One test, more answers with Whole Genome Sequencing

Whole Genome Sequencing is the most advanced testing solution for detecting known and potential disease-causing variants.

Whole Genome Sequencing (WGS) is the most comprehensive test available through Baylor Genetics. It analyzes up to 98% of the human genome, detecting known and potential disease-causing variants that may not be identified on more targeted genetic testing. Additionally, WGS covers both the protein-coding exons and clinically significant non-coding regions of the genome.

As the most comprehensive genetic test available, WGS captures virtually all disease-causing genetic variations including single-nucleotide variants, small insertion/deletions, copy number variants, and a comprehensive set of tandem repeat disorders. In addition, WGS also captures variants within the mitochondrial genome which further increases clinical utility.

END YOUR PATIENT’S DIAGNOSTIC ODYSSEY

Getting a diagnosis that explains your patient’s symptoms can be life changing. Results provide treatment options, inform medical management, and open additional research opportunities so you can focus on the best care for your patient.
EARLY DIAGNOSIS FOR PATIENT CARE
• 32% of affected individuals had changes in medical care1 [superscript 1]
• Save an average of $12k – $15k per patient1 [superscript 1]
• On average, avoid ~525 days of hospitalization1 [superscript 1]
• 3 out of 4 families want answers and are in favor of diagnostic tests2 [superscript 2]
SOURCES:
1. Am J Hum Genet.2021 Jul 1; 108(7): 1231–1238.
2. Child Neurology Foundation 2020 Assessment Survey Summary

BAYLOR GENETICS IS COMMITTED TO FINDING ANSWERS FOR YOU AND YOUR PATIENTS

To assist with providing answers, our WGS includes the following features:
• RNA sequencing (RNAseq), is available for WGS and Rapid WGS (rWGS). It is performed when a qualified variant has been reported and the ordering provider has opted in.* Any findings will be provided as an updated (addendum) report.

*A qualified variant means that it meets our prediction algorithm criteria (Splice AI) that RNAseq will provide additional functional information. RNAseq is not currently available as a standalone test.

Whole Genome Sequencing (WGS) is the most comprehensive test available through Baylor Genetics. It analyzes up to 98% of the human genome, detecting known and potential disease-causing variants that may not be identified on more targeted genetic testing. Additionally, WGS covers both the protein-coding exons and clinically significant non-coding regions of the genome.

As the most comprehensive genetic test available, WGS captures virtually all disease-causing genetic variations including single-nucleotide variants, small insertion/deletions, copy number variants, and a comprehensive set of tandem repeat disorders. In addition, WGS also captures variants within the mitochondrial genome which further increases clinical utility.

END YOUR PATIENT’S DIAGNOSTIC ODYSSEY

Getting a diagnosis that explains your patient’s symptoms can be life changing. Results provide treatment options, inform medical management, and open additional research opportunities so you can focus on the best care for your patient.
EARLY DIAGNOSIS FOR PATIENT CARE
• 32% of affected individuals had changes in medical care1 [superscript 1]
• Save an average of $12k – $15k per patient1 [superscript 1]
• On average, avoid ~525 days of hospitalization1 [superscript 1]
• 3 out of 4 families want answers and are in favor of diagnostic tests2 [superscript 2]

SOURCES:
1. Am J Hum Genet.2021 Jul 1; 108(7): 1231–1238.
2. Child Neurology Foundation 2020 Assessment Survey Summary

BAYLOR GENETICS IS COMMITTED TO FINDING ANSWERS FOR YOU AND YOUR PATIENTS

To assist with providing answers, our WGS includes the following features:
• RNA sequencing (RNAseq), is available for WGS and Rapid WGS (rWGS). It is performed when a qualified variant has been reported and the ordering provider has opted in.* Any findings will be provided as an updated (addendum) report.

*A qualified variant means that it meets our prediction algorithm criteria (Splice AI) that RNAseq will provide additional functional information. RNAseq is not currently available as a standalone test.

