenatal diagnostic test on your patient and sending Blueprint Genetics a fetal sample, you agree that:

  • you take responsibility for the appropriateness of the requested testing.
  • you have explained the purpose of the prenatal testing you have requested to the patient.
  • you have provided appropriate genetic counseling to the patient.
  • the patient had an opportunity to ask questions as they arose.
  • you are responsible for obtaining and documenting written or verbal informed consent ensuring your patient understands the risks, benefits and limitations of the testing you have requested in addition to the implications of the results.
  • you have arranged for maternal cell contamination (MCC) studies to be performed to rule out significant maternal cell contamination as (MCC) can affect the performance of prenatal diagnostic testing and interpretation of test results.

What prenatal tests does Blueprint Genetics perform?

For ongoing pregnancies where the sample is fetal in origin, we will perform:

  • Panel testing for diagnostic purposes
  • Single gene testing for diagnostic purposes
  • Family Member Testing (FMT)
    • If known variant testing is requested for a previously identified CNV, we are unable to test for the CNV via qPCR due to the sample quality of DNA extracted from prenatal samples. We will instead do single gene NGS for the detection of previously identified CNVs. If requested on the requisition, we will limit our report to the variants previously identified in the family. For pricing, please refer to our regular fee schedule.
    • Please note that fetal samples from an ongoing pregnancy are not eligible for FMT as part of the Family Extension Service. FMT for fetal samples can be done as part of our regular FMT Service. For information about the Family Extension Service, click here.

I want to do prenatal FMT but the testing for the index patient was done at a different laboratory. Will Blueprint Genetics do the prenatal FMT?

Prenatal testing is time sensitive. For this reason, Blueprint Genetics only performs prenatal FMT when the index patient was tested at Blueprint Genetics.

Does Blueprint Genetics perform whole exome sequencing (WES) for prenatal samples?

At this time, we do not perform WES for ongoing pregnancies where the fetus is the index patient. We will accept samples for WES from terminated pregnancies, spontaneous losses or stillbirths where there is an indication for WES.

We will accept samples for WES where there is an ongoing pregnancy in the family, and the index patient is not a fetus. Our WES TAT is up to 8-10 weeks.  We will make every effort to prioritize WES when there are implications for an ongoing pregnancy. In such cases, WES Family (WES trio) is strongly recommended.

Are there any circumstances where Blueprint Genetics will not do prenatal testing?

We do not perform prenatal testing for:

  • Fetal sex determination
  • Preimplantation diagnosis

What fetal samples does Blueprint Genetics accept for prenatal testing?

We will accept the following samples for prenatal testing:

  • DNA extracted from direct or cultured amniocytes or chorionic villi (MCC required)
  • DNA extracted from fresh or frozen fetal tissue obtained after birth/delivery (MCC not required)
  • DNA extracted from fetal blood (MCC required)
  • Umbilical cord blood after birth/delivery (MCC studies at client’s discretion)

Currently we are not able to perform cell culturing, and therefore do not accept direct or cultured amniotic fluid or chorionic villi. We do not accept DNA extracted from fetal liver or formalin fixed or paraffin embedded samples.

Does Blueprint Genetics perform maternal cell contamination studies (MCC)?

At this time, we do not perform MCC. We therefore require that MCC studies be performed locally.

MCC studies can be done prior to sending the prenatal sample to Blueprint Genetics or concurrently. Please indicate on the requisition that MCC is negative or is pending to ensure timely processing and testing of the fetal sample.

What is the turn-around time (TAT) for prenatal testing for ongoing pregnancies at Blueprint Genetics?

The typical TAT for panel testing and for Familial Variant Testing (FVT) (where the variant has been previously identified at our laboratory) is approximately 3-4 weeks and 2-4 weeks, respectively, from the receipt of sample and confirmation of payment/funding.

At this time, we do not offer a formal priority testing service, however, our laboratory will make every effort to prioritize fee for service testing of fetal samples or samples when there is an ongoing pregnancy.

Is there an additional charge to perform prenatal testing?

There is currently no additional charge for prenatal testing.

What does Blueprint Genetics need in order to perform prenatal testing for an ongoing pregnancy?

