What is an insurance Benefit Investigation (BI)?
Blueprint Genetics will contact the patient’s insurance provider and verify 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. BPG has billing specialists that 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 and will assist patients when an 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, 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, 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 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.
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.
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.
- 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 firstname.lastname@example.org
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 email@example.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.
What is Connecting Clinicians?
Connecting Clinicians is a service we have built that connects clinicians in Nucleus based on matching variants found in patient cases. With this service we are providing you with the possibility to connect with other physicians and share knowledge as well as phenotypes in cases of rare variants that have been classified as VUS or Likely Pathogenic.
What information is shared with the connection?
Connections are created only between users that have agreed to be part of the Connecting Clinicians program. Nucleus connects users based on rare variants that have been classified as VUS or Likely Pathogenic. Only the variant information with your contact information is shared to the connection. Nucleus doesn’t share any information regarding the patient.
As a default the connection sees your name, email address and the hospital/institution your Nucleus account is connected to. You can also add your phone number to your profile (from Profile settings) if you wish. If you have a phone number added to your profile, the connection sees that as well. You get each other’s contact details and can choose to contact each other and discuss the matched cases. Nucleus does not host the conversations, but merely provides the contact information needed for you to do this on your own.
How are the connections made?
At the moment, Connecting Clinicians is matching variants that are graded as VUS or Likely Pathogenic by Blueprint Genetics and have a perfect match in our database (meaning that the exact same genetic change was reported for someone else). We are planning to expand the service to create connections also for close-by matches.
Connections are created only between users that have agreed to be part of Connecting Clinicians. When our system founds a new match and creates a connection, it first appears as a pending connection for both of the connecting users. Only after both of the users have agreed to connect for that certain variant, the connection is confirmed and the connecting users can see each other’s contact information. If you feel like you do not want to share information for a particular case/variant, you can choose to reject the connection and it will be removed from the pending connections.
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.
What payment methods can I use?
You can use either bank transfer, Credit Card or PayPal.
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.
Who can order genetic tests from Blueprint Genetics?
Our genetic tests can be ordered only by qualified healthcare professionals.
What should I consider before ordering a test?
Before ordering a test, a healthcare professional should explain to the patient to be tested:
- What is the purpose of the test
- What the test results mean (including positive, negative and possible uncertain results)
- That the results might reveal information about patient’s family members’ health.
If you are not sure whether Blueprint Genetics has a test for your patient or what would be the optimal test for your patient, please first review our diagnostic panels in the website top bar menu under ‘tests’ where each panel is shortly described including a list of covered genes and regions within each gene, analytic performance and potential limitations. If the phenotype is partly unclear and you are still unsure which test to pick up, send us a consultation preferably by email or phone (see contact section). Please do not insert patient’s name or social security number (or equivalent) in emails. Customer will be advised by email within 24 hours from the request.
Prenatal testing at Blueprint Genetics
Contamination of a prenatal specimen (chorionic villus biopsy, amniotic fluid sample or fetal cord blood sample) by maternal cells is a potential source of error in diagnostic prenatal genetic testing.
At this time, Blueprint Genetics does not perform maternal cell contamination (MCC) testing. However, maternal cell contamination results are critical in interpreting the prenatal genetic testing results correctly.
Thus, until we are performing maternal cell contamination studies in our laboratory, we only offer prenatal testing for cases where the maternal cell contamination studies (MCC) have been done or will be done by a local genetic laboratory. The referring clinician is responsible for the final interpretation of the prenatal test results combining the results of prenatal genetic testing (panel or targeted mutation testing with Sanger sequencing) with the results of the maternal cell contamination test performed in another laboratory.
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 firstname.lastname@example.org.
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:
- VEP (https://www.ensembl.org/info/docs/tools/vep/index.html)
- ANNOVAR (http://annovar.openbioinformatics.org/en/latest/)
- SnpEff (http://snpeff.sourceforge.net)
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.
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.