Rapid Trio WGS

Rapid Duo WGS

Rapid Proband WGS

Test Code

1822

1823

1829

Consent

REQUIRED

REQUIRED

REQUIRED

Parents Needed

REQUIRED

REQUIRED

OPTIONAL

Parental Report Included

NOT INCLUDED

TAT (days)

5

5

5

Can Elect to Receive Incidental Finding(s)

Raw Data Available

Indications for Testing

MULTIPLE CONGENITAL ANOMALIES

NEURODEVELOPMENTAL DISORDERS

INTELLECTUAL DISABILITY AND/OR

DEVELOPMENTAL DELAY

FAILURE TO THRIVE

DYSMORPHIC FEATURES

EPILEPSY SYNDROMES

EXTENSIVE DIFFERENTIAL DIAGNOSIS

PREVIOUS GENETIC TESTING UNINFORMATIVE

Trio WGS

Duo WGS

Proband WGS

Test Code

1800

1803

1810

Consent

REQUIRED

REQUIRED

REQUIRED

Parents Needed

REQUIRED

REQUIRED

OPTIONAL

Parental Report Included

TAT (weeks)

3

3

3

Can Elect to Receive Incidental Finding(s)

Raw Data Available

Indications for Testing

MULTIPLE CONGENITAL ANOMALIES

NEURODEVELOPMENTAL DISORDERS

INTELLECTUAL DISABILITY AND/OR

DEVELOPMENTAL DELAY

FAILURE TO THRIVE

DYSMORPHIC FEATURES

EPILEPSY SYNDROMES

EXTENSIVE DIFFERENTIAL DIAGNOSIS

PREVIOUS GENETIC TESTING UNINFORMATIVE

RNA Sequencing

RNA sequencing (RNAseq), is available for WGS and Rapid WGS (rWGS). It is performed when a qualified variant has been reported and the ordering provider has opted in.* Any findings will be provided as an updated (addendum) report.

*A qualified variant means that it meets our prediction algorithm criteria (Splice AI) that RNAseq will provide additional functional information. RNAseq is not currently available as a standalone test.
†The TAT for RNAseq is calculated from the release date of the WGS report or from date of sample receipt if an additional sample is requested by the laboratory.

Sample Requirements

(if additional sample is required)

  Blood in EDTA

TAT (days)

28†

Report

Provided as an updated

(addendum) report

Positive Results

Positive or “abnormal” results mean there is a genetic change related to the patient’s medical issues. Positive results can include the following types of genetic changes:

Related to the Patient’s Indications

  • Single nucleotide variants/indels (SNV)
  • Short Tandem Repeats (STR) for 27 genes 
  • Mitochondrial Genome variants 
  • Copy number variants (CNV)
    • Structural variants (SV)
    • Absence of Heterozygosity (AOH)
    • Uniparental Disomy (UPD)

Negative Results

Negative results mean no relevant genetic change could be detected using WGS. Genetic testing, while highly accurate, might not detect a change present in the genes tested. This can be due to limitations of the information available about the genes being tested, or limitations of the testing technology. 

Results of Unclear Significance

WGS can detect change(s) in DNA that do not have a clear meaning known as a variant of uncertain significance (VUS). Every person has changes in their DNA; not all of these changes cause medical issues. Studies of family members may help resolve the uncertainty. As our understanding of genetics increases, it may also be possible to determine the significance of these variants. 

Additional Reporting Options: Available on an Opt-in Basis

ACMG Secondary Findings

The American College of Medical Genetics (ACMG) has published a series of guidelines for the reporting of these types of medically actionable or secondary findings (including PMID: 34012068). These guidelines include a list of genes, which are updated occasionally, that are considered medically actionable and indicate laboratories should report pathogenic (disease-causing) and likely pathogenic findings in these genes. In accordance with an update to this policy statement (PMID: 25356965), you may choose to opt in to receive this information.

Potential clinically significant findings in genes with no known disease association (WGS Trio only)

Rare variants including homozygous, hemizygous, compound heterozygous, and/or de novo variants in candidate genes for which there is limited available evidence of disease association are reported as variants of uncertain significance. Relevant literature is referenced if available. These are considered research findings, and further information would be required to determine the relationship to the patient’s condition.

