Illumina Clinical Services Laboratory
`Illumina Inc.
`9865 Towne Centre Dr
`San Diego, CA 92121, USA
`Phone: (858) 736-8080
`Fax: (858) 736-8600
`PersonalGenomeInquiries@Illumina.com
`
`Individual Genome Sequence Report
`
`Dr. Naviaux
`UCSD School of Medicine
`214 Dickinson St., Room C-103,
`San Diego, CA 92103-8467
`Tel: (619) 543-2904
`
`Physician Name
`
`Patient Sex
`
`Patient Record Number
`
`Laboratory Tracking
`
`Date Reported
`
` Dr. Naviaux
`
`Male
`
`N/A
`
` PG0000021-BLD
`
`January 19, 2010
`
`Blood Sample
`
`Saliva Sample
`
`Collected
`
`Received
`
`11/16/2009
`
`11/17/2009
`
`11/16/2009
`
`11/17/2009
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`
`
`
`Results
`
`
`Summary Statistics
`
`Base pairs reported (consensus)
`
`Percentage NCBI reference covered
`
`
`
`2,715,363,145
`
`95.1%
`
`Number of SNPs detected relative to NCBI reference* 3,414,889
`
`Number of dbSNPs genotyped*
`
`Number of novel SNPs detected*
`
`12,809,716
`
`361,510
`
`Average depth of coverage across reference genome 95.1%
`
`91,979,393,847
`
`Number of bases used to generate consensus
`
`Note: The National Center for Biotechnology Information (NCBI) website
`(http://www.ncbi.nlm.nih.gov/) is a curated database sponsored by the National
`Institutes of Health that contains reference sequences, including the officially
`released builds of the human genome. The official reference build 36.1 was used to
`align the Personal Genome Sequence reported on here.
`
`*The numbers reported here reflect different ways of measuring variation, and are
`not mutually exclusive. These numbers are further explained below.
`
`
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`
`Genomic Coverage
`
`This graph reports on the coverage (as a percentage of the alignable NCBI
`published reference genome) of the patient’s Individual Genome Sequence per
`chromosome and total. Coverage is shown by chromosome (1-22, X, Y and M,
`where M is mitochondria). The parts of the genome not covered here mostly
`comprise identical repeat sequences, which are present in the raw reads but cannot
`be aligned to a unique position on the reference sequence.
`
`
`Coverage
`
`100%
`
`90%
`
`80%
`
`70%
`
`60%
`
`50%
`
`40%
`
`30%
`
`20%
`
`10%
`
`0%
`
`
`
`Total
`
`X Y M
`
`22
`
`21
`
`20
`
`19
`
`18
`
`17
`
`16
`
`15
`
`14
`
`13
`
`12
`
`11
`
`10
`
`1 2 3 4 5 6 7 8 9
`
`
`
`Single Nucleotide Polymorphisms (SNPs)
`
`Chromosome
`
` A
`
` polymorphism is a site or region of the genome that is variable. When a single
`base is variable, it is reported as a single nucleotide polymorphism (SNP).
`
`Variability can be measured by comparing the genome to the NCBI reference
`genome; the genome reported here was different from the NCBI reference at
`3,414,889 sites.
`
`NCBI also curates a database on single nucleotide polymorphisms (SNPs)
`(http://www.ncbi.nlm.nih.gov/SNP/). Of the more than 13 million SNPs
`documented in dbSNP (version 129), 12,809,716 SNPs are reported here.
`
`Finally, 361,510 SNPs were detected in this genome that have not been
`documented elsewhere. These SNPs are labeled as “Novel”, however this should
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`
`
`not be interpreted as SNPs unique to the individual. As the public database
`becomes more extensive, the number of documented SNPs should increase.
`
`For all of the following graphs, variation is reported using the NCBI reference
`genome as the comparison.
