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.

Family member samples (comparators), typically the biological mother and biological father, can be included in this test to help identify potential candidate DNA changes. The inheritance information from biologically related individuals improves filtering of rare variants and increases the likelihood of identifying a clinically meaningful result.

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.

Exome Singleton Sequencing (Proband-Only Exome Sequencing) refers to exome sequencing performed on a single individual, typically the affected person (proband) without sequencing biological parents or other relatives. This approach analyzes both coding and non-coding regions of the genome to detect single nucleotide variants, small insertions/deletions, copy number variants, aneuploidy, and regions of homozygosity. While it can identify many clinically relevant variants, interpretation may be more challenging than family-based sequencing because inheritance patterns and de novo status cannot be evaluated.

Exome Sequencing with Comparators (Family-Based Duo/Trio/Quad Exome Sequencing) refers to exome sequencing performed on the affected individual along with one or more biologically related individuals (such as parents or siblings). The comparator samples are used to help interpret the proband’s genetic variants by determining inheritance patterns, including whether variants are inherited or occurred de novo. This approach improves variant interpretation, reduces the number of candidate variants, and increases the likelihood of identifying a clinically meaningful result by providing genetic context that is not available with proband-only sequencing.

Please indicate the number of samples being sent as comparators on the test requisition form. Exome sequencing is performed on comparator samples. Variants present in family members included in this analysis are not independently evaluated or reported.

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 and Genome 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. 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/Cultured amniocytes or chorionic villus cells/Extracted DNA from blood, chorionic villi, and amniocyte. Direct chorionic villi, amniocyte, or amniotic fluid testing require Genetics Director approval. Please call the lab at 206-598-7021. Saliva (collected from Oragene Dx OGD- 500 or Oragene Dx OGD- 575). Please contact the Genetics laboratory at 206-598-1149 to request a kit.

Collection

Acceptable:

Whole blood:5 mL lavender top (EDTA) tube or yellow (ACD) top tube or 2 mL microtainer lavender top tube.
Extracted DNA from blood, chorionic villi, and amniocytes: 500 ng (concentration >10 ng/uL).
Cultured amniocytes/chorionic villi: MCC is required for testing fetal samples. See Maternal Cell Contamination, Fetal [MCC].
Saliva (collected from Oragene Dx OGD- 500 or Oragene Dx OGD- 575). Please contact the Genetics laboratory to request for the kit.

Unacceptable: Heparin green top tubes, buccal swab

Forms & Requisitions

GSTL Exome and Genome Requisition

Quantity

Requested: Entire sample
Minimum: Blood: 1 mL. If volume is less than 1mL, do not cancel. Send to Genetics lab. Confluent cultured cells: One (1) T25 flask. Extracted DNA: 250 ng

Processing

Receiving Instructions

UW SPS: Log and forward to Genetics

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

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.

Note: Please include clinical history.

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 Candace Myers, PhD Colin Pritchard, MD, PhD Vera Paulson, MD, PhD Eric Konnick, MD, MS He Fang, PhD Ghayda Mirza, MD Kristyn Galbraith, MD Annie Garcia, MD Karen Chisholm, MD, PhD

Billing & Coding

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

Exome Full Test Panel Billing