Incidental Findings

Medically actionable variants are changes found in genes known to be associated with disease but not associated with the current symptoms or clinical presentation. These variants are reported as they may cause severe, early-onset disease or may have implications for treatment and prognosis.

Rapid Trio WGS

Rapid Duo WGS

Rapid Proband WGS

Test Code

1822

1823

1829

Consent

REQUIRED

REQUIRED

REQUIRED

Parents Needed

REQUIRED

REQUIRED

OPTIONAL

Parental Report Included

NOT INCLUDED

TAT (days)

5

5

5

Can Elect to Receive Incidental Finding(s)

Raw Data Available

Indications for Testing

MULTIPLE CONGENITAL ANOMALIES

NEURODEVELOPMENTAL DISORDERS

INTELLECTUAL DISABILITY AND/OR

DEVELOPMENTAL DELAY

FAILURE TO THRIVE

DYSMORPHIC FEATURES

EPILEPSY SYNDROMES

EXTENSIVE DIFFERENTIAL DIAGNOSIS

PREVIOUS GENETIC TESTING UNINFORMATIVE

Trio WGS

Duo WGS

Proband WGS

Test Code

1800

1803

1810

Consent

REQUIRED

REQUIRED

REQUIRED

Parents Needed

REQUIRED

REQUIRED

OPTIONAL

Parental Report Included

TAT (weeks)

3

3

3

Can Elect to Receive Incidental Finding(s)

Raw Data Available

Indications for Testing

MULTIPLE CONGENITAL ANOMALIES

NEURODEVELOPMENTAL DISORDERS

INTELLECTUAL DISABILITY AND/OR

DEVELOPMENTAL DELAY

FAILURE TO THRIVE

DYSMORPHIC FEATURES

EPILEPSY SYNDROMES

EXTENSIVE DIFFERENTIAL DIAGNOSIS

PREVIOUS GENETIC TESTING UNINFORMATIVE

RNA sequencing (RNAseq), is available for WGS and Rapid WGS (rWGS). It is performed when a qualified variant has been reported and the ordering provider has opted in.* Any findings will be provided as an updated (addendum) report.

*A qualified variant means that it meets our prediction algorithm criteria (Splice AI) that RNAseq will provide additional functional information. RNAseq is not currently available as a standalone test.
†The TAT for RNAseq is calculated from the release date of the WGS report or from date of sample receipt if an additional sample is requested by the laboratory.

Sample Requirements

(if additional sample is required)

  Blood in EDTA

TAT (days)

28†

Report

Provided as an updated

(addendum) report

Positive Results

Positive or “abnormal” results mean there is a genetic change related to the patient’s medical issues. Positive results can include the following types of genetic changes:

Related to the Patient’s Indications

  • Single nucleotide variants/indels (SNV)
  • Short Tandem Repeats (STR) for 27 genes 
  • Mitochondrial Genome variants 
  • Copy number variants (CNV)
    • Structural variants (SV)
    • Absence of Heterozygosity (AOH)
    • Uniparental Disomy (UPD)

Negative Results

Negative results mean no relevant genetic change could be detected using WGS. Genetic testing, while highly accurate, might not detect a change present in the genes tested. This can be due to limitations of the information available about the genes being tested, or limitations of the testing technology. 

Results of Unclear Significance

WGS can detect change(s) in DNA that do not have a clear meaning known as a variant of uncertain significance (VUS). Every person has changes in their DNA; not all of these changes cause medical issues. Studies of family members may help resolve the uncertainty. As our understanding of genetics increases, it may also be possible to determine the significance of these variants. 

Additional Reporting Options: Available on an Opt-in Basis

ACMG Secondary Findings

The American College of Medical Genetics (ACMG) has published a series of guidelines for the reporting of these types of medically actionable or secondary findings (including PMID: 34012068). These guidelines include a list of genes, which are updated occasionally, that are considered medically actionable and indicate laboratories should report pathogenic (disease-causing) and likely pathogenic findings in these genes. In accordance with an update to this policy statement (PMID: 25356965), you may choose to opt in to receive this information.