In order to perform prenatal testing, we require the following:

  • Fully completed Nucleus order or paper requisition
  • Extracted fetal DNA
  • Maternal cell contamination studies must be performed locally (indicate MCC is ongoing or complete on the requisition to avoid delays in processing and testing)
  • Signed consent form
  • Retention of a back-up culture is strongly recommended

What variants will Blueprint Genetics report from prenatal testing?

We will report pathogenic or likely pathogenic variants in addition to variants of uncertain significance (VUS) felt to be related to the reported phenotype. We do not report likely benign or benign variants.

Please note that there are some panels that include genes where bi-allelic variants cause a childhood onset condition but where a single heterozygous variant causes an increased risk for an adult onset condition, e.g., the Limb Malformations Panel includes BRCA2.  Bi-allelic variants are associated with Fanconi anemia while heterozygous pathogenic/likely pathogenic variants are associated with an increased risk of breast and ovarian cancer. It is the responsibility of the ordering health care provider to be aware of the genes on the selected panel and to counsel their patient accordingly.

Will Blueprint Genetics do prenatal testing for a VUS?

We will do prenatal testing for one or more VUS(s).  Genetic counseling is strongly recommended prior to testing and after results are available to ensure the patient is aware of the risks and limitations of prenatal testing for a VUS. It is important to note that clinical decisions should not be made based on the presence or absence of a VUS.

Does Blueprint Genetics perform paternity testing?

No, we do not perform paternity testing.

What is the policy for DNA Banking and Return of Samples?

Please note the options for DNA storage at Blueprint Genetics on our consent form. If you wish the fetal sample returned to you after testing is complete, please see our policy for Sample return (FAQ>Shipping) or contact our Customer Support Team at support@blueprintgenetics.com.

Raw Data

Does Blueprint Genetics provide raw data?

Yes, we provide raw data for Whole Exome Sequencing (WES) and panel orders.

What is raw data used for?

Raw data is typically a resource for researchers or experts that are skilled at bioinformatics. Raw data requires specialized bioinformatic tools to open the files and further analyze or visualize them.

What file formats does Blueprint Genetics provide for raw data?

Blueprint Genetics delivers raw data in BAM and / or VCF file formats.

  • For WES cases, we provide unannotated VCF or BAM files.
  • For panels, we provide unannotated VCF including genetic variants detected in panel target regions, unless the full raw data set is specifically requested.

VCF (Variant Call Format) is a standard file format storing a list of sequence variants and their genomic positions. The VCF file does not contain detailed annotations of the variants such as the gene name or population frequency of the variant. It is ~2 MB in size.

BAM (Binary sequence Alignment Map) is a standard file format that contains sequence reads mapped to the human reference genome, including base quality and mapping quality scores.  BAM files are ~20-30GB in size.

Please note that the file size for raw data is large and the data requires further processing with bioinformatic tools to produce meaningful results. Links to commonly used and freely available tools are provided below.

Who can request raw data?

The data can be requested by the health care provider who placed the original order or by a health care provider with whom the results have been shared in Nucleus.

Any raw data requests from an organization or institution other than the original ordering organization or institution require a PHI Release form signed by the patient / legal representative. Please contact our Support for further assistance at support.us@blueprintgenetics.com.

How do I request raw data?

Download the correct form to request raw data for your previous order. Complete the Raw Data Request form and send it to us (by land mail or fax). E-mail should not be used. Please note there are separate Raw Data Request forms for WES raw data and panel raw data.

Alternatively, you can request raw data at the time you order a panel or WES for your patient by sending the Raw Data Request form with the patient sample and test requisition or by attaching the form to Nucleus at the time you create your order. Please note that attaching documents in Nucleus after placing an order is not yet possible.

Is there a time limit for requesting raw data?

The data can be requested up to 2 years after the initial report.

How long does it take to receive the raw data once it has been requested?

The data is delivered approximately 1 month after the results are reported, and the request and all required forms are received.

Is there a fee for requesting raw data?

Raw data for WES and panels requested within two years after the original report is provided at no cost. WES raw data for a previous panel order is available for a fee. Contact our Support for more information on pricing.

How is the raw data provided to me?

You will receive an email notification and instructions for downloading the data from our Support team. There will be a download link which will remain active for 14 days. Please download the data as soon as you receive the download link to ensure enough time for technical assistance should it be needed. If the data is not retrieved during that 14-day window, a new link can be requested by contacting Support.

