Diagnosis made possible with Whole Exome Sequencing

When a patient’s medical history and physical exam suggests an underlying genetic cause, we recommend Whole Exome Sequencing through Baylor Genetics.

Whole exome sequencing (WES) is comprehensive genetic testing which assesses the exome, the set of all exons (protein-coding sections within genes) within the human genome. Most genetic conditions are caused by variants found within these exons.

Older testing technologies only look at one or a few genes at a time, which is time-consuming and leads to several rounds of testing to reach a diagnosis. Using next-generation sequencing, WES accelerates the testing process by simultaneously analyzing thousands of genes at the same time.

Finding the reason for your patient’s medical condition 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.

When a patient’s medical history and physical exam strongly suggests an underlying genetic cause, we recommend Whole Exome Sequencing.

Whole exome sequencing (WES) is available to patients who are searching for a unifying diagnosis for multiple medical issues. Unlike older technology where only one gene could be tested at a time, Baylor Genetics uses state-of-the-art technology to study a person’s exome. The exome refers to all our exons, which are the important protein-coding sections of DNA that are contained in our genes. The majority of DNA changes that may cause a genetic disorder are found in exons.

Scientists know what the sentences should say. Sequencing is a technology that looks at each letter in every sentence of DNA in the exome allowing scientists to compare the DNA of a person who has medical issues to the DNA from a person without medical issues. WES simultaneously looks at thousands of portions of genetic material at the same time. However, this technology cannot see all genetic changes that may lead to genetic conditions, which is why additional testing may be recommended. Finding an answer to your patient’s medical condition through whole exome sequencing can be life changing. Results can open options to treatment and additional research opportunities through Baylor College of Medicine.

Baylor Genetics Exome Diagnosis Rates

The exome diagnosis rate at Baylor Genetics is ~30% for proband or trio exome, and ~40% for prenatal trio and rapid trio. Ordering the exome test with a shorter turn-around time can impact health outcomes in a significant way, especially for younger patients. 

Indications for Testing:

MULTIPLE CONGENITAL ANOMALIES

AUTISM SPECTRUM DISORDERS

NEURODEVELOPMENTAL DISORDERS

DEVELOPMENTAL DELAY

INTELLECTUAL DISABILITY

PREVIOUS GENETIC TESTING WAS UNINFORMATIVE

FAILURE TO THRIVE

DYSMORPHIC FEATURES

EPILEPSY SYNDROMES

PATIENTS WITH AN EXTENSIVE

DIFFERENTIAL DIAGNOSIS

Baylor Genetics Exome Diagnosis Rates

The exome diagnosis rate at Baylor Genetics is approximately 30% for proband or trio exome, and approximately 40% for prenatal trio and critical trio exome. Ordering the exome test with a shorter turn-around time can impact health outcomes in a significant way, especially for younger patients.

Indications for Testing

EXHAUSTED GENETIC TESTING OPTIONS

PATIENTS WITH A LONG LIST OF DIFFERENTIAL DIAGNOSES

ATYPICAL PRESENTATION OF DISEASE

PROBAND WES

RAPID PROBAND WES

DUO WES

RAPID DUO WES

TRIO
WES

RAPID TRIO WES

BLUEPRINT CUSTOM
PANEL

TOTAL BLUEPRINT PANEL

ADULT SCREENING
EXOME

Test Code

1500

1729

1603

1723

1600

1722

1300

1390

1605

Consent

REQUIRED

REQUIRED

REQUIRED

REQUIRED

REQUIRED

REQUIRED

REQUIRED

MD ONLY

REQUIRED

Parents Needed


RECOMMENDED

RECOMMENDED

REQUIRED

REQUIRED

REQUIRED

REQUIRED

RECOMMENDED

RECOMMENDED

RECOMMENDED

Parental Report
Included

TAT (weeks)

10

5 days

6

5 days

6

5 Days

6

8

10

Can Elect to
Receive 
Incidental Finding

Standard Reporting

Raw Data
Available

Consent Available in
Other Language

  • null
    Saliva
  • null
    Blood

Prenatal WES Trio is used when prenatal imaging detects an anomaly that strongly suggests there is an underlying genetic etiology. Prenatal WES Trio is often considered after fetal chromosomal microarray analysis or other prenatal testing has been non-diagnostic.

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

Consent

REQUIRED

Parents Needed


REQUIRED

Method of Parent Testing

EXOME

TAT (weeks)

2 (not including tissue culture)

Can Elect to Receive Incidental Finding FETAL


PARENTAL

Raw Data Available

Consent Available in Other Language

Rapid WES Testing
When a baby is critically ill, rapid results are necessary. Both biological parents must be available for this test.

Proband Only Testing
Proband WES is an option when biological parents are not available.  

Duo Testing
Duo WES is an option when one biological parent is available. 

Trio Testing
Trio WES has the highest diagnostic rate of all WES testing options and is available when both biological parents are available. 

BluePrint Custom Panel (1300) 
The BluePrint panel is a genetic test that enables ordering a customized panel of up to 1,000 genes based on a patient’s clinical symptoms.