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 is usually performed as a tool to help the physician make a diagnosis and thus improving risk assessment, prevention and treatment strategies for the disease. Results of genetic testing are sometimes complicated and difficult to understand, so that special knowledge is essential in order to explain the consequences of the test outcome. Results of genetic testing may lead to immediate change of life style, treatment or need of additional testing, which all need to be explained to the patient by his/her physician to make sure that the final decisions are done by an expert who knows all aspects of the patient’s situation.
The test results have been lost or were never received. Can you resend them?
Results are available for the ordering physician at our online reporting system, where copies can be taken. We cannot send results to the patient or other physicians who were not registered in our system when preliminary order was done without a signed release from the ordering physician authorizing us to do so. When asking a new report, please contact our customer service.
I received an email saying that the test results are ready. How can I see them?
You can access the results by our ordering and reporting system, Nucleus. We send login details by email to all of our unregistered customers after they have placed an order. If you can’t find/remember your password, you can order a new one using the “Forgot password?” link. If you asked for the results to be sent by regular mail, they are sent to you via priority mail the same or the following business day after the notification email. If you asked for the results to be faxed to you, they are faxed the same or the following business day after the notification email.
How do I know that my test results are ready?
Our tests take normally 3-4 weeks to complete. Your physician can track the laboratory process from our online system. As soon as a test is completed, your physician will be notified by email that your test results are available at our online reporting system.
What kind of patient samples do you accept?
Whole Exome Sequencing, Panels and Family Member Tests
- EDTA blood, min. 1 ml
- Purified DNA, min. 3μg* in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit)
When Whole Exome Family or Whole Exome Family Plus products are ordered, we require that samples from first-degree relatives of the index patient are sent already at the start of testing.
We accept extracted or isolated DNA only from qualified laboratories. Please attest that extracted nucleic acid submitted for testing has been isolated or extracted in an appropriately qualified laboratory. The qualified laboratories have either 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 fluorescence based DNA quantification method such as Qubit, 3 µg of DNA would be enough, but when the measurement is done using spectrophotometric methods a two times higher amount is needed due to likely overestimation of true amount. If our DNA quality and quantity control show that customer has provided DNA less than needed, it will delay testing due to need for additional sample material before analysis can be initiated.
We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.
Blueprint Genetics accepts DNA extracted from liver tissue only for Family member tests for variants found in Sequence analysis. This is due to the fact that many liver cells are polyploid.
Contact customer support if you are wishing to send any other material. It is mandatory that the customer notifies Blueprint Genetics if the patient has received bone marrow transplant. This is due to the risk of misinterpretation when analyzing blood or saliva samples as starting material for the analysis.
How should samples be collected, labeled and stored before shipping?
Blood sample should be collected to an EDTA tube designated for blood samples. The tube should be labeled with patient name, date of birth and date of sample collection. The blood tube should be labeled with “infectious” if the sample is known to contain HB-, HC- or HI-virus. Ideal is to send the sterile blood sample as soon as possible after sample collection. It can be sent in ambient temperature. Overnight shipment is recommended. In hot weather a cool pack should be enclosed. If storing of the sample is the only option, the blood sample can be refrigerated for a couple of days before shipment. For longer storage the sample should be frozen. The yield and quality of isolated DNA determines whether the sample can be analyzed. Blood specimens will be rejected if hemolyzed or clotted. Blood is accepted for all tests except if the patient has ever received a heterologous bone marrow transplant. We recommend using transport tubes in accordance with IATA regulations 650.
DNA samples should be sent in TE buffer or equivalent or any standard elution buffer used in DNA isolation. Sample tube should be labeled with patient name, date of birth, DNA concentration and volume. The sample can be sent in ambient temperature. If the sample needs to be stored before shipment, it can be refrigerated for a couple of days. For longer storage the sample should be frozen. The quality and quantity of DNA will be tested at arrival at Blueprint Genetics and the customer will be asked to send a new sample if the DNA quality or quantity is not sufficient for the analysis. We recommend using transport tubes in accordance with IATA regulations 650.
Sample tube should be labeled with patient name, date of birth and date of sample collection. Collect the sample according to the manufacturer’s instructions to the tube provided in the kit. Samples not collected properly (e.g. sample is mainly mucus not saliva) will be rejected. The sample can be stored and sent in ambient temperature.