What should I expect when I download the raw data file(s)?

The file size can be large, so we recommend that you reserve several hours for the download. It is possible to use a web browser to download the files, but we encourage you to use a command line utility to download files on a computer that is capable of storing and processing large quantities of data.

  • The VCF file size (~2MB) is not typically problematic in size for a regular computer. VCF files require bioinformatic tools for processing. However, it can be opened in any text editor or Excel after unzipping the gz-formatted VCF file.
  • With BAM files (~20-30GB), it is important to use a computer that is capable of storing and processing large quantities of data. One can use bioinformatic tools to access the BAM file and make variant calls (which generates a VCF) or visualize sequence reads and variants.

What software do I need to read the raw data?

Analysis of the raw sequence data requires bioinformatics expertise and software.

For annotation and analysis of sequence variants in the VCF file there are several commercial and non-commercial tools available. Commonly used and freely available command line tools include:

There are also several non-commercial and commercial web browser-based or stand-alone software for variant annotation and analysis. For sequence read analysis, GATK is one of the most commonly used toolkits https://software.broadinstitute.org/gatk/.

To visualize the content of VCF or BAM files in genomic context the Integrative Genome Browser (IGV) can be used, both as a stand-alone application and a web-browser interface.

http://software.broadinstitute.org/software/igv/.

Does Blueprint Genetics offer technical support if I have a question about raw data?

Blueprint Genetics provides technical instructions and general assistance for receiving and downloading the data, however, we do not provide assistance with the bioinformatic analysis of the raw data. To support the work of clinicians, Blueprint Genetics has already provided a thorough clinical analysis and interpretation of the data in the Clinical Statement.

Raw Data Request forms

Download the correct form to request raw data for your previous order. Complete the Raw Data Request form and send it to us (by land mail or fax). E-mail should not be used. Please note there are separate Raw Data Request forms for WES raw data and panel raw data.

Results and Analysis

Why are the results of testing sent directly to the referring physician rather than the patient or parent of a patient?

Genetic testing offered by Blueprint Genetics must be ordered by a healthcare professional, and we only share the results with the individual ordering the test. Genetic test results can establish the correct diagnosis in a patient, determine the most appropriate treatment strategies and provide a risk assessment the patient/family. This type of information is best communicated in the context of a patient’s medical/family history by a healthcare professional involved in the patient’s care.

How can I view the results of the tests I have ordered?

Results can always be viewed online or downloaded as a PDF through our online portal, Nucleus. By request, the results can also be sent by fax or regular mail.

How will I know when my test results are ready?

Throughout the ordering process, we keep you up-to-date on the status of your order by email. You can also log in to Nucleus to track the progress of your order through the various steps of the analysis. When the analysis is complete, you will receive an email notifying you that results are now ready to be reviewed in Nucleus.

If you haven’t created a Nucleus account for yourself, you can create an account here or our support team can do this for you. If you can’t recall your password, you can use the “Forgot password?” link to create a new one.

If you wish to have results mailed to you, these will be sent via mail the same or next business day following the notification email. If you have requested a faxed copy of your results, these will be sent shortly after the notification email is sent. Downloading the report directly from Nucleus is the quickest, and most reliable, way to review and receive test results.

When can I expect results to be ready?

The majority of our tests are completed within 28 days from the time the sample is received in the laboratory with all required information. The turn-around time for Whole Exome Sequencing is approximately 8-10 weeks. Ordering online and providing complete clinical information facilitates the processing and interpretation of results.

Does Blueprint Genetics offer an expedited or priority analysis?

Currently, Blueprint Genetics does not offer expedited analysis of samples. We do aim to prioritize the analysis of samples where the results will directly impact medical management (eg. treatment, interventions or a pregnancy). If this is the case for your patient, please contact our Client Services team at support@blueprintgenetics.com.

Sample Requirements

What kind of patient samples do you accept?

Sample types and requirements:

  • Minimum 2 μg** in TE buffer or equivalent (please do not dilute in water)
  • Concentration > 20 ng/μl (optimal concentration 20 – 150 ng/μl) and with a minimum volume of at least 40 μl. Please ensure to provide at least 2 μg extracted DNA.
  • Stored in a DNase-free microcentrifuge tube (ideal: 1.5 ml snap-cap microcentrifuge tube).