Total BluePrint Panel (1390)
The Total BluePrint Panel will analyze all exonic regions of the 4,800 known Mendelian disease-causing genes simultaneously to identify the rare changes in an individual’s DNA that are contributing to your patient’s medical condition.

Adult Screening Exome Sequencing (1605)
The Adult Screening Exome Sequencing test is used when an individual’s medical history and physical exam findings are normal, but the person desires information about the potential future risk of developing a genetic disorder.

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. 

Results of Unclear 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. 

Potentially Clinical 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. 

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.  

Take the first step with WES

Specimen Requirements
SAMPLE TYPE REQUIREMENTS SHIPPING CONDITIONS

Blood

Draw blood in an EDTA (purple-top) tube(s). Send at least 5cc (children) or 10cc (adults).

Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. The sample must arrive within 7 days.

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.

Cultured Skin Fibroblast

Send 2 T25 flasks at 80-100% confluence.

Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. The sample must arrive within 7 days.

Purified DNA

Send at least 20ug of purified DNA (minimal concentration of 50ng/uL; A260/A280 of ~1.7).

Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. The sample must arrive within 7 days.

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.

Vice President, Clinical Genomics
AVP, Clinical Reporting
Genetic Counselor
Reanalysis of Clinical Exome Sequencing Data

Liu, P., Meng, L., Normand, E.A., Xia, F., Song, X., Ghazi, A., Rosenfeld, J., Magoulas, P.L., 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, P.J., Bernstein, J.A., Eble, T., Eroglu, Y., Erwin, D., Escobar, L., Gibson, J.B., Gripp, K., Kleppe, S., Koenig, M.K., Lewis, A.M., Natowicz, M., Mancias, P., Minor, L., Scaglia, F., Schaaf, C.P., Streff, H., Vernon, H., Uhles, C.L., Zackai, E.H., Wu, N., Sutton, V.R., Beaudet, A.L., Muzny, D., Gibbs, R.A., Posey, J.E., Lalani, S., Shaw, C., Eng, C.M., Lupski, J.R., and Yang, Y. (2019). Reanalysis of Clinical Exome Sequencing Data. N Engl J Med 380, 2478-2480. PMID: 31216405

Germline Mutations in ABL1 Cause an Autosomal Dominant Syndrome Characterized by Congenital Heart Defects and Skeletal Malformations

Wang X, Charng WL, Chen CA, Rosenfeld JA, Shamsi AMA, Gazali LA, McGuire M, Mew NA, Arnold G, Qu CJ, Ding Y, Muzny DM, Gibbs RA, Eng CM, Walkiewicz M, Xia F, Plon SE, Lupski JR, Schaaf CP, Yang Y. Germline Mutations in ABL1 Cause an Autosomal Dominant Syndrome Characterized by Congenital Heart Defects and Skeletal Malformations. Nat Genet. 2017 Apr;49(4):613. PMID: 28288113

Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features

Santiago-Sim T, Burrage LC, Ebstein F, Tokita MJ, Miller M, Bi W, Braxton AA, Rosenfeld JA, Shahrour M, Lehmann A, Cogné B, Küry S, Besnard T, Isidor B, Bézieau S, Hazart I, Nagakura H, Immken LL, Littlejohn RO, Roeder E; EuroEPINOMICS RES Consortium Autosomal Recessive working group, S. Hande Caglayan., Kara B, Hardies K, Weckhuysen S, May P, Lemke JR, Elpeleg O, Abu-Libdeh B, James KN, Silhavy JL, Issa MY, Zaki MS, Gleeson JG, Seavitt JR, Dickinson ME, Ljungberg MC, Wells S, Johnson SJ, Teboul L, Eng CM, Yang Y, Kloetzel PM, Heaney JD, Walkiewicz MA. Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features. Am J Hum Genet. 2017 Apr 6;100(4):676. PMID: 28343629

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. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 Feb 23;168(5):830. PMID: 28235197

Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation

Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, Coban Akdemir ZH, Walkiewicz M, Bi W, Xiao R, Ding Y, Xia F, Beaudet AL, Muzny DM, Gibbs RA, Boerwinkle E, Eng CM, Sutton VR, Shaw CA, Plon SE, Yang Y, Lupski JR. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med. 2017 Jan 5;376(1):21. PMID: 27959697

MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death

Eldomery MK, Zeynep C, Akdemir, Vögtle F, Charng W, Mulica P, Rosenfeld J, Gambin T, Gu S, Burrage L, Shamsi A, Penney S, Jhangiani S, Zimmerman H, Muzny D, Wang X, et al. (2016) MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile deathGenome Medicine 20168:106. https://doi.org/10.1186/s13073-016-0360-6

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

Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans

Vetrini F, D’Alessandro LC, Akdemir ZC, Braxton A, Azamian MS, Eldomery MK, Miller K, Kois C, Sack V, Shur N, Rijhsinghani A, Chandarana J, Ding Y, Holtzman J, Jhangiani SN, Muzny DM, Gibbs RA, Eng CM, Hanchard NA, Harel T, Rosenfeld JA, Belmont JW, Lupski JR, Yang Y. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. Am J Hum Genet. 2016 Oct 6;99(4):886. PMID: 27616478

