-1-NationaJ•srand
`COMPUTATION NOTEBOOK
`Department
`B10 EN 1;,r fiiETfiY Nh
`(/rp,il CJ.oo8 ...: Oct- aoo8)
`Subject
`4
`Name
`Cff{?.tS11tl/! fNv
`Address Cl-M{~ E. ?oo c c1l.ll11~f tlrB)
`43 .. 648
`N~onaFDran:~,::e:t::n:m~r: Quad., 11~3/4" X 9 1/4"
`
`under littlln horn Avery OennJson Olllce
`Product,. anll dlstrilluted by Reclfform Jn~,
`
`0
`
`STANFORD EXHIBIT 2110
`SEQUENOM v. STANFORD
`CASE IPR2013-00390
`
`

`

`Panel
`ID
`
`Sample lnf FAM-MGB
`Name
`1 S01
`2 S02
`3 S03
`4 S04
`5 S05
`6 S06
`7 S07
`a soa
`9 S09
`10 S10
`11 S11
`12 S12
`
`length
`
`~0
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`13oo
`
`62
`148
`175
`74
`56
`182
`182
`97
`1392
`
`278
`663
`784
`332
`251
`815
`815
`435
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`

`

`mum 0! mm
`3
`tr~of · IH!dt
`0
`
`v
`
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`
`5
`
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`
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`
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`
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`16D
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`

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`r •
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`

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`an
`
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`16F
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`

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`II
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`454 P25
`
`"
`..
`•
`....
`
`•
`
`•
`
`y = -5525.2K + 0 .8278
`R2 = 0 .4226
`
`y = -6181.2x + 1.0438
`R' = 0.3441
`
`-
`Ill -
`
`• <220bp
`• overall
`--Linear (<220bp)
`--Linear (overall)
`
`1.2
`
`0.8
`
`0.6
`
`0.4
`
`0
`
`0.000005
`
`0.00001
`
`0.00002
`0.000015
`gene density
`
`0 .000025
`
`0.00003
`
`0.000035
`
`1.20
`
`1.10
`
`1.00
`
`0.90
`
`0.80
`
`0.70
`
`0.60
`
`0.50
`
`0.40
`35
`
`454 P25
`
`y ,. -0.0082x + 1.3243
`R2 = 0.1378
`
`~
`
`• -
`
`• overall
`• <220bp
`--Linear {<220bp)
`--Linear (overall)
`
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`
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`
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`
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`
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`
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`
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`
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`
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`
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`
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`
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`y = · 0.0079x + 1.1014
`R'"' 0.1952
`
`37
`
`39
`
`41
`
`43
`GCcontent
`
`45
`
`47
`
`49
`
`51
`
`16G
`
`

`

`59:22, DWbm‘m
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`
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`161
`
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`1\1\e&ttt. = I =r 5~r
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`3000 r--------.--------.----.----.-------~--------~------~
`
`2500
`
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`
`1500
`
`1000
`
`500
`
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`
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`
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`
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`9 ~------~--~----~------~~--------~------~
`
`8
`
`7
`
`6
`
`5
`
`4
`
`3
`
`2
`
`1
`
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`
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`
`100
`
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`
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`
`250
`
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`
`IO
`
`41
`
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`
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`
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`
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`
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`

`2500
`2500
`
`7
`
`2000
`
`1500
`
`1000
`
`500 ‘
`
`7
`
`7
`
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`
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`
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`
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`
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`
`050
`
`I
`
`100
`
`150
`
`200
`
`250
`
`3007
`
`350 (LP)
`350 ( bf )
`
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`16N
`
`

`

`>it:~ cb s.Jh h .P\?" f1{J att r 4L-<eA LP J
`~ ~ ~lit t-o h ~ r R C u..ti~CJ..)U )
`
`700 ~------~------~------~--------~------~------~
`
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`f'IIRfAA
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`( 0 o/o {'"1(\'f
`
`600
`
`500
`
`400
`
`300
`
`200
`
`100
`
`100
`
`150
`
`200
`
`250
`
`300
`
`350
`
`160
`
`

`

`Statistics of Sequences Mapped to hg 18
`
`#- S~{Qt :: 3d3~ I
`i'ul~ 1Y14p~
`
`tnetAn : Cf(, . f~
`!h tit : ":f37·
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`
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`
`ot"lih;
`
`•
`
`10
`
`16P
`
`

