Exome Sequencing

Performing Lab: 
UCSF Genomic Medicine Lab
CPT Code: 
81415, 81416

Specimen Type:
Peripheral blood, Saliva (collected in Oragene kit), Buccal cells, Cultured cells, DNA (minimum 2 micrograms)

Methodology: Next-generation sequencing

Turnaround Time: 4-12 weeks

TEST INDICATIONS: 

For best results:

  • Include samples from both biological parents to improve exome yield.
  • Provide a detailed phenotypic/clinical description of your patient. Phenotypic information is essential for optimal test performance. This information is used to assess the relevance of candidate genes.
  • Please specify any specific genes of interest on the Test Requisition Form.
  • Consider sending other preliminary genetics studies before requesting exome sequencing.  Exome sequencing does not assess all types of genetic variation (e.g. DNA repeats, large copy number variations, mitochondrial DNA).
  • We encourage referral to the UCSF General Genetics Clinic for detailed phenotypic assessment, consideration of ancillary testing, family member inclusion and informed consent.

Important points to consider:

  • Informed consent and signatures are required for all individuals undergoing sequencing.
  • Please review the informed consent form in detail with each individual whose specimens are submitted for testing.
  • Exome sequencing may reveal additional findings unrelated to the indication for testing. Please be sure to have the patient indicate their preference for receiving additional findings.
    • Our group follows recommendations by the American College of Medical Genetics/Genomics for reporting of additional findings.
HOW THE TEST WORKS: 

Genomic DNA is extracted for library preparation.  Target enrichment is performed by hybrid capture using custom oligonucleotides (IDT xGen Exome Research Panel v1.0).  Sequencing of captured libraries is performed on an Illumina HiSeq 2500 in rapid run mode (2 X 101 bp read length).  Sequence reads are de-duplicated to allow for accurate allele frequency determination and copy number calling.  The analysis uses open source or licensed software for alignment to the human reference sequence UCSC build hg19 (NCBI build 37) and variant calling.  Common germline polymorphisms were eliminated from analysis using the complete list of germline mutations from dbSNP.  Additional filtering to eliminate technology specific sequencing artifacts was performed before analyzing the data. This test was validated by the UCSF Genomic Medicine Laboratory to confirm performance characteristics, in compliance with current guidelines for clinical implementation

SPECIMEN REQUIREMENTS FOR A SUCCESSFUL TEST: 
  • EDTA (lavender top), 3cc
  • Saliva in Oragene collection kit, minimum 1 cc
  • Buccal swabs, minimum 3 swabs
  • Cultured cells, minimum 2 x T25 flasks (confluent)
  • DNA, minimum 2 micrograms
HOW TO ORDER THE TEST: 

UCSF Clinicians — blood draws can be ordered through APeX

117878 GML EXOME PROBAND PERIPHERAL BLOOD DRAW (GMLEXP)
117882 GML EXOME FAMILY MEMBER PERIPHERAL BLOOD DRAW (GMLEXF)
Please use the paper requisition form to provide the test request details.
Please use the paper consent form to document informed consent.
Other forms:
GML Buccal Collection Instructions.pdf
Instructions Shipping Samples UCSF Exome.pdf
Oragene Saliva Collection Instructions.pdf
For all specimens, an interpretation of this test by a laboratory physician will automatically be performed and billed for separately.