Please note that:

  • As many liver cells are polyploid, DNA extracted from liver tissue is only accepted for Familial Variant Testing of a known sequence variant (not accepted for NGS based tests or copy number changes).
  • We do not perform maternal cell contamination (MCC) studies for prenatal samples (chorionic villus samples, amniocytes, fibroblasts, amniotic fluid samples etc.). We recommend MCC testing be performed locally for any prenatal testing sent to Blueprint Genetics.
  • We do not accept DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue.

*DNA must be extracted by a qualified laboratory with one or more of the following certifications / accreditations: CLIA certification, CAP accreditation, accreditation equivalency as determined by CMS, accreditations and certifications from established international organizations and/or government agencies)

**If DNA concentration is measured using a fluorescence-based DNA quantification method such as Qubit, 2 µg of DNA is sufficient. However, if the measurement is done using spectrophotometric methods, twice as much DNA is required as the concentration has likely been overestimated. If our DNA quality and quantity control demonstrate that the amount of DNA provided is less than what is required, we will request a new sample before beginning the analysis.

How should samples be collected, labeled and stored before shipping?

Blood

  • Blood should be collected in an EDTA tube (lavender top) designated for blood samples.
  • The tube should be labeled with the patient’s name, date of birth and date of sample collection.
  • The blood tube should be labeled with “infectious” if the sample is known to contain infectious material, for example, Hepatitis B-, Hepatitis C- or HI-virus.
  • If the patient has received an allogenic hematopoietic stem cell transplant, blood is not accepted.
  • Hemolyzed or clotted blood samples will not be accepted.
  • The blood sample should be sent as soon as possible after it has been collected. The sample can be sent at room temperature. We recommend using transport tubes in accordance with IATA regulations 650. For more information, please see FAQ > Shipping.
  • If it is necessary to store the sample prior to shipping, it should be refrigerated immediately. If the sample will be stored for longer than 3 days, the sample should be kept frozen until shipped.

Extracted DNA

  • DNA samples should be sent in TE buffer or equivalent, or in any standard elution buffer used for DNA isolation.
  • The sample tube should be labeled with the patient’s name, date of birth, DNA concentration and volume. Ideally, a 1.5 ml snap-cap microcentrifuge tube sealed with parafilm should be used.
  • DNA quality and quantity will be evaluated upon arrival at Blueprint Genetics. We will request a new sample sample if the DNA quality or quantity does not meet our standards for analysis.
  • DNA should be extracted or isolated in laboratory qualified with one or more of the following certifications / accreditations:
    – CLIA certification
    – CAP accreditation
    – accreditation equivalency as determined by CMS
    – accreditations and certifications from established international organizations and/or government agencies
  • The sample can be sent at room temperature. We recommend using transport tubes in accordance with IATA regulations 650. For more information, please see FAQ > Shipping.

Saliva

Saliva samples should be collected in the tube provided in the kit. Please follow the manufacturer’s collection instructions carefully (DNA Genotek > Collection Instructions). Instructions are provided in the kit and can be found on the manufacturer’s website in multiple languages. Samples collected improperly (e.g. sample is mainly mucus not saliva) will not be accepted.

The sample tube must be labeled with the patient’s name, date of birth and date of sample collection. Samples without proper labeling will not be accepted.

The sample can be stored and sent at room temperature. For more information, please see the FAQ > Shipping.

I am ordering more than one test on the same patient. Do I need to provide a separate sample for each test?

No, one sample is typically sufficient for multiple tests. If an additional sample is required, our client services team will contact you directly.

Which buffer should I use to extract the DNA?

TE buffer is often used. Other options are nuclease free water or elution buffer provided by standard DNA extraction kits.
 

My patient had a blood transfusion. What sample types are accepted?

If your patient has received any blood product containing white blood cells (leukocytes), wait 2 weeks from the time of transfusion before collecting a sample.

Transfusions of packed red blood cells, plasma or platelets are not expected to affect the analysis. Patients who have received these blood products can provide a sample at anytime.

My patient has hematological disease such as myelodysplastic syndrome or leukemia. What sample types are accepted?

