Northwest Clinical Genomics Laboratory
University of Washington
Department of Genome Sciences
3720 15th Avenue NE, Seattle, WA 98195
Phone: (206) 685-8886; FAX: (206) 543-3050
Subject Name:
Subject DOB:
Gender:
Medical Record #:
Date Obtained:
Date Received:
Subject ID:
Referring Physician: F. Hisama, MD
Report date:
Whole Exome Sequencing – Incidental Finding Report
This individual has enrolled in a research study aimed at understanding the application of whole exome
sequencing to clinical care, in the care of individuals with a personal and/or family history of colon cancer
and/or polyps. Genetic findings related to colon cancer and/or polyps are reported separately.
A subset of pharmacogenetic variants, and sequence variants in a subset of non-colon cancer and/or polyp
related genes, were also identified by this assay as incidental findings and are reported below. Only currently
known pathogenic mutations are reported here, variants of uncertain significance are not reported.
Sequencing technology is continually evolving, and the interpretation of genetic findings may change over time.
If you believe your patient has a genetic condition, evaluation by a genetic specialist to determine the need for
additional genetic testing may be warranted.
Indication: 67 year old man with colon cancer diagnosed at 42 years old. Family history of sister with breast
cancer diagnosed in her 50s and melanoma diagnosed in her 20s, a paternal grandmother with breast cancer
and a paternal uncle with leukemia.
Molecular Test Results:
Gene
Variant
1.
CYP2C9
*1/*3
2.
VKORC1
-1639GA
Clinical Significance
Recommendation
Consideration of reduced
Warfarin (Coumadin) Sensitivity
doses of warfarin (Coumadin).
(http://www.ncbi.nlm.nih.gov/pubmed/21900891) Contact a pharmacist for more
information.
Interpretation:
1. & 2. CYP2C9 *1/*3 (rs1057910) and VKORC1 -1639GA (rs9923231)
Gene and
Chromosome
Variant Position
(hg19)
CYP2C9
Genbank file:
NM_000771.3
Chromosome 10
Chr10: 96741053
Nucleotide variant
(1 = the A of the initiator
methionine codon)
*1 = Ref allele
*3 = c.1075A>C
Heterozygous
Protein variant
(1 = the initiator methionine, the first translated
amino acid of the precursor protein)
p.Ile359Leu
Heterozygous
The single nucleotide substitution described above results in the change of arginine to cysteine at position 144 of
the amino acid sequence.
Gene and
Chromosome
Variant Position
(hg19)
VKORC1
Genbank file:
NM_024006.4
Chromosome 16
Chr16:31107689
Nucleotide variant
(1 = the A of the initiator
methionine codon)
-1639G>A
Heterozygous
Protein variant
(1 = the initiator methionine, the first translated
amino acid of the precursor protein)
N/A
Gene variants in CYP2C9 and VKORC1 may affect the metabolism of several drugs, including warfarin (Coumadin).
Warfarin is an anticoagulant that is used to prevent blood clots. This individual has CYP2C9 *1/*3. *1 is equivalent to the
reference allele, and *3 is associated with decreased CYP2C9 enzyme activity. This individual has the VKORC1
promoter genotype (GA), which is associated with decreased VKORC1 enzyme activity. Decreased CYP2C9 and
VKORC1 enzyme activity both lead to warfarin sensitivity and increased bleeding risk at standard doses1-3. Consideration
of reduced doses of warfarin for warfarin-sensitive individuals is recommended.
Recommendations: A variety of known and unknown genetic and environmental factors affect warfarin dosing.
Several algorithms to estimate stable doses of warfarin have been developed that take into account CYP2C9 and
VKORC1 enzyme activity. www.warfarindosing.org is a free website that provides estimates for warfarin dosing in patients
starting therapy. The Clinical Pharmacogenetics Implementation Consortium has also published warfarin dosing
guidelines based on CYP2C9 and VKORC1 causative variations, or mutations
(http://www.ncbi.nlm.nih.gov/pubmed/21900891).
References:
1. Warfarin dose and the pharmacogenomics of CYP2C9 and VKORC1 - rationale and perspectives. Tong Yin, and
Toshiyuki Miyata. Thrombosis Research (2007) 120(1):1-10. Epub 2006 Dec 11. Review.
