Clinical Workflow for Whole Genome Sequencing

Whole Genome Sequencing

The PANDA Core for Genomics and Microbiome Research at the University of Arizona's Steele Children’s Research Center offers Whole Genome Sequencing (WGS) to identify a genetic basis for a disease in an affected individual. This rapid, robust, and comprehensive test is a phenotype-based “one-step” test providing an insight into coding and non-coding elements of a genome, as well as regulatory elements and mitochondrial genes. 

WGS allows to identify a molecular basis for many genetic disorders in individuals with:

  • a disease with an uncertain differential diagnosis;
  • atypical presentation of a genetic disorder;
  • long and exhausting diagnosis odyssey;
  • polygenic disease.

Offering WGS as a diagnostic test to clinicians, the PANDA Core aims to provide assistance in the diagnostic process and aid in making disease-specific treatment decisions. Our goal is to improve the lives of critically-ill babies, children, and their families.

The PANDA Core has partnered with Illumina in genomic sequencing and data science. By leveraging AI and a focus on process engineering, we can deliver the fastest, most accurate results. We provide a quick turnaround time, offering actionable results to improve patient outcomes. The average time for a WGS final report is 14-21 days. 

Whole Genome Sequencing (WGS) diagnostic test involves analyzing an individual's entire genome to identify genetic variations, mutations, or markers associated with specific diseases or conditions. This comprehensive analysis can provide valuable information for diagnosing genetic disorders, predicting disease risk, and guiding personalized treatment strategies. It is the most efficient, accurate, and actionable test to end a diagnostic odyssey, or prevent it from even beginning. WGS diagnostic tests can be particularly valuable for diagnosing rare or complex genetic disorders, identifying inherited conditions in individuals with undiagnosed symptoms, and informing precision medicine approaches for targeted therapies.

PANDA Core offers:

  1. WGS Proband (<4 weeks, test code PG41), and rWGS Proband (7-14 days, test code PG21):
    • The proband is a person whose entire genome is sequenced to search for genetic variants associated with a particular disease, disorder, or trait.
  2. WGS Duo (<4 weeks, test code PG42), and rWGS Duo (7-14 days, test code PG22):
    • In a duo testing, genetic analysis is performed on two genetically related individuals. This involves a proband and a parent. In duo testing, both individuals' genomes are sequenced to compare genetic variants and identify potential disease-causing mutations or genetic factors contributing to a trait or condition.
  3. WGS Trio (<4 weeks, test code PG43), and rWGS Trio (7-14 days, test code PG23):
    • A trio testing involves three related individuals, typically a proband and both biological parents. In WGS trio testing, the genomes of all three individuals are sequenced. This approach allows for the analysis of genetic inheritance patterns, such as identifying de novo mutations (mutations present in the child but not in either parent), as well as assessing genetic contributions from both parents to the child's phenotype.
  4. WGS re-analysis  (test code PG90)

 

SUBMIT A CLINICAL ORDER

 

WGS Workflow

 

1

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Sample Collection and DNA Extraction: A sample is collected and DNA is extracted from a biological sample, such as saliva (buccal swab OCD-100) or whole blood (coming soon) obtained from the individual undergoing testing

2

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Library Preparation: Using PCR-free technology a sequencing library is prepared from patient's genomic DNA

3

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Sequencing and Base Calling: Samples are sequenced on Illumina NovaSeq6000 sequencing platform using 2x150bp paired-end reads

4

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Alignment, Variant Calling and Annotation: Alignment and detection of variants were performed with DRAGEN bioinformatics pipeline version 4.2, with GRCh38 as the human genome reference. Based on validation studies, the pipeline showed 98.2% sensitivity and 100% precision in areas with coverage greater than 30x and high mapping quality. Variants were annotated with the public and internal bioinformatics/genetics resources

5

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Filtration and Prioritization: All variants unlikely to be relevant to the phenotype or disease are removed and the remaining variants are prioritized based on their likelihood of being associated with the phenotype or disease under investigation

6

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Curation and Reporting: Selected variants are organized and interpreted by trained geneticists and presented to a patient, patient's family and ordering providers as a useful and understandable clinical report