Acquired somatic mutations present in many hematologic diseases may complicate the interpretation of next generation sequencing (NGS) results. Therefore, DNA isolated from sources containing leukocytes (blood, saliva, oral rinse and buccal swabs) is not accepted. DNA extracted from cultured skin fibroblasts or another non-hematologically derived tissue is required.

My patient had an allogenic hematopoietic stem cell transplant. What sample types are accepted?

DNA extracted from cultured skin fibroblasts is the only post-transplantation source of DNA that is accepted if the patient had an allogeneic hematopoietic stem cell transplant.

Submitting a DNA sample from other sources in this situation increases the risk of contamination by donor DNA and false negative results. If available, a DNA sample taken prior to transplantation can be submitted.

You must indicate on the test requisition or in Nucleus that your patient has undergone an allogenic hematopoietic stem cell transplant in addition to the source of the extracted DNA.

When should I send family member samples for the Whole Exome Family test?

For our Whole Exome Family test, we require that samples on participating family members be sent at the same time as the index case’s sample.

If you are ordering our Expand to Exome service (expanding from a single gene or panel to Whole Exome Family test) and we already have a sample on the index patient, samples on participating family members should be sent at the time of the order. The Expand to Exome order will only be processed once we have received samples from all family members that are to be included in the analysis.

Shipping

Where do I send the sample?

Shipping from:

US and South America

Please send to:

Blueprint Genetics
2505 3rd Ave
Suite 204
Seattle
WA 98121
United States

Europe, Middle East, Canada, Asia and Australia

Please send to:

Blueprint Genetics
Keilaranta 16 A-B,
02150 Espoo
Finland

How do I send the sample?

Sending samples by using the Specimen kit

Follow the orders and use the packing materials provided in the kit.

Sending samples without the Specimen collection kit

How should samples be collected, labeled and stored before shipping?

Blood

  • Blood should be collected in an EDTA tube (lavender top) designated for blood samples.
  • The tube should be labeled with the patient’s name, date of birth and date of sample collection.
  • The blood tube should be labeled with “infectious” if the sample is known to contain infectious material, for example, Hepatitis B-, Hepatitis C- or HI-virus.
  • The blood sample should be sent as soon as possible after it has been collected. The sample can be sent at room temperature. We recommend using transport tubes in accordance with IATA regulations 650.
  • If it is necessary to store the sample prior to shipping, it should be refrigerated immediately. If the sample will be stored for longer than 3 days, the sample should be kept frozen until shipped.
  • If the patient has received an allogenic hematopoietic stem cell transplant, blood is not accepted. DNA extracted from a non-hematopoietic tissue is acceptable.
  • Hemolyzed or clotted blood samples will not be accepted.

Extracted DNA

  • DNA should be extracted or isolated in laboratory qualified with one or more of the following:
    – CLIA certification
    – CAP accreditation
    – accreditation equivalency as determined by CMS
    – accreditations and certifications from established international organizations and/or government agencies
  • The sample tube should be labeled with the patient’s name, date of birth, DNA concentration and volume. Ideally, a 1.5 ml snap-cap microcentrifuge tube sealed with parafilm should be used.
  • The sample can be sent at room temperature. We recommend using transport tubes in accordance with IATA regulations 650.
  • DNA samples should be sent in TE buffer or equivalent, or in any standard elution buffer used for DNA isolation.
  • DNA quality and quantity will be evaluated upon arrival at Blueprint Genetics. We will request a new sample if the DNA quality or quantity does not meet our standards for analysis.

Saliva

  • Saliva samples must be collected in the tube provided in our Saliva Sample Collection kit.
  • The sample tube must be labeled with the patient’s name, date of birth and date of sample collection.
  • Instructions are provided in the kit and can be found on the manufacturer’s website in multiple languages. Please follow the manufacturer’s collection instructions carefully (DNA Genotek > Collection Instructions).
  • The sample can be stored and sent at room temperature.
  • Samples collected improperly (e.g. sample is mainly mucus not saliva) or without proper labeling will not be accepted.

Does Blueprint Genetics pay for shipping?

  • Our Specimen Collection Kits contain all shipping materials in addition to prepaid return shipping paid by Blueprint Genetics.
  • If you prefer, you can use your own test tubes and shipment method.
  • If you are unsure about the sample collection and shipping, please don’t hesitate to contact our customer support at support@blueprintgenetics.com.

