throbber
Table S1. Comparison of SOLiD sequencing, Illumina SNP arrays, and Digital Karyotyping for analysis of copy number alterations
`SOLiD sequencing
`Digital Karyotyping
`Illumina SNP Arrays
`
`Left
`Boundary
`41,273,307
`
`Right
`Size (bp)
`Boundary
`43,008,812 1,735,506
`
`Tag Density
`Ratio*
`9.1
`
`Left
`Boundary
`41,419,345
`
`Right
`Boundary
`42,485,546
`
`Size (bp)
`1,066,202
`
`Log R
`Ratio*
`1.9
`
`Left
`Boundary
`41,418,000
`
`Right
`Size (bp)
`Boundary
`42,537,000 1,119,001
`
`Tag Density
`Ratio*
`16.4
`
`Tumor
`Sample Chr
`
`Amplification Co84C 6
`
`Amplification Co84C 8
`
`127,618,526 128,009,287
`
`390,762
`
`Amplification Co84C 8
`
`128,750,189 128,857,861
`
`107,673
`
`Amplification Co84C 8
`
`129,473,672 129,667,129
`
`193,458
`
`Amplification Co84C 11
`
`34,337,207
`
`35,266,401
`
`929,195
`
`19.2
`
`8.3
`
`13.8
`
`33.0
`
`127,621,008
`
`127,995,012
`
`374,005
`
`128,750,181
`
`128,848,183
`
`98,003
`
`129,472,209
`
`129,677,099
`
`204,891
`
`34,359,268
`
`35,265,359
`
`906,092
`
`109,108,212
`
`109,557,712
`
`449,501
`
`2.7
`
`2.0
`
`3.4
`
`3.0
`
`2.3
`
`127,617,000 128,010,000
`
`393,001
`
`128,748,000 128,859,000
`
`111,001
`
`129,471,000 129,678,000
`
`207,001
`
`34,338,000
`
`35,268,000
`
`930,001
`
`109,107,000 109,557,000
`
`450,001
`
`150.0
`
`43.1
`
`116.6
`
`91.2
`
`33.6
`
`Amplification Co84C 13
`
`109,096,557 109,553,930
`
`457,374
`
`Amplification Co84C 15
`
`88,545,070
`
`89,258,106
`
`713,037
`
`Amplification Co84C 19
`
`34,570,450
`
`34,641,949
`
`71,500
`
`Amplification Co84C 19
`
`34,956,853
`
`35,344,522
`
`387,670
`
`Amplification Co84C 19
`
`36,274,262
`
`36,388,331
`
`114,070
`
`9.2
`
`26.2
`
`7.9
`
`14.3
`
`6.2
`
`Amplification Co84C 19
`8.4
`143,419
`54,643,655
`54,500,237
`* Values for Tag Density Ratios and Log R Ratios represent observed maximum values for amplifications.
`
`88,561,995
`
`89,253,599
`
`691,605
`
`3.6
`
`34,561,976
`
`34,641,548
`
`79,573
`
`34,966,463
`
`35,321,409
`
`354,947
`
`36,281,540
`
`36,385,232
`
`103,693
`
`54,520,709
`
`54,622,533
`
`101,825
`
`2.2
`
`2.6
`
`2.5
`
`2.1
`
`88,542,000
`88,983,000
`89,133,000
`89,208,000
`
`88,953,000
`89,118,000
`89,166,000
`89,256,000
`
`411,001
`135,001
`33,001
`48,001
`
`34,548,000
`
`34,641,000
`
`93,001
`
`34,956,000
`
`35,346,000
`
`390,001
`
`36,273,000
`
`36,396,000
`
`123,001
`
`54,498,000
`
`54,636,000
`
`138,001
`
`93.2
`32.8
`84.8
`50.3
`
`33.9
`
`36.8
`
`21.2
`
`41.8
`
`LEARY ET AL. SUPPLEMENTARY MATERIAL, PAGE 1
`
`Foresight EX1026
`Foresight v Personalis
`
`

