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Diagnosis made possible with
Whole Exome Sequencing

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Whole Exome Sequencing (WES) —
a comprehensive precision diagnostic test
for actionable insights.

Finding the reason for your patient’s medical condition can be life-changing.

Whole Exome Sequencing (WES) assesses the exome, the set of all protein coding sections within
the human genome. As most genetic conditions are caused by variants found within those exons,
WES provides a higher diagnostic yield compared to Chromosomal Microarray Analysis (CMA) and
targeted panel testing to allow for more clinically actionable insights.

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.
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Patient Case

Whole Exome Sequencing (WES)

Whole Exome Sequencing identifies two intronic variants to help explain a neurodevelopmental disorder case.

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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
  • Save an average of $12k – $15k per patient1
  • On average, avoid ~525 days of hospitalizations
  • 3 out of 4 families want answers and are in favor of diagnostic tests2

 

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

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

In the NICU/PICU

With written results as early as five days, consider Rapid Whole Exome Sequencing (rWES) for your patients when a genetic etiology is suspected.

Gene Coverage

  • All genes
  • Single nucleotide variants/indels in coding regions
  • Copy number variants (CNV) >3 exons & homozygous copy number changes of any size
  • Depth/Coverage: Average 100x genome-wide
  • 2x150bp Sequencing Length: Better mapping for complex genomic regions
  • Bioinformatic analysis is performed on human reference genome build GRCh37 (HG19) for WES

Methodology

  • Proprietary-developed bioinformatics pipeline
PROBAND WES
RAPID PROBAND WES
DUO WES
RAPID DUO WES
TRIO WES
RAPID TRIO WES
Test Code
1500
1729
1603
1723
1600
1722
Parental Report Included*
No
No
Yes
Yes
Yes
Yes
TAT (weeks)
3
5 days
3
5 days
3
5 days
Can Elect to Receive Incidental Finding
Yes
Yes
Yes
Yes
Yes
Yes
Raw Data Available
Yes
Yes
Yes
Yes
Yes
Yes

*Parental Report is only included for certain test codes and if the parent(s) provide a sample. For Duo Whole Exome Sequencing, only one parent is required to submit a sample.

Baylor Genetics is committed to finding answers for you and your patients, which is why we offer companion testing for complementary insights.

To assist with providing answers, our WES includes the following features:

  • RNA sequencing (RNAseq), available as a reflex test for WES and Rapid WES (rWES), can help reclassify qualifying variants
  • WES Reanalysis (Test Code 1900)
  • CMA (Test Code 8665)
    • Proband WES + CMA (Test Code 1530)
  • Global MAPS® (Test Code 4900 & 4901)
  • Comprehensive Mitochondrial DNA (mtDNA) Analysis (Test Code 2055)
    • Trio WES + mtDNA (Test Code 1532)
    • Trio rWES + mtDNA (Test Code 1533)
  • Additional Affected Sibling (Test Code 1602)

Positive Results
Positive or “abnormal” results mean there is a change in the genetic material related to the patient’s medical issues.

Negative Results
Negative results mean no relevant genetic change could be detected using WES. 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. 

Variants of Uncertain Significance
WES 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. 

ACMG Secondary Findings
The American College of Medical Genetics (ACMG) has published guidelines for the reporting of medically actionable or secondary findings (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) findings in these genes. These findings are available on an opt-in basis. 

Incidental Findings
Medically actionable variants are changes found in genes known to be associated with disease but not associated with your 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. These findings are available on an opt-in basis.  

Potential Clinically Significant Findings in Genes With No Known Disease Association (Trio Only)
Rare variants in candidate genes for which there is limited available evidence of disease association. Relevant rare homozygous, hemizygous, compound heterozygous, and/or de novo variants are reported. The variants reported within this category will be classified as of uncertain significance. Any relevant literature will be referenced when available. Further information would be required to understand if any human disease association exists. These findings are available on an opt-in basis.

RNA Sequencing

RNA Sequencing (RNAseq) is a reflex option to our WES offerings to help reclassify qualifying variants.