Can I send samples in ambient temperature?

  • Blood samples collected on a Friday evening or over a weekend should be kept in the refrigerator and shipped on the next business day for overnight delivery. Keeping the specimen refrigerated over the weekend will not compromise the quality of the specimen.
  • Blood, DNA and saliva samples can be sent in ambient temperature.
  • Samples that were previously frozen can also be shipped at ambient temperature.
  • Express shipping should be used for blood and DNA samples.

Can Blueprint Genetics return samples to customers?

By request, samples can be returned to customers after testing has been completed as long as the entire sample was not used in our analysis. Samples are only returned once our testing is complete.  The sample types that will be returned may be extracted DNA, blood, or saliva.

If a sample is returned to you, please note that we will require a new sample from the patient should you wish to pursue additional testing eg. with Expand to Exome or Re-analysis service.

Required:

  1. A completed Sample shipment form. Please contact our customer support (support(at)blueprintgenetics.com) for more information.
  2. A FedEx shipping account number

OR

  1. If you do not have a FedEx shipping account number, we will return the sample for a fee.

Please note that samples are not shipped until payment is received.

Blueprint Genetics stores samples for 1 year from the time of receipt of samples unless the patient has consented to long term storage. Please see storage options on our consent form here.

Whole Exome Sequencing

When should whole exome sequencing (WES) be considered?

WES is the analysis of the protein-coding regions of all ~20,000 genes of the human genome (known as the exome) using next generation sequencing technologies. While the exome constitutes only ~1% of the whole genome, ~85% of all established disease-causing variants are located within the exome.

The diagnostic yield of WES is higher than many traditional genetic diagnostic methods such as multi-gene panels. A diagnosis is made in 20-60% of cases with severe, early onset disorders having the highest diagnostic rates.

WES is most suitable for individuals with:

  • A complex, non-specific genetic disorder with multiple differential diagnoses
  • A genetically heterogeneous disorder where stepwise testing of genes significantly increases costs
  • A suspected genetic disorder where a specific genetic test is not available
  • Previous genetic testing that has not been diagnostic

What platform does Blueprint Genetics use?

High-quality exome capture is performed using an in-house designed WES platform and the Illumina NovaSeq sequencing system.

What is the coverage / read depth of Blueprint Genetics WES?

We have performed an extensive assay validation to determine the coverage, accuracy and precision of our WES data.

Highly uniform sequencing depth across all protein-coding genes:

  • On average, median sequencing depth of 174X
  • On average, ≥99.4% of the base pairs (bp) in target coding regions covered at ≥20X

Highly sensitive and specific detection of SNVs and indels

  • 99.7% sensitivity and >99.99 specificity for SNV detection within target coding regions
  • 97% sensitivity and >99.99% specificity for indel detection within target coding regions (up to 220 bp)

Best-in-class sensitivity for the detection of copy number variants (CNVs)

  • Most 1 exon deletions detected and >99% sensitivity to detect 5 exon del/dup
  • 100% sensitivity to detect known microdeletion and microduplication syndromes

Deep intronic disease causing variants included in every WES

  • Assessment of >1500 non-coding disease causing variants listed in ClinVar and HGMD are included in every WES

Assay performs with high precision

  • The within run precision (repeatability) is 99.7% for SNVs

Do you provide coverage information specific to my patient?

Yes. The median sequencing depth and ≥20x coverage are reported for each individual included in the WES analysis. In addition, we include a coverage plot detailing the target region coverage for each individual included in the WES analysis.

How do I know if my gene(s) of interest is well covered?

We do not report coverage for individual genes on the WES report. If there is a gene or a differential diagnosis that you suspect, please include this information with the referral. Our interpretation team will specifically examine your gene(s) of interest at the time of reporting.

Does Blueprint Genetics WES detect mtDNA variants?

There are >1,500 currently known nuclear encoded genes affecting mitochondrial function and 37 genes encoded by mitochondrial DNA.

According to Koenig (2008), adults are more likely to have well-defined mitochondrial syndrome and carry mutations in mtDNA while children are more likely to have non-specific symptoms and have mutations in the nuclear DNA. Lamont et al. (1998), suggested that mtDNA mutations account for <10% of all mitochondrial disorders in children.