`

`Table S2. Putative copy number alterations identified by SOLiD sequencing in Co84 that
`were not identified by Illumina SNP arrays or Digital Karyotyping
`
`Left Boundary
`Chromosome
`Alteration Type
`83,388,000
`1
`Homozygous deletion
`151,188,000
`1
`Amplification
`159,393,000
`1
`Amplification
`172,101,000
`1
`Amplification
`179,910,000
`1
`Amplification
`200,238,000
`1
`Amplification
`204,168,000
`1
`Amplification
`9,804,000
`4
`Homozygous deletion
`69,066,000
`4
`Homozygous deletion
`147,138,000
`4
`Homozygous deletion
`31,749,000
`5
`Amplification
`114,279,000
`5
`Homozygous deletion
`38,358,000
`7
`Homozygous deletion
`145,698,000
`8
`Amplification
`66,978,000
`10
`Homozygous deletion
`108,681,000
`13
`Homozygous deletion
`110,139,000
`13
`Amplification
`54,357,000
`16
`Homozygous deletion
`59,112,000
`16
`Homozygous deletion
`76,467,000
`17
`Amplification
`14,268,000
`18
`Homozygous deletion
`50,271,000
`19
`Amplification
`25,404,000
`20
`Amplification
`49,050,000
`X
`Homozygous deletion
`121,650,000
`X
`Homozygous deletion
`* Values for Tag Density Ratios represent observed maximum values for amplifications.
`
`Right Boundary Size (bp)
`83,532,000
`144,001
`151,194,000
`6,001
`159,414,000
`21,001
`172,107,000
`6,001
`179,916,000
`6,001
`200,256,000
`18,001
`204,186,000
`18,001
`9,813,000
`9,001
`69,171,000
`105,001
`147,147,000
`9,001
`31,755,000
`6,001
`114,288,000
`9,001
`38,364,000
`6,001
`145,725,000
`27,001
`66,984,000
`6,001
`108,687,000
`6,001
`110,157,000
`18,001
`54,378,000
`21,001
`59,130,000
`18,001
`76,482,000
`15,001
`14,289,000
`21,001
`50,277,000
`6,001
`25,428,000
`24,001
`49,059,000
`9,001
`121,734,000
`84,001
`
`Tag Density
`Ratio*
`0.0
`11.2
`9.7
`18.1
`17.4
`9.6
`13.2
`0.0
`0.0
`0.0
`12.3
`0.0
`0.0
`11.5
`0.0
`0.0
`22.5
`0.0
`0.0
`17.8
`0.0
`9.3
`13.1
`0.0
`0.0
`
`LEARY ET AL. SUPPLEMENTARY MATERIAL, PAGE 2
`
`Foresight EX1026
`Foresight v Personalis
`
`