Sample Requirements

(if additional sample is required)

A red drop of blood   Blood in EDTA

TAT (days)

28¶

Report

Provided as an updated

(addendum) report

¶ The TAT for RNAseq is calculated from the release date of the WES report or from date of sample receipt if an additional sample is requested by the laboratory.

Prenatal WES Trio is used when prenatal imaging or other testing detects an anomaly that strongly suggests there is an underlying genetic etiology.

INDICATIONS FOR TESTING

  • Prenatal ultrasound with abnormal findings
  • Positive prenatal screening tests
  • Uninformative prior prenatal diagnostic testing

FETAL REPORT INCLUDES:

  • Pathogenic or likely pathogenic variants in disease genes related to the prenatal indications
  • Variants in disease genes unrelated to the prenatal indications, but likely to cause severe childhood-onset disorders

Test Code

1622

Accepted

Sample Types*

 A blue outline of a fetus inside a circle, with the umbilical cord trailing to the left

Amniotic

Fluid

 A red outline of a fetus inside a circle with a needle piercing the outer circle.

Chorionic Villus

Sampling (CVS)

 A vertical stack of three circles with a tan circle in the middle flanked by red circles on the top and bottom

Cultured

Cells

Consent

REQUIRED FOR ALL SAMPLE TYPES

Parents Needed

 A red drop of blood

Blood

OR

REQUIRED

 Illustration of the tip of a sterile swab

Buccal Swab

TAT (weeks)†

2
(not including tissue culture)

Can Elect to Receive

Incidental Finding

FETAL

PARENTAL

Raw Data Available

† Tissue culturing typically takes two weeks to complete. However, this may take longer depending on the quality and/or quantity of sample received by the laboratory.

BLUEPRINT CUSTOM PANEL

TOTAL BLUEPRINT PANEL

Test Code

1300

1390

Parental Report Included
No
No

TAT (weeks)

3

3

Can Elect to Receive Incidental Finding
Yes
Yes

Raw Data Available
Yes
Yes

ADULT SCREENING EXOME
Test Code
1605
Parental Report Included
No
TAT (weeks)
3
Can Elect to Receive Incidental Finding
Standard Reporting
Raw Data Available
Yes

Diagnosis made possible with WES

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Product Overview
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Requisitions
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Specimen Requirements
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Online Order
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Request Test Kit

How It Works:

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Order appropriate testing for your patient.

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The patient’s sample is collected.

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The patient’s sample is sent to Baylor Genetics.

StartingAt5Days

Written results are sent to the physician.

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Discuss the results with the patient.

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More questions? Please contact us by calling 1.800.411.4363.

Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits

Yuan, B., Schulze, K. V., Assia Batzir, N., Sinson, J., Dai, H., Zhu, W., Bocanegra, F., Fong, C. T., Holder, J., Nguyen, J., Schaaf, C. P., Yang, Y., Bi, W., Eng, C., Shaw, C., Lupski, J. R., & Liu, P. (2022). Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Medicine, 14(1), 113. PMID: 36180924.

Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis

Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. Chen, C. A., Lattier, J., Kumar, R. D., Meng, L., Liu, P., Miyake, C. Y., Worley, K. C., Bi, W., & Lalani, S. R. American Journal of Medical Genetics. 2022 Sep 6. https://doi.org/10.1002/ajmg.a.62967.

Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies

Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. Chen CA, Lattier J, Zhu W, Rosenfeld J, Wang L, Scott TM, Du H, Patel V, Dang A, Magoulas P, Streff H, Sebastian J, Svihovec S, Curry K, Delgado MR, Hanchard NA, Lalani S, Marom R, Madan-Khetarpal S, Saenz M, Dai H, Meng L, Xia F, Bi W, Liu P, Posey JE, Scott DA, Lupski JR, Eng CM, Xiao R, Yuan B.  Genet Med. 2021 Nov 16; S1098-3600(21)05245-X. PMID: 34906496

Contribution of uniparental disomy in a clinical trio exome cohort of 2,675 patients

Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. Wang L, Liu P, Bi W, Sim T, Wang X, Walkiewicz M, Leduc MS, Meng L, Xia F, Eng CM, Yang Y, Yuan B, Dai H. Mol Genet Genomic Med. 2021 Sep 29; e1792. PMID: 34587367.

CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels

CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. Genet Med. 2020 Jun 24. PMID: 32576985

Reanalysis of Clinical Exome Sequencing Data

Reanalysis of Clinical Exome Sequencing Data. Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, Dong J, Gijavanekar C, Benke PJ, Bernstein JA, Eble T, Eroglu Y, Erwin D, Escobar L, Gibson JB, Gripp K, Kleppe S, Koenig MK, Lewis AM, Natowicz M, Mancias P, Minor L, Scaglia F, Schaaf CP, Streff H, Vernon H, Uhles CL, Zackai EH, Wu N, Sutton VR, Beaudet AL, Muzny D, Gibbs RA, Posey JE, Lalani S, Shaw C, Eng CM, Lupski JR, Yang Y. N Engl J Med. 2019 Jun 20; 380(25):2478-2480. PMID: 31216405

Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected mendelian disorder

Normand, E. A., Braxton, A., Nassef, S., Ward, P. A., Vetrini, F., He, W., Patel, V., Qu, C., Westerfield, L. E., Stover, S., Dharmadhikari, A. V., Muzny, D. M., Gibbs, R. A., Dai, H., Meng, L., Wang, X., Xiao, R., Liu, P., Bi, W., Xia, F., … Yang, Y. (2018). Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Medicine, 10(1), 74. https://doi.org/10.1186/s13073-018-0582-x. PMID: 30266093. 

Use of exome sequencing for infants in intensive care units: Ascertainment of severe single-gene disorders and effect on medical management

Meng, L., Pammi, M., Saronwala, A., Magoulas, P., Ghazi, A. R., Vetrini, F., Zhang, J., He, W., Dharmadhikari, A. V., Qu, C., Ward, P., Braxton, A., Narayanan, S., Ge, X., Tokita, M. J., Santiago-Sim, T., Dai, H., Chiang, T., Smith, H., Azamian, M. S., … Lalani, S. R. (2017). Use of Exome Sequencing for Infants in Intensive Care Units: Ascertainment of Severe Single-Gene Disorders and Effect on Medical Management. JAMA Pediatrics, 171(12), e173438. https://doi.org/10.1001/jamapediatrics.2017.3438. PMID: 28973083.

Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders

Bostwick, B. L., McLean, S., Posey, J. E., Streff, H. E., Gripp, K. W., Blesson, A., Powell-Hamilton, N., Tusi, J., Stevenson, D. A., Farrelly, E., Hudgins, L., Yang, Y., Xia, F., Wang, X., Liu, P., Walkiewicz, M., McGuire, M., Grange, D. K., Andrews, M. V., Hummel, M., … Lalani, S. R. (2017) Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Genome Medicine 9:73. PMID: 28807008.

An Organismal CNV Mutator Phenotype Restricted to Early Human Development

An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. Cell. 2017. Feb 23;168(5):830-842.e7. PMID: 28235197

Prenatal Diagnostic Exome Sequencing: A Review

Westerfield L., Braxton A., Walkiewicz, M. Prenatal Diagnostic Exome Sequencing: A Review. Current Genetic Medicine Reports (2017) 5: 75. https://doi.org/10.1007/s40142-017-0120-y.

Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation

Posey, J. E., Harel, T., Liu, P., Rosenfeld, J. A., James, R. A., Coban Akdemir, Z. H., Walkiewicz, M., Bi, W., Xiao, R., Ding, Y., Xia, F., Beaudet, A. L., Muzny, D. M., Gibbs, R. A., Boerwinkle, E., Eng, C. M., Sutton, V. R., Shaw, C. A., Plon, S. E., Yang, Y., … Lupski, J. R. (2017) Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. New England Journal of Medicine, (1):21. PMID: 27959697

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

James RA, Campbell IM, Chen ES, Boone PM, Rao MA, Bainbridge MN, Lupski JR, Yang Y, Eng CM, Posey JE, Shaw CA. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Medicine. 2016 Feb 2;8(1):13. PMID: 26838676

Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene.