Our WES products detect variants in nuclear encoded mitochondrial genes. At this time, mtDNA variants are not targeted in our WES.

How does Blueprint Genetics filter the variants?

WES generates thousands of variants. Our proprietary bioinformatics pipeline distinguishes disease-relevant variants from the many benign variants present in the exome. The pipeline determines the consequence of variants and performs filtering steps to remove common variants based on allele frequencies in population cohorts. We review the literature and various databases to determine the association between the identified variants and the genes’ association with relevant diseases.

To further aid the process of variant interpretation, observed variants are matched against a comprehensive set of databases of disease-related mutations, collected, and curated in-house, and accessed from the public domain or licensed from commercial sources.

The analysis of the WES data is individually tailored. During the analysis process, the clinical and family history of the patient, including symptoms, age of onset, prevalence, and inheritance patterns are taken into consideration. The precise filters used in the variant analysis are then selected based on this information.

What is Blueprint Genetics approach to reporting variants identified in the proband?

Blueprint Genetics analyzes WES data using a ‘genotype-first’ approach. In the genotype-first approach, the genetic data is primarily utilized to establish the diagnosis. This is in contrast to the ‘phenotype-first’ approach where WES data is filtered for genes that are known to be associated with the symptoms observed in the patient. The genotype-first approach allows for a diagnosis of an unexpected or atypical presentation of a disorder associated with previously established disease genes.

The WES data is first analyzed for variants in genes that are known to be associated with conditions showing overlap with that of the patient. If this is inconclusive, the data is then analyzed for variants that are not located within known clinically associated genes, but have properties that make them candidates for potentially disease–causing variants.

Variants are reported based on the clinical information provided. It is therefore extremely important to provide detailed clinical information with the patient sample to maximize the diagnostic yield of the genotype-first approach.

If, over time, other patients with similar phenotypes and variants in the same gene are identified, the variant may be reclassified as a likely cause of the disorder. In this circumstance, an updated report will be sent to the ordering clinician.

Does Blueprint Genetics report secondary findings?

As WES covers all protein-coding genes of the genome, it enables detection of variants that are not associated with the indication for performing WES but are of medical value for patient care. These findings are known as secondary findings.

Blueprint Genetics follows the ACMG Recommendations for Reporting Secondary Findings in Clinical Exome and Genome Sequencing, 2016 Update to seek and report clinically actionable variants in genes determined by ACMG. These guidelines are followed if the patient or caregiver has opted-in for analysis and reporting of secondary findings.

If parents or other family members are also participating in the WES analysis, they have the option to opt-in for analysis and reporting of secondary findings.

Secondary findings for additional family members are reported in a separate clinical statement than that of the index patient and is independent of the secondary findings reported in the index patient.

Does Blueprint Genetics report other findings not related to the patient’s phenotype?

We do not currently report variants other than those that are considered to be associated with the indication for performing WES or that are within the ACMG defined list of secondary findings genes.

We also do not report carrier status of variants in autosomal or X-linked recessive disease genes that are not linked with the indication for performing WES for the patient.

Lastly, pharmacogenetics variants are currently not reported.

Is anything not included in the report?

Family members participating in WES for the benefit of segregation analysis and variant interpretation in the proband may have a variant(s) in a gene(s) unrelated to the proband’s phenotype that is not reported.

If an individual (or their caregiver) participating in WES does not opt in to analysis and reporting of secondary findings, a disease-causing variant may be present and not reported.

Further, variants that are benign or likely benign are considered negative and therefore these variants are not generally reported.

Does Blueprint Genetics issue separate reports for family members?

If samples are received on the index patient and one or more family members, all variants and segregation analysis relating to the cause of the index patient’s phenotype are reported in the index patient’s report.

Secondary findings for family members participating in WES are reported in separate, individual reports if the family member chooses to receive this information.

Can I see a sample WES result?

To view a sample WES report, please click here.

How long will results take?

Results are available within 8-10 weeks from receipt of (all required) samples, consent forms, and billing requirements.

Can results be expedited?

While we do not offer a formal expedited WES service at this time, we will do our best to accommodate requests for expedited WES results if there is a clinical indication to do so. Please contact our Support team for additional information.

