What is Whole Genome Sequencing?

WHAT IS WHOLE GENOME SEQUENCING?

A staggering 400 million people are affected by genetic and rare conditions globally, with 15 million affected children in the United States alone. Some newborn babies in the neonatal and pediatric intensive care units (NICU/PICU) with severe illnesses will not be diagnosed with standard tests and imaging. Additionally, it often takes an average of 8 years to reach a medical diagnosis for these patients. This long road to a diagnosis, also known as the diagnostic odyssey, presents one of the greatest challenges affecting the health and well-being of the individual. The diagnostic odyssey for rare diseases may be tackled and eliminated by improving access to quality genetic testing services. Making a genetic diagnosis can help have a significant impact on prognosis, and medical management, and thereby influence infant mortality and morbidity.   

Whole Genome Sequencing (WGS) has shown promise in becoming a first-tier diagnostic test for patients due to its impact on rare and genetic diseases.¹ This article will help you understand WGS, its benefits, limitations, and its influence on clinical care. We will also briefly cover the importance of WGS in the NICU and PICU settings and how it can further promote medical treatment and management. Finally, we will briefly discuss the significance of Baylor Genetics’ WGS. 

INTRODUCTION TO WHOLE GENOME SEQUENCING

WGS is a single, all-encompassing test that can be ordered to analyze your patient’s genome. Additionally, WGS can detect a wide spectrum of genetic abnormalities like single nucleotide variants (SNV), structural variants (SV), copy number variants (CNV), mitochondrial variants (MV), short tandem repeats (STR) in coding and non-coding regions, and more. Usually, WGS can provide a diagnosis for most genetic disorders, such as rare Mendelian disorders caused by germline mutations.⁵  

WGS is classified into de novo and resequencing depending on whether there is a reference genome, which makes the DNA assembly simple and rapid. Pioneered by the Human Genome Project WGS is a powerful second-generation platform that has enabled the sequencing of millions of DNA molecules simultaneously using capillary electrophoresis and massively parallel next-generation sequencing (NGS).  This powerful tool has revolutionized the future of precision medicine and clinical diagnostics by offering a high throughput option and shows promise in guiding therapeutic intervention with efficiency and panache.

WHOLE GENOME SEQUENCING WORKFLOW

We’ve created a simplified overview of the WGS lab process based on the article titled, “Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease,” in NPJ Genomic Medicine, which was co-authored by Dr. Pengfei Liu, Associate Clinical Director of NGS and Molecular at Baylor Genetics. 

The article highlights that WGS can be divided into three main stages of wet lab processes and bioinformatics:¹  

• Primary 
  • In the primary stage, the genomic DNA is fragmented and indexed for library preparation. Then, the library samples are purified and pooled for sequence analysis on a sequencing machine, converting raw sequencing instrument signals into nucleotides and sequence reads.  
• Secondary 
  • In the secondary stage, DNA variants are identified through read alignment and variant calling. 
• Tertiary 
  • In the tertiary stage the lab performs variant annotation, filtering, prioritization, classification, interpretation, and reporting. This procedure is common in most laboratories that perform high-throughput sequencing tests and informatics pipelines. However, the difference in the data quality and accuracy of results depends on the components and algorithms used for processing the data. 

WHOLE GENOME SEQUENCING AS A COMBINATION TEST

WGS is equal to a combination of multiple tests that include whole exome sequencing (WES), chromosomal microarray analysis (CMA), and mitochondrial DNA testing (mtDNA). 

• Whole Exome Sequencing:  
  • WES is a genome sequencing technique that sequences all the protein-coding regions (exome) of the genome. While the exome only makes up about 1 – 2% of the genome, it is estimated to contain 85% of disease-causing mutations.^2,5 However, any DNA mutation outside the exon that can affect gene activity and protein production leading to genetic disorders, might be missed by WES. 

• Chromosomal Microarray Analysis: 
  • CMA measures additions and deletions of DNA throughout the human genome. It can identify chromosomal aneuploidy, large changes in the structure of chromosomes, and submicroscopic abnormalities that are too small to be detected by traditional modalities.   

• Mitochondrial DNA Testing: 
  • Most of the inherited DNA is in the nucleosome of the cell. However, a small amount of maternally inherited DNA is found in the mitochondria. Nuclear DNA is linear, whereas the mtDNA is circular, short, and has 37 genes. ATP produced by the genes in the mitochondria provides the cell energy. Mutations in the mitochondria affect the brain and muscles that require a high level of ATP.   

Several studies have shown that WGS has the potential to identify nearly all forms of genetic variation.⁴ In the pediatric populations, WGS analyses have shown identification of clinically relevant variants in about 40% of those with autism spectrum disorders and around 60% of those with intellectual disabilities. Overall, WGS is expected to have a tremendous impact for pediatric patients and potentially replace CMA and WES as a first-tier diagnostic test.⁴  

WHO CAN BENEFIT FROM WHOLE GENOME SEQUENCING? 