Bekheirnia MR, Bekheirnia N, Bainbridge MN, Gu S, Coban Akdemir ZH, Gambin T, Janzen NK, Jhangiani SN, Muzny DM, Michael M, Brewer ED, Elenberg E, Kale AS, Riley AA, Swartz SJ, Scott DA, Yang Y, Srivaths PR, Wenderfer SE, Bodurtha J, Applegate CD, Velinov M, Myers A, Borovik L, Craigen WJ, Hanchard NA, Rosenfeld JA, Lewis RA, Gonzales ET, Gibbs RA, Belmont JW, Roth DR, Eng C, Braun MC, Lupski JR, Lamb DJ. Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. 2016, Genet Med. epub. doi:10.1038/gim.2016.131

Molecular diagnostic experience of whole-exome sequencing in adult patients

Posey JE, Rosenfeld JA, James RA, Bainbridge M, Niu Z, Wang X, Dhar S, Wiszniewski W, Akdemir ZH, Gambin T, Xia F, Person RE, Walkiewicz M, Shaw CA, Sutton VR, Beaudet AL, Muzny D, Eng CM, Yang Y, Gibbs RA, Lupski JR, Boerwinkle E, Plon SE. Molecular diagnostic experience of whole-exome sequencing in adult patients. Genet Med. 2016 Jul;18(7):678. PMID: 26633545

Retinal diseases caused by mutations in genes not specifically associated with the clinical diagnosis

Wang X, Feng Y, Li J, Zhang W, et al. (2016) Retinal diseases caused by mutations in genes not specifically associated with the clinical diagnosis. PLoS ONE 11(10): e0165405. PMID: 27788217

Whole Exome Sequencing Identifies the First STRADA Point Mutation in a Patient with Polyhydramnios, Megalencephaly, and Symptomatic Epilepsy Syndrome (PMSE).

Bi W, Glass IA, Muzny DM, Gibbs RA, Eng CM, Yang Y, Sun A. (2016). Whole Exome Sequencing Identifies the First STRADA Point Mutation in a Patient with Polyhydramnios, Megalencephaly, and Symptomatic Epilepsy Syndrome (PMSE). Am J Med Genet A. 170(8):2181-2185. PMID: 27170158

Molecular findings among patients referred for clinical whole exome-sequencing

Yang, Y., Muzny, D. M., Xia, F., Niu, Z., Person, R., Ding, Y., Ward, P., Braxton, A., Wang, M., Buhay, C., Veeraraghavan, N., Hawes, A., Chiang, T., Leduc, M., Beuten, J., Zhang, J., He, W., Scull, J., Willis, A., Landsverk, M., … Eng, C. M. (2014). Molecular findings among patients referred for clinical whole-exome sequencing. JAMA, 312(18), 1870–1879. https://doi.org/10.1001/jama.2014.14601. PMID: 25326635.

Comprehensive analysis of Stargardt macular dystrophy patients reveals new genotype-phenotype correlations and unexpected diagnostic revisions

Zaneveld J, Siddiqui S, Li H, Wang X, et al. (2014) Comprehensive analysis of Stargardt macular dystrophy patients reveals new genotype-phenotype correlations and unexpected diagnostic revisions. Genetics in Medicine 174. PMID: 25474345

Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements

Wang F, Wang H, Tuan H, Nguyen D, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, et al. (2013) Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Human Genetics 133, 331-345. PMID: 24154662

Clinical whole exome sequencing for the diagnosis of Mendelian disorders

Yang Y, Muzny DM, Reid JG,  Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z,  Hardison M,  Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon, SE,  Lupski JR, Beaudet AL,  Gibbs RA, Eng CM. Clinical whole exome sequencing for the diagnosis of Mendelian disorders. N Engl J Med. 2013 Oct ;369(16): 1502. PMID: 24088041

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