2. A novel functional VKORC1 promoter polymorphism is associated with inter-individual and inter-ethnic differences
in warfarin sensitivity. Hsiang-Yu Yuan, Jin-Jer Chen, M.T. Michael Lee, Ju-Chieh Wung, Ying-Fu Chen, Min-Ji Charng,
Ming-Jen Lu, Chi-Ren Hung, Chun-Yu Wei, Chien-Hsiun Chen, Jer-Yuarn Wu and Yuan-Tsong Chen Human Molecular
Genetics (2005) Jul 1;14(13):1745-51. Epub 2005 May 11.
3. Genetic Determinants of Response to Warfarin during Initial Anticoagulation. Ute I. Schwarz, Marylyn D. Ritchie, Yuki
Bradford, Chun Li, Scott M. Dudek, Amy Frye-Anderson, Richard B. Kim, Dan M. Roden, and C. Michael Stein. The New
England Journal of Medicine (2008) 358(10): 999-1008.
Test: Whole Exome Sequencing (WXS)
WXS was performed in a research environment to screen the coding portion of the subject’s genome (exome) for DNA
sequence variants in genes known to cause colon cancer and/or polyps. Sequence variants in a set of non-colon cancer
or polyposis related ‘actionable genes’ were also identified by this assay as incidental findings. These actionable genes
were chosen based on their association with adult onset conditions for which there is recommended screening and/or
treatment. Thus, this individual’s exome was not comprehensively interrogated.
Only pathogenic variants are reported for incidental findings—variants of uncertain significance are not returned. Positive
findings were validated to clinical standards in a CLIA compliant laboratory; however, the performance characteristics of
exome sequencing for negative results (the absence of mutations) were not validated to clinical standards in a CLIA
compliant laboratory.
This laboratory test was developed and its performance characteristics determined by the Northwest Clinical Genomics
Laboratory (CLIA-certified). Consistent with laboratory-developed tests, this test has not been cleared or approved by the
U.S. Food and Drug Administration.
Procedure:
I.
Whole Exome Sequencing
Genomic DNA was extracted from blood using standard procedures. A library of DNA fragments was constructed and
enriched for protein and RNA coding portions of the human genome using the SeqCap EZ Exome v3.0 (NimbleGen)
capture system. Paired-end sequencing of the enriched library was performed using standard TruSeq v3.0 (Illumina)
chemistry on a HiSeq 2000 (Illumina) sequencer according to the manufacturer’s recommended protocol. Resulting
sequences were aligned to the human genome reference (hg19) using the Burrows-Wheeler Aligner (BWA) and
variants identified with the Genome Analysis Took Kit (GATK). A modified version of the SeattleSeq tool was used to
annotate variants found within a defined set of colon cancer and actionable genes.
Limitations:
1. This assay does not detect large deletions or duplications and has limited ability to identify small insertions and
deletions. This test is also has limited ability to detect mosaicism.
2. The assay does not detect variants located: 1) outside the captured exome, 2) in regions of insufficient coverage,
3) in regions containing paralogous genes or pseudogenes, or 4) where the reference genome is inaccurate or
contains gaps and insertions.
3. Variants of uncertain significance are not reported
4. Genes not associated with treatable genetic conditions at the time this test was performed were not analyzed
II. Validation of Sequence Variants (CLIA-accredited)
Primers based on the hg19 (February 2009) version of the human genome sequence, were used to amplify
targets containing WXS-identified sequence variants. PCR-amplified fragments were sequenced using
standard dye-terminator chemistry.
__________________________________
Peter H. Byers, M.D.
Laboratory Director
____________________________________
Michael O. Dorschner, Ph.D.
Laboratory Director
__________________________________
Laura Amendola, M.S., C.G.C.
Licensed Genetic Counselor
Contact Information:
Northwest Clinical Genomics Laboratory
University of Washington
Laura Amendola, MS CGC
Phone: (206) 685-8886; FAX: (206) 543-3050
EMAIL: lauraa7@uw.edu
CLIA ID: 50D2050662
Genetic Medicine Clinic
University of Washington
Fuki Hisama, MD
Robin Bennett, MS CGC
Phone: (206) 598-4030; Fax: (206) 598-3269
EMAIL: fmh2@u.washington.edu
robinb@u.washington.edu