Making a genetic diagnosis is crucial. With the advent of high-throughput parallel sequencing techniques such as WGS, potential genetic causes can be determined sooner. If your patient has a broad spectrum of phenotypic features with an obvious clinical diagnosis, WGS could replace multiple tests. Ultimately, this can help reduce your patient’s diagnostic odyssey.⁵ Alternatively, for newborns and children in the NICU and PICU with complex medical issues, a comprehensive approach such as WGS may be the appropriate first-line test.⁶ 

In November 2021, the American College of Medical Genetics and Genomics (ACMG) published an evidence-based clinical guideline recommending the use of exome and genome sequencing as a first-tier or second-tier test for pediatric patients with congenital anomalies, intellectual disability, and developmental delay.²  

WHOLE GENOME SEQUENCING TESTING OPTIONS AT BAYLOR GENETICS

To make the testing more accessible, we offer multiple options for WGS, which include rapid and non-rapid tests. 

Rapid Whole Genome Sequencing (rWGS): Starting turnaround time (TAT) of five days 

• Rapid Proband WGS (test code 1829) 
• Rapid Duo WGS (test code 1823) 
• Rapid Trio WGS (test code 1822) 

Whole Genome Sequencing: Starting TAT of 10 weeks 

• Proband WGS (test code 1810) 
• Duo WGS (test code 1803) 
• Trio WGS (test code 1800) 

In December 2022, Baylor Genetics launched WGS Reanalysis. This test enables healthcare providers to provide options for reanalysis and interpretation for their patients who had WGS performed at Baylor Genetics.  

RAPID TURNAROUND TIME 

For rapid WGS, test results are available in just five days. And for babies in the NICU, five days can mean a lifetime. 

“Without rapid diagnostic testing, many patients with genetic disorders leave the hospital, and some even pass away before they ever get a diagnosis,” said Christina Settler, Associate Vice President of Medical Affairs at Baylor Genetics. 

At Baylor Genetics we prioritize our rapid TAT and provide prompt responses to our clients so that you can provide your patients with the information they need to make important decisions.  

FEATURES & BENEFITS OF BAYLOR GENETICS’ WHOLE GENOME SEQUENCING  

To advance our understanding of the underlying concepts of genetics, it is crucial to use a high efficiency and robust substrate for a comprehensive analysis of the human genome.³  Baylor Genetics’ bioinformatics analysis is performed on the newest human reference genome assembly, GRCh38, which plays a central role in nearly all aspects of clinical research. 

Baylor Genetics’ WGS is designed to: 

• Be an effective diagnostic strategy for clinical diagnosis of genetic and inherited disorders 
• Provide rapid results for patients who are critically ill with undiagnosed genetic syndrome
• Provide a diagnosis for patients that show symptoms of developmental delay, intellectual disability, autism spectrum disorders, multiple congenital anomalies, epilepsy syndromes, dysmorphic features, and more 
• Aid in medical management and treatment

Advantages of WGS at Baylor Genetics:²  

• In one test, every single variant is detected whether small SV or large CNV leading to a thorough genotype and phenotype analysis
• Can detect multiple types of structural variants in the genome (e.g., SNVs, indels, deletions, duplications, rearrangements, aneuploidy)
• Reliable and in-depth sequence coverage of coding and non-coding regions, including a high coverage across the genome
• Uniform coverage, when compared to WES
• Detailed analysis helps identify monogenic diseases (e.g., thalassemia) and polygenic diseases (e.g., type 2 diabetes mellitus)
• Provides the most detailed genetic information, when compared to other DNA sequencing methods
• Acts as a screening tool to identify carriers of recessive diseases such as cystic fibrosis
• Testing can help future parents receive genetic counseling or even pre-implantation genetic screening if needed
• Partnership with the Undiagnosed Diseases Network as its main sequencing core for WGS and WES.

General Limitations of WGS: 

• Large amounts of data  
• Difficulty in interpretation of variants in noncoding regions 
• Higher cost, when compared to WES and other genetic testing methods        
• Low mosaicism  

IS WHOLE GENOME SEQUENCING MY PATIENTS BEST OPTION?

Given the severity of genetic conditions, the complexity involved in a diagnosis, and where time is of the essence, rWGS might be the most comprehensive and powerful diagnostic tool available – especially for babies and children in the NICU and PICU.

This clinical genetic test has the potential to replace most standard tests and medical evaluations. Additionally, WGS has a wide array of benefits such as providing information about human health, ascertaining diseases and abnormalities in the DNA, how disease can be treated efficiently, knowledge about potential genetic conditions that might be transmitted to the offspring, and more.

In conclusion, with results obtained in five days, Baylor Genetics’ rWGS can help resolve critical and complex cases for providers, detect chromosomal abnormalities, and reduce the diagnostic time involved.

For more details on WGS and to start a test order with Baylor Genetics, click here.

References:

1. Marshall, C.R., Chowdhury, S., Taft, R.J. et al. Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease. npj Genom. Med. 5, 47 (2020). https://doi.org/10.1038/s41525-020-00154-9
2. Baylor Genetics. Whole Genome Sequencing. (2023, January). https://www.baylorgenetics.com/whole-genome-sequencing/
3. Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10. PMID: 28396521; PMCID: PMC5411779.
4. Stavropoulos, D., Merico, D., Jobling, R. et al. Whole-genome sequencing expands diagnostic utility and improves clinical management in pediatric medicine. npj Genomic Med 1, 15012 (2016). https://doi.org/10.1038/npjgenmed.2015.12
5. Gilissen C, Hoischen A, Brunner HG, Veltman JA. Unlocking Mendelian disease using exome sequencing. Genome Biol. 2011 Sep 14;12(9):228. doi: 10.1186/gb-2011-12-9-228. PMID: 21920049; PMCID: PMC3308044.