What if a family member wants testing for a variant identified with WES?

Family members can be tested for variants identified by WES as part of our Familial Variant Testing (FVT) service. For more information, please click here.

Does Blueprint Genetics offer prenatal WES?

At this time, we do not accept prenatal samples for WES when the index patient is a fetus and the pregnancy is on-going, however, we are able to accept fetal samples for WES from a deceased fetus.

Please note, only extracted fetal DNA is accepted at this time. In addition, Blueprint Genetics currently does not offer maternal cell contamination (MCC) studies. Therefore, ordering clinicians need to ensure that any prenatal sample sent to Blueprint Genetics has MCC studies done locally.

Blueprint Genetics will accept prenatal samples for panel testing or Family Member Testing (FMT) at our standard fee when requested.

Will Blueprint Genetics re-analyze WES data?

The WES Re-analysis service will be available in summer 2019. WES orders placed after November 27th, 2017 are eligible for this service. For additional information, please read more here or contact our Support team.

Is the WES raw data available?

Yes, we provide raw data for WES and panel orders. Read more about raw data here.

What are the limitations of WES?

  • At present, it is not possible to capture and sequence 100% of the exome. We cover, on average, >99.4% of base pairs with at least 20X depth within the target coding regions.
  • It is possible that a variant is identified in a gene not currently known to be associated with disease. Given the incomplete knowledge of the function of all the genes in the genome, this variant may not be recognized as a factor in a patient’s disease.
  • WES is not optimized to detect certain variants such as trinucleotide repeats and may not reliably detect variants in genes with pseudogenes or segmental duplication.
  • At this time, we are not targeting variants in mtDNA.
  • This test is not designed to detect complex inversions, gene conversions or balanced translocations.
  • This test is not designed to detect variants in regulatory or non-coding (intronic variants located deeper than 20 nucleotides from the exon-intron boundary) regions, however, we are specifically targeting >1500 non-coding disease causing variants listed in ClinVar and HGMD.
  • This test may not reliably detect low level mosaicism or stretches of mononucleotide repeats.
  • A negative result does not exclude a genetic condition.

How much does WES cost?

Please click here for information regarding pricing.

I would like to order WES. What do I need to send?

  • Sample from the index patient (see below for sample types accepted)
  • Completed requisition for the index patient
  • Completed consent form for the index patient
  • Detailed clinical information including consult notes, symptoms, and age(s) of onset pedigree, previous test results (genetic and others like ECG, MRI, etc). It is strongly preferred that these are provided in English.
  • Samples from additional family members, if applicable
  • Consent forms for additional family members, if applicable

If Whole Exome Family Plus is being ordered, please send parental/familial and index patient samples at the same time.

What sample types are accepted?

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Read more about our sample requirements here.

What are the different WES tests offered by Blueprint Genetics?

All WES orders from North and South America include copy number variant diagnostics (Plus analysis). Our flagship WES offering is the Whole Exome Family Plus test. Details include:

  • WES and deletion/duplication (copy number variant) analysis for the proband and the biological parents
  • Including parental samples provides the following benefits:
    • Improved variant filtering and analysis
    • Reduced rate of uncertain findings
    • Increased diagnostic rate
    • Reduced overall turn-around time

In addition, we also offer the following:

  • Whole Exome Plus – Proband only WES and deletion/duplication (copy number variants)

Our Whole Exome Family product include WES for the index patient and biological parents, however, other family members can be analyzed upon request.

Customization in reporting is available. Please contact our team for additional details.

How do I decide what test to order?

 

Test Test code Considerations
Whole Exome Plus WE0301
  • Both biological parents are NOT available
  • Analysis for deletions and duplications is desired
Whole Exome Family Plus WE0401
  • Both biological parents are available
  • Analysis for deletions and duplications is desired
  • The most comprehensive reporting and interpretation of variants is desired at the time the report is issued

Does WES detect copy number variants (CNVs)?

Yes, Blueprint Genetics includes assessment of deletions or duplications (CNVs) for all of our Whole Exome products. The detection limit for Del/Dup (CNV) analysis varies throughout the genome depending on exon size, sequencing coverage and sequence content. In our validation study, 92% of single exon deletions were detected.

Last modified: 02.13.2019