De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive

Tokita MJ, Braxton AA, Shao Y, Lewis AM, Vincent M, Küry S, Besnard T, Isidor B, Latypova X, Bézieau S, Liu P, Motter CS, Melver CW, Robin NH, Infante EM, McGuire M, El-Gharbawy A, Littlejohn RO, McLean SD, Bi W, Bacino CA, Lalani SR, Scott DA, Eng CM, Yang Y, Schaaf CP, Walkiewicz MA. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive. Am J Hum Genet. 2016 Sep 1;99(3):720. PMID: 27545676

Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO

Scott DA, Hernandez-Garcia A, Azamian MS, Jordan VK, Kim BJ, Starkovich M, Zhang J, Wong LJ, Darilek SA, Breman AM, Yang Y, Lupski JR, Jiwani AK, Das B, Lalani SR, Iglesias AD, Rosenfeld JA, Xia F. Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO. J Med Genet. 2016 Aug 22. PMID: 27550220

Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia due to Bi-allelic TANGO2 Mutations

Lalani SR, Liu P, Rosenfeld JA, Watkin LB, Chiang T, Leduc MS, Zhu W, Ding Y, Pan S, Vetrini F, Miyake CY, Shinawi M, Gambin T, Eldomery MK, Akdemir ZH, Emrick L, Wilnai Y, Schelley S, Koenig MK, Memon N, Farach LS, Coe BP, Azamian M, Hernandez P, Zapata G, Jhangiani SN, Muzny DM, Lotze T, Clark G, Wilfong A, Northrup H, Adesina A, Bacino CA, Scaglia F, Bonnen PE, Crosson J, Duis J, Maegawa GH, Coman D, Inwood A, McGill J, Boerwinkle E, Graham B, Beaudet A, Eng CM, Hanchard NA, Xia F, Orange JS, Gibbs RA, Lupski JR, Yang Y. Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia due to Bi-allelic TANGO2 Mutations. Am J Hum Genet. 2016 Feb 4;98(2):347-57. PMID: 26805781

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

ADIPOR1 is mutated in syndromic retinitis pigmentosa

Mingchu Xu, Aiden Eblimit, Jing Wang, Jianli Li, Feng Wang, Li Zhao, Xia Wang, et al. (2015) ADIPOR1 is mutated in syndromic retinitis pigmentosaHuman Mutation 10, 1002. PMID: 26662040

Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome

Thaker VV, Esteves KM, Towne MC, Brownstein CA, James PM, Crowley L, Hirschhorn JN, Elsea SH, Beggs AH, Picker J, Agrawal PB. “Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome.” J Clin Endocrinol Metab. 2015 May;100(5):1723-30. PMID: 25781356

De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome

Burrage LC, Charng WL, Eldomery MK, Willer JR, Davis EE, Lugtenberg D, Zhu W, Leduc MS, Akdemir ZC, Azamian M, Zapata G, Hernandez PP, Schoots J, de Munnik SA, Roepman R, Pearring JN, Jhangiani S, Katsanis N, Vissers LE, Brunner HG, Beaudet AL, Rosenfeld JA, Muzny DM, Gibbs RA, Eng CM, Xia F, Lalani SR, Lupski JR, Bongers EM, Yang Y. De Novo GMNN Mutations Cause Autosomal-Dominant Primordial Dwarfism Associated with Meier-Gorlin Syndrome. Am J Hum Genet. 2015 Dec 3;97(6):904, featured article. PMID: 26637980

De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea

Xia F, Bainbridge MN, Tan TY, Wangler MF, Scheuerle AE, Zackai EH, Harr MH, Sutton VR, Nalam RL, Zhu W, Nash M, Ryan MM, Yaplito-Lee J, Hunter JV, Deardorff MA, Penney SJ, Beaudet AL, Plon SE, Boerwinkle EA, Lupski JR, Eng CM, Muzny DM, Yang Y, Gibbs RA. De novo truncating mutations in AHDC1 in individuals with syndromic expressive language delay, hypotonia, and sleep apnea. Am J Hum Genet. 2014 May 1;94(5):784. PMID: 24791903

Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism

Schaaf CP, Gonzalez-Garay ML, Xia F, Potocki L, Gripp KW, Zhang B, Peters BA, McElwain MA, Drmanac R, Beaudet AL, Caskey CT, Yang Y. Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism. Nat Genet. 2013 Nov;45(11):1405. PMID: 24076603

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

Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis

Wang X, Wang H, Cao M, Li Z, Chen X, Patenia C, Gore A, Abboud EB, Al-Rajhi AA, Lewis RA, Lupski JR, Mardon G, Zhang K, Muzny D,Gibbs RA,Chen R. Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with Leber congenital amaurosis .Human mutation,2011,32(12):1450-1459. PMID: 21901789

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