Potential clinically significant findings in genes with no known disease association (WGS Trio only)

Rare variants including homozygous, hemizygous, compound heterozygous, and/or de novo variants in candidate genes for which there is limited available evidence of disease association are reported as variants of uncertain significance. Relevant literature is referenced if available. These are considered research findings, and further information would be required to determine the relationship to the patient’s condition.

Incidental Findings

Medically actionable variants are changes found in genes known to be associated with disease but not associated with the current symptoms or clinical presentation. These variants are reported as they may cause severe, early-onset disease or may have implications for treatment and prognosis.

All it takes is one test to get more answers

Specimen Requirements

Extracted DNA

SAMPLE TYPE REQUIREMENTS SHIPPING CONDITIONS

Blood

Draw blood in an EDTA (purple-top) tube(s) and send 3-5 cc for adults/children or 3 cc for infants < 2 years.

Attach clinical notes and concurrent laboratory reports.

Ship at room or refrigerated temperature in an insulated container by overnight courier. Do not heat or freeze. Specimen should arrive in the laboratory within 24-48 hours of collection.

Buccal Swab

Collect with ORAcollect•Dx (OCD-100) self-collection kit (provided by Baylor Genetics with instructions).

We highly recommend the sample be collected by a healthcare professional.

Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. Sample must arrive within 72 hrs.

Cultured Skin Fibroblasts

Send 2 T25 flasks at 80-100% confluence.

Ship at ambient temperature (18-25°C/64-77°F) in an insulated container by overnight courier. Cell line specimens should arrive in the laboratory within 48 hrs of collection. Do not heat or freeze.

Extracted DNA

Send at least 20 ug with a minimum average concentration of 50 ng/μL.

Attach clinical notes and/or concurrent laboratory reports as applicable. Extracted DNA will only be accepted if the isolation of nucleic acids for clinical testing occurs in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS.

Ship at room temperature in an insulated container by overnight courier. May also be shipped frozen on a minimum of 10 lbs of dry ice in an insulated container by overnight courier.

Saliva

 

Collect with Oragene DNA Self-Collection Kit.

Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze.

How It Works:

Order appropriate testing for your patient.

The patient’s sample is collected.

The patient’s sample is sent to Baylor Genetics.

StartingAt5Days

Results are sent to the physician.

Discuss the results with the patient.

More questions? Please contact us by calling 1.800.411.4363.

Christine Eng
Chief Medical Officer, Chief Quality Officer
MicrosoftTeams-image
Associate Clinical Director, NGS/Molecular 
Performance of Whole Genome Sequencing

A summary of the analytical validation to determine performance of a Whole Genome Sequencing test and implications of testing in the NICU environment. Read the full white paper by clicking here.

Best practices for the interpretation and reporting of clinical whole genome sequencing

Austin-Tse, C. A., Jobanputra, V., Perry, D. L., Bick, D., Taft, R. J., Venner, E., Gibbs, R. A., Young, T., Barnett, S., Belmont, J. W., Boczek, N., Chowdhury, S., Ellsworth, K. A., Guha, S., Kulkarni, S., Marcou, C., Meng, L., Murdock, D. R., Rehman, A. U., Spiteri, E., … Medical Genome Initiative* (2022). Best practices for the interpretation and reporting of clinical whole genome sequencingNPJ genomic medicine7(1), 27. PMID: 35395838.

Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease

Borja, N., Bivona, S., Peart, L. S., Johnson, B., Gonzalez, J., Barbouth, D., Moore, H., Guo, S., Undiagnosed Disease Network, Bademci, G., & Tekin, M. (2022). Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease. Molecular Genetics & Genomic Medicine10(4), e1892. https://doi.org/10.1002/mgg3.1892. PMID: 35247231.

Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory

Meng, L., Attali, R., Talmy, T., Regev, Y., Mizrahi, N., Smirin-Yosef, P., Vossaert, L., Taborda, C., Santana, M., Machol, I., Xiao, R., Dai, H., Eng, C., Xia, F., & Tzur, S. (2023). Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratoryGenetics in Medicine: Official Journal of the American College of Medical Genetics25(6), 100830. Advance online publication. PMID: 36939041.