`

`Type
`
`Primer 1
`
`Sample
`
`Primer 2
`
`Table S3. Confirmed somatic rearrangements in breast and colorectal cancer samples*
`Reverse tag
`Forward tag
`Chromosome
`Position
`Chromosome
`Position
`TATATTGGAAGAATAGAAATGAATGG
`AAGTTTTTCAAGCTTTACCTGAAGT
`AAC
`3
`52,573,088
`3
`52,638,626
`B5C
`GCACACTGTTTGCAGGAATG
`AGCCAAGTGCAATTCTCCAG
`BAC
`4
`-93,105,085
`4
`93,109,700
`B5C
`AAGCTTTGTTTGGTTGTTCTCA
`GCCACCTTTCTTTCTTTCTGA
`C**
`8
`-48,889,516
`11
`57,713,780
`B5C
`TCCTTTCTGCCCATTAGGG
`TGGCTTTCAAAACCCACTG
`C**
`20
`-29,591,944
`18
`19,141,985
`B5C
`CACACCGCATTCACACAAAC
`TCATGGTTTATCCACGGTGT
`C**
`2
`-104,047,142
`22
`48,743,603
`B5C
`CGCATCCAAAGTATTAATAGCAA
`TCAAAACAGAAAGCATTAGGC
`C**
`7
`65,542,257
`1
`-96,237,189
`B7C
`CCAAATTGCCTGCTTAAGAGAT
`AACTCCTCCCACCTCAAAATC
`AAC
`2
`113,761,988
`2
`197,428,606
`B7C
`TACCGTCCTCCAGGCATGT
`TGCTACCAATACTTCCCACTTG
`C**
`3
`185,241,029
`2
`-32,084,286
`B7C
`TCCCTCATCAGAGCAAATCA
`GGAGAAAACCCTGGTTATTTTTA
`C**
`18
`53,562,784
`2
`114,604,628
`B7C
`TCTGAACATGCCTGATCTCATC
`AAATTGGGAAGGATCATACTGAC
`3
`-115,651,310 AAC
`3
`-115,579,348
`B7C
`TTGCTAAGTGATGCTACCTGTG
`CTGAACTCCTGGGCTGAA
`4
`733,804
`AAC
`4
`785,983
`B7C
`TGAAGAATCCTTCTAGTGATGGAA
`CCTGGCCCCTTAGGTAAGAT
`5
`107,231,803
`AAC
`5
`107,405,959
`B7C
`CTGCCAGTCCAAACTGGTG
`TGCAGCTTTTCTCTGTCTTCA
`10
`-44,715,202
`C**
`5
`38,284,430
`B7C
`TGAAATTAGGACCTGGAGCAC
`TGCTGTTTCAAATTCCTACAGTC
`6
`90,853,847
`AAC
`6
`106,401,376
`B7C
`GATGCAGGAAGTTGACAGCA
`GCCAGGTAACATGCTCACTTT
`6
`102,444,426
`ABC
`6
`101,933,981
`B7C
`GCCATGTGCAAGTCAAGAAG
`GGGCTAAGCTTAAGAGTCTGG
`9
`21,761,298
`AAC
`9
`22,003,033
`B7C
`TAAGGGCGATGTGAACAAGG
`TCTGCCGGCATACTGGAC
`11
`-6,519,897
`AAC
`11
`-6,436,033
`B7C
`AACATCTCTTCCTTTTGAAGATCC
`GCCCTATTTTCAGAGAAAGTGGTA
`12
`65,923,399
`AAC
`12
`65,950,588
`B7C
`AGCTGAATCAAAATTTCCAATG
`AATTTGCTCTCATCGTATTGTGT
`13
`52,159,979
`AAC
`13
`60,438,525
`B7C
`AATGGGTTAAGCAGTTTAGGG
`CTGAATCTCTTTCCAGCAAAAT
`X
`31,179,704
`AAC
`X
`31,583,118
`B7C
`AAAGGTTAAAGGACTGTTTTAAGTTG
`TAGCATGCACCACTTTAGGC
`5
`-104,930,827
`C**
`2
`191,184,628
`Co108C
`GTTAAGATCAACATTTTTGTTTCAAG
`GGTTCTGGAGGGTTGGAGA
`6
`-13,299,323
`C**
`2
`78,849,963
`Co108C
`TCCCAGTGCAATAAAACCAA
`TATGCCACCATCGCTTAGGT
`6
`13,299,385
`C**
`2
`-7,268,710
`Co108C
`CGATCTATACACCACCCCACA
`GGTGTTCTCTCTCCCATACCA
`13
`96,916,170
`C**
`2
`-141,266,018
`Co108C
`GCTGATTTGTTTATACCCAGTGC
`TGCTTTTAGTTTTGGGTACGG
`3
`-60,437,489
`AAC
`3
`-60,400,269
`Co108C
`AACCCCATCCTGAAGCTACC
`ATCCTCGGACTGGACTGAGA
`3
`-60,498,861
`AAC
`3
`-60,365,933
`Co108C
`GCTCTCAATTTGTGTGATTTGG
`GGGTTATCTCAAAAGGGCAGA
`3
`60,472,593
`AAC
`3
`60,573,034
`Co108C
`GACTACAAATGGCCCAGACTC
`TGTGTTCCTCTCCTCTTAAGCAT
`15
`54,039,041
`C**
`4
`81,934,151
`Co108C
`CCCAGCCATATGTTGGTTTA
`ATCCCCACATTCCCAACC
`5
`157,523,537
`C**
`6
`-13,299,291
`Co108C
`TCAATGGGGGAGAGAGAGC
`GTATTTGTTCATGTTTGTTAGGTGTT
`2
`-20,956,947
`C**
`6
`13,299,271
`Co108C
`CCAGATGGCTGGGTTAAATAAA
`ACGTGTGTATTGGGGGTAGC
`10
`67,756,452
`C**
`13
`34,581,537
`Co108C
`GGCTTCTGTAGAGTGCACATGA
`AGCTAGGTGGAGAATTTGTCG
`19
`49,144,200
`C**
`8
`128,442,121
`Co84C
`CTGCAGGAACTGTCTCATTCTT
`AAGGAGATTGGTTATTGTGGAAA
`13
`109,267,462
`C**
`11
`34,790,251
`Co84C
`TGGTGATTCCACTGAGGTGA
`TGCTGAATCATTCTCCCAACT
`15
`88,736,701
`C**
`11
`-34,405,644
`Co84C
`GGAAACCGTTAGTGGAAAAGTC
`GCATTCTAAAGATGAAGTCCCATT
`8
`127,747,412
`C**
`15
`-89,096,347
`Co84C
`TTTGGGTTCAGTTCTATTTGAAGA
`CAGGTGATATACCAAAGAAAATTAGG
`4
`156,043,548
`C**
`8
`96,971,644
`Hx402x
`TGGGCATGAGCAAGATATTC
`AGTCAACGCCCTAGCATGG
`5
`-137,521,052 AAC
`5
`-100,413,406
`Hx402x
`GTGACAGGCTGGGTGTCC
`AATCACGTTGGGTGACTGTG
`8
`-144,787,051 AAC
`8
`-144,771,376
`Hx402x
`TGTATGAAACATTGTAGAGGCTGT
`TGAAGGTTGAGTTGCCAGTG
`14
`-85,560,400
`AAC
`14
`-85,526,541
`Hx402x
`GGTGATTTTCAATGCATATTTCA
`AGGAGGAAAGCAACACATAGAG
`1
`-119,550,445 BBC
`1
`119,547,240
`Hx403x
`CAAAAGATTTCCAAATGCAGGT
`AATTACCACAACTCCCAGCAG
`5
`27,150,736
`BBC
`5
`-27,160,637
`Hx403x
`CACTTGAGAATCAATGATATGCAG
`TGAATCAGAAAGTCTGGCAGT
`11
`66,662,814
`AAC
`11
`66,674,459
`Hx403x
`TTTGTGTACCTAGACATTCATCCAA
`CCTAGCCCTTTGTTCCCTGT
`16
`6,727,736
`AAC
`16
`6,343,641
`Hx403x
`AGCCAAGATCAAGCCACAGA
`GCAGAGAACAGCAGAAAAGTTG
`16
`6,759,729
`AAC
`16
`6,574,321
`Hx403x
`TTGATGATTTAGAAACTCTAGCCTGT
`TTCTCTTTCTCTGCCTTCAGTG
`16
`-26,582,595
`BBC
`16
`26,579,136
`Hx403x
`CTGCTGACGTGCTGGTCTT
`GGCTCCCCTCTCCATTCC
`17
`-34,624,284
`BBA
`17
`34,622,352
`Hx403x
`* A single representative mate pair is shown for each rearrangement. Forward and reverse tags and their genomic coordinates correspond to F3 and R3 SOLiD mate pair
`tags. The type of rearrangement corresponds to the categories described in http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/
`documents/generaldocuments/cms_058717.pdf. AAC corresponds to mate pairs spanning deletions; codes starting with B denote incorrect strand orientation; codes
`containing a B at the middle position denote incorrect ordering; and C** corresponds to interchromosomal translocations. Primers 1 and 2 correspond to primers used for
`confirming tumor-specific rearranged sequences.
`
`LEARY ET AL. SUPPLEMENTARY MATERIAL, PAGE 3
`
`Foresight EX1026
`Foresight v Personalis
`
`

