Exome Sequencing

General Information

Lab Name

Exome Sequencing

Lab Code

EXOME

Epic Name

Exome Sequencing

Description

Exome analysis targets protein coding genes and other clinically relevant regions of the genome to identify differences with a human reference sequence. Exome analysis is recommended as a first-tier test for individuals with developmental delay, intellectual disability, unexplained epilepsy, or multiple congenital anomalies.

Exome Trio Sequencing: the proband, biological mother, and biological father are sequenced. The inheritance information from each biological parent improves filtering of rare variants and helps to identify potential candidate DNA changes.

Family member samples (comparators) must be received within 4 weeks. If comparator samples are not received, a change in the test codes will be required which can impact billing and prior authorization investigations.

Exome Singleton Sequencing: If one or both biological parents are not available for testing, exome singleton sequencing is performed with or without additional comparators.

Additional Exome Comparator: Comparator exome sequencing is an adjunct to exome sequencing of the proband (either exome singleton or exome trio) and inheritance information from affected and/or unaffected family members improves filtering of rare variants and helps to identify potential candidate DNA changes. Please indicate the number of samples being sent as comparators (example: for a proband-mother duo, exome singleton is ordered with an additional comparator). Exome sequencing is performed on comparator samples.

Comparator samples must be received within 4 weeks. If comparator samples are not received, a change in the test codes will be required which can impact billing and prior authorization investigations.

Optional Mitochondrial Genome Sequencing Analysis. If requested, mitochondrial genome analysis is provided with exome analysis.

Optional Secondary Findings in Medically Actionable Genes. If requested, the laboratory will report genetic variants unrelated to the primary indication for testing that are considered potentially medically actionable (termed "secondary findings").

Forms & Requisitions

GSTL Exome Requisition

Synonyms

Extracted DNA, Saliva, Whole blood (EDTA tube)

Components

Code	Name
EXRES	Exome Sequencing Result

Interpretation

Guidelines

Genetics and Solid Tumor Diagnostic Testing

Method

Exome DNA Sequencing

Next generation DNA sequencing is performed to identify small variants (SNV and INDEL), copy number variants >1 Kb, and regions of homozygosity in protein coding genes and other clinically relevant regions of the genome. If requested, mitochondrial genome analysis is provided. Clinical regions of interest are sequenced to an average read depth of 35x and compared to the GRCh38 human genome reference and the revised Cambridge Reference Sequence. Sequence alignment and variant detection are performed using Illumina’s DRAGEN pipeline. All called variants are assigned a quality score for filtering. Variants are assessed for pathogenicity using available information from population, clinical, and genetic resources. Variant prioritization and analysis are performed in Emedgene software (Illumina).

Based on analytical validation studies, our assay showed >99.7% sensitivity and 99.8% specificity for SNVs and small insertions and/or deletions (indels) that were ≤50 bp in regions with high mapping quality, and 92.3% sensitivity and 92.6% specificity for copy number variants >1kb. Clinical validation studies showed 100% sensitivity and specificity for small variants (SNVs, indels) and CNVs.

Reference Range

See individual components

Interferences and Limitations

Some types of variation are not reliably detected by this assay, including complex structural variants, DNA methylation, nucleotide repeat expansions/contractions, mosaic variants with allele frequencies lower than 20%, and, rarely, misannotated variants due to limitations in variant calling with overlapping benign polymorphisms or other complexities. Variants occurring in regions containing paralogous genes, pseudogenes, repeat or homopolymer tracks, high GC content, or otherwise low coverage, may impair the accuracy of the results.

Ordering & Collection

Specimen Type: Blood, saliva, cultured cells
Collection: BLOOD is the Preferred Specimen drawn in a lavender top tube (EDTA):
Adults: 5-10cc
Children: 3-5cc
Infants: 2-3cc
If necessary, whole blood may be stored up to 5-7 days in the refrigerator before shipping.

Saliva (Oragene kit) or DNA extracted from blood, saliva, amniocytes, or fibroblasts (minimum 5ug) are also acceptable. If there are difficulties with arranging for laboratory blood draw and shipment, please contact the laboratory for saliva collection or blood tube kits.
Forms & Requisitions: GSTL Exome Requisition
Handling Instructions: SPS specimen handling:

Whole blood sample: store in the refrigerator

Cultured amniocytes/chorionic villi: store at room temperature. Call the Genetics lab upon receipt (206)598-7021.

Extracted DNA: store in the refrigerator

Saliva: store at room temperature

Any other samples contact the Genetics Lab.

Processing

Receiving Instructions: UW SPS: Log and forward to Genetics

NWH, Fred Hutch, all other SPS: Send to UW SPS

Misc Sendout

Performance

Lab Department

Genetics(GEN)

Frequency

Results within 4-6 weeks.

Available STAT?

Performing Location(s)

UW-MT	Genetics Attention: Genetics Lab Clinical lab, Room NW220 University of Washington Medical Center 1959 NE Pacific Street Seattle, WA 98195 Tel: 206-598–6429 M–F (7:30 AM–4:00 PM) Fax: 206-616-4584 Lab email: cgateam@uw.edu Tel (EXOME only): 206-543-0459	Faculty Jillian Buchan, PhD, FACMG Runjun Kumar, MD, PhD Regina Kwon, MD, MPH Christina Lockwood, PhD, DABCC, DABMGG Abbye McEwen, MD, PhD Candace Myers, PhD Colin Pritchard, MD, PhD Vera Paulson, MD, PhD Eric Konnick, MD, MS He Fang, PhD

Billing & Coding

LOINC: 86205-2
Interfaced Order Code: UOW5865
Billing Comments: We offer full insurance prior authorization services.

Exome Full Test Panel Billing