If more than one test is being ordered from the same patient, is it better to provide a new tube of blood for each test?
There is usually no need for another sample. Blueprint Genetics obtains enough DNA from one sample to complete a number of tests. In case we run out of sample material, you are contacted by our customer support.
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.
Where do I send the sample?
US and South America
1268 Missouri Street
San Francisco, CA 94107
Biomedicum Helsinki 1,
1268 Missouri Street
San Francisco, CA 94107
Europe, Middle East, Asia and Australia
Biomedicum Helsinki 1,
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 kit
An express courier service should be used for sending blood samples from outside the Nordic countries. Blood samples can be sent in ambient temperature if overnight shipping is used. Blood samples fall under Biological substance category B (UN3373) and should be packaged and sent according to IATA 650 guidelines. The primary receptacle (=tube) needs to be leak proof and should be placed into a leak proof secondary package (e.g. sealed plastic bag or falcon tube) with some absorbent material. The secondary package should then be placed into a rigid outer package. The outer package needs to include the text “Biological Substance, Category B” next to a diamond-shaped UN3373 label.
DNA samples can be sent either via an express courier service or regular mail depending on your country’s postal service and their regulations. They can be sent in ambient temperature if express shipping is used. DNA samples are considered noninfectious and can be sent as exempt human specimens. They should however be packaged in a triple package. The primary receptacle (=tube) needs to be leak proof and should be placed into a leak proof secondary package (e.g. sealed plastic bag or falcon tube) with some absorbent material. The secondary package should then be placed into a sturdy outer package. The outer package needs to include the text “Exempt human specimen”.
Saliva samples can be sent either via an express courier service or regular mail depending on your country’s postal service and their regulations. They can be sent in ambient temperature. Saliva samples are considered noninfectious and can be sent as exempt human specimens. They should however be packaged in a triple package. The saliva tube should be placed into a leak proof secondary package (e.g. sealed plastic bag or falcon tube) with some absorbent material. The secondary package should then be placed into a sturdy outer package. The outer package needs to include the text “Exempt human specimen”.
Does Blueprint Genetics pay for shipping?
When using our Specimen Kit, the shipping has been prepaid by Blueprint Genetics. For sending samples without the specimen kit, contact our customer support (support(at)blueprintgenetics.com).
Can I send samples in ambient temperature?
Blood, DNA and saliva samples can be sent in ambient temperature. Express shipping should be used for blood and DNA samples. 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.
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.
- A completed Sample shipment form. Please contact our customer support (support(at)blueprintgenetics.com) for more information.
- A FedEx shipping account number
- 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.
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
Non-coding disease causing variants included in every WES
- Assessment of >1200 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 coverage, mean coverage, and percent bases covered at ≥10X, ≥15X and ≥20 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?
Our WES products detect variants in nuclear encoded mitochondrial genes, however, 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. Pathogenic and likely pathogenic variants are confirmed by Sanger sequencing.
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.
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.
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.
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 Family Member Testing (FMT) 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?
Is the WES raw data available?
Yes, after analysis of the WES data and delivery of the final report, Blueprint Genetics will provide the WES raw sequence data if requested. Special software, not provided by Blueprint Genetics but publically available, is required to view, analyze, and interpret the data.
Please note that the data is released to be used on a research basis only, not for clinical purposes. Raw WES data may include secondary and incidental findings and variants that may be potential sequencing artifacts.
To request the raw WES data, please request and complete a Whole Exome Sequencing Raw Data Consent Form.
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 >1200 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?
Blueprint Genetics accepts the following samples for WES:
- EDTA blood (minimum 1 ml)
- Extracted DNA (minimum 3μg) in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit and Oragene DNA OGD-500 kit [US ONLY])
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?
|Whole Exome Plus||WE0301||
|Whole Exome Family Plus||WE0401||
Does WES detect copy number variants (CNVs)?
Yes, Blueprint Genetics includes assessment of deletions or duplications (CNVs) for all of our Whole Exome Plus products in North America and South America.