`
`Novel SNPs
`361,510
`10.60%
`
`SNPs in
`dbSNP
`3,049,525
`89.40%
`
`
`
`
`
`
`
`
`
`The distribution of SNPs is shown below:
`
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`SNP distribution
`
`Novel SNPs
`
`SNPs in dbSNP
`
`
`
`300,000
`
`250,000
`
`200,000
`
`150,000
`
`100,000
`
`50,000
`
`0
`
`1
`
`2
`
`3
`
`4
`
`5
`
`6
`
`7
`
`8
`
`9
`
`10
`
`11
`
`12
`
`13
`
`14
`
`15
`
`16
`
`17
`
`18
`
`19
`
`20
`
`21
`
`22
`
`X
`
`Y M
`
`
`Heterozygous and homozygous sites
`
`The human genome is diploid (individuals possess two copies, one inherited from
`each parent) for chromosomes 1-22 (and in females, for the X chromosome as
`well). When the two copies differ at a particular site, the individual is said to be
`heterozygous for that site. The overall ratio of heterozygous to homozygous SNPs
`was 1.53.
`
`The breakdown of heterozygous to homozygous sites at each chromosome is
`displayed below:
`
`
`dbSNP SNPs heterozygotes
`to homozygotes
`
`Novel SNPs heterozygotes to
`homozygotes
`
`Heterozygotes
`
`Homozygotes
`
`Heterozygotes
`
`Homozygotes
`
`35,000
`
`30,000
`
`25,000
`
`20,000
`
`15,000
`
`10,000
`
`5,000
`
`0
`
`1
`
`3
`
`5
`
`7
`
`9 11 13 15 17 19 21 X M
`
`1
`
`3 5
`
`7
`
`9 11 13 15 17 19 21 X M
`
`250,000
`
`200,000
`
`150,000
`
`100,000
`
`50,000
`
`0
`
`
`
`
`
`
`
`
`
`
`
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`
`
`Methodology
`
`
`Sequence was generated from DNA that was extracted from whole blood. DNA
`extracted from the whole blood was sequenced using the Illumina GAII sequencer.
`Briefly, DNA was fragmented, and the fragments were attached to the surface of a
`glass microscope slide. The fragments were then sequenced using fluorescently
`labeled nucleotides, which were excited by a laser and imaged using digital
`equipment.
`
`These fragments were then assessed for quality using a variety of metrics to ensure
`that only robust sequences were analyzed. Fragments were aligned to the NCBI
`reference sequence. Fragments that aligned to more than one region of the
`reference genome were excluded from the report. Additionally, fragments were
`excluded from the analysis on the basis of quality and alignment scores. Each
`nucleotide site reported was sequenced an average of 30 times, so there was on
`average 30-fold redundancy for each base pair reported.
`
`Illumina, Inc. made rigorous efforts to report a high quality consensus sequence,
`however due to a variety of factors, this genome report should not be considered
`complete or perfect. The regions of the genome not reported here include regions
`where the human reference genome has not been completely resolved, or are
`duplications of genetic regions make it impossible to align the fragments accurately.
`Although the error rates for this kind of technology are believed to be quite low, the
`sequence provided here cannot be considered as diagnostic. Clinical action for
`any variants of potential medical concern should only be considered
`after further investigation confirms the presence of the variant using
`alternative, more focused testing specifically developed for that
`variant.
`
`This test was developed and its performance characteristics determined by Illumina
`Clinical Services Laboratory. It has not been cleared or approved by the U.S. Food
`and Drug Administration.
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`Illumina Clinical Services Laboratory
`Physician: Dr. Naviaux
`Laboratory Tracking: PG0000021-BLD
`
`
`References
`Bentley et al. (2008) Accurate whole human genome sequencing using reversible
`terminator chemistry. Nature 456:53-59.
`Wheeler et al. (2008) The complete genome of an individual by massively parallel
`DNA sequencing. Nature 452:872-876.
`Levy et al. (2007) The diploid genome sequence of an individual human. PLoS
`Biology 5(10):e254.
`Wang et al. (2008) The diploid genome sequence of an Asian individual. Nature
`456:60-66.
`The International Human Genome Sequencing Consortium (2004) Finishing the
`euchromatic sequence of the human genome. Nature 431:931-945.
`
`
`
`
`
`
`
`_______________________
`
`Philip D. Cotter, Ph.D., FACMG
`Director, Clinical Laboratory
`
`
`
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