`

`
`
`Tumor-derived mate-pair library
`
`Normal tag
`libraries
`
`Single tag data
`
`Group tag data
`bins and
`generate tag
`densities
`
`Filter out normal
`variants and
`identify tumor
`specific variants
`
`High-copy amplifications
`
`Single copy changes
`
`Homozygous deletions
`
`Mate-pair data
`
`Matched
`normal library
`
`Mate-pairs associated with
`copy number alterations
`
`Interchromosomal
`translocations
`
`Matched
`normal library
`
`Candidate somatic intra-
`and inter-chromosomal
`rearrangements
`
`PCR confirmation of tumor
`and matched normal DNA
`
`Individualized PCR assay
`for plasma DNA samples
`
`
`
`
`Fig. S1. Flow chart of approach used to identify rearranged sequences
`
`LEARY ET AL., PAGE 4
`
`Foresight EX1026
`Foresight v Personalis
`
`

`

`Digital Karyotyping
`
`100
`
`80
`
`60
`
`40
`
`20
`
`0
`120,000,000
`
`125,000,000
`
`130,000,000
`
`135,000,000
`
`140,000,000
`
`Illumina SNP array
`
`012345
`
`Fold Amplification
`
`Fold Amplification
`
`120,000,000
`
`125,000,000
`
`130,000,000
`
`135,000,000
`
`140,000,000
`
`SOLiD sequencing
`
`100
`
`80
`
`60
`
`40
`
`20
`
`Fold Amplification
`
`0
`120,000,000
`
`125,000,000
`
`130,000,000
`
`135,000,000
`
`140,000,000
`
`Chromosome 8 position
`
`
`Fig. S2. Comparison of Digital Karyotyping, Illumina SNP array, and SOLiD
`sequencing results on chromosome 8.
`
`
`
`LEARY ET AL., PAGE 5
`
`Foresight EX1026
`Foresight v Personalis
`
`

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