`

`file:///E:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`Distribution of Reads
`
`Sample:P25 46XY
`
`Chf1
`
`chr1
`3Jr----r----r----r----~---r----~---,
`
`25
`
`20
`
`15
`
`10
`
`25
`
`20
`
`3J
`
`25
`
`20
`
`15
`
`10
`
`60
`t.t reads par 500kb
`
`chr2
`
`100
`
`120
`
`60
`t.t roads per 500kb
`
`Ill
`
`100
`
`120
`
`chr3
`
`chr coan:hnale
`
`chr2
`
`chr coordinate
`
`chr3
`
`X 10°
`
`120
`
`100
`
`Ill
`
`0 ..,
`;;
`a ,.,
`g
`i 60
`~
`
`50
`
`45
`
`40
`
`J5
`
`{l
`~
`
`'0 I
`
`~
`
`10
`
`0
`·5
`
`I of8
`
`0
`
`10
`chi coordmate
`
`15
`
`:aJ
`X 107
`
`0
`·20
`
`0
`
`till
`#reads per 5lllkb
`
`Ill
`
`100
`
`120
`
`6/16/2008 2:22 PM
`
`16Q
`
`

`

`file:///E:/Down%20Syndromc%20Diagnostics/sequencing/454/P25/ ...
`
`ch••
`M r-----~----~------~----~-----,
`
`chr•
`:11.----,----~-----r----,-----r----,----~
`
`25
`
`:II
`
`25
`
`20
`
`j
`..
`~ 15
`
`5
`
`0
`-20
`
`:II
`
`25
`
`20
`~
`a 15
`..
`
`10
`
`BO
`
`100
`
`120
`
`II' 10ado por !iOOkb
`
`chr5
`
`Ill
`# roads per 500kb
`
`BO
`
`100
`
`120
`
`chr6
`
`chr coordinate
`
`chr!i
`
`x~o'
`
`5D
`
`•5
`•o
`35
`
`~
`
`..
`~ :II
`!25
`~
`I
`
`chr coordinate
`
`chr6
`
`X 107
`
`10
`
`0
`-5
`
`5D
`.s
`
`ft
`
`35
`"" ~:II
`"0
`~25
`il-20
`~
`15
`
`10
`
`chr coordinate
`
`x107
`
`~ 0
`
`# ntads per 5DOkb
`
`BO
`
`100
`
`120
`
`2 of8
`
`16R
`
`6/16/2008 2:22 PM
`
`

`

`AO
`
`35
`
`i~
`I 15
`
`10
`
`5
`
`AS
`
`file:///E:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`18
`
`16
`
`14
`
`0
`
`a
`6
`chr coordinate
`
`12
`
`14
`
`16
`x107
`
`II roads pQr Slllkb
`
`eo
`
`100
`
`1:10
`
`chill
`~----~--~----T----r----~--~---.
`
`20
`
`M 15
`:i
`
`a .. 10
`
`till
`# reads per 500kb
`
`Ill
`
`120
`
`chr9
`15r---~----~----~--~----~----~---,
`
`t:hr caord•nale
`
`x107
`
`ill reads per !mkb
`
`1:10
`
`3 of8
`
`16S
`
`v 6/16/2008 2:22 PM
`
`

`

`file:///E:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`12
`
`chr coordtnate
`
`X 107
`
`60
`II reads per 500kb
`
`chr11
`
`100
`
`120
`
`fill
`
`!il
`
`i-40
`
`!!
`1;
`~
`~
`w
`
`-20
`
`10
`
`4 of8
`
`chr coord•nate
`
`chr12
`
`X 107
`
`11 road• per 500kb
`
`chrl2
`
`l!!
`:l5
`~
`-"
`~
`
`..
`
`6
`
`0
`
`2
`
`6
`chr coordtna1c
`
`B
`
`10
`
`12
`
`14
`x m'
`
`~
`
`fill
`# reada per 500kb
`
`Ill
`
`100
`
`120
`
`16T
`
`6/1612008 2:22 PM
`
`

`

`file:///E:/Down%20Syndrome%20Diagnosticslsequencing/454/P25/ ...
`
`thr13
`OOr---~----~-----r----,-----~--~~---,
`
`thr13
`
`45
`
`45
`
`35
`
`15
`
`10
`
`100
`
`120
`
`thrU
`14r---~----~~--r---~----~----r----,
`
`12
`
`10
`
`0
`
`100
`
`120
`
`thr15
`14r---~----~----r---~----~----r----,
`
`12
`
`~2~--~0---
`
`6
`Lhr coordinah:!
`
`a
`
`10
`
`12
`r107
`
`60
`II reads per SOOkb
`
`1CO
`
`120
`
`5 of8
`
`16U
`
`6/16/2008 2:22PM
`
`

`

`70
`
`45
`
`filc:///E:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`ch!l6
`
`thr16
`
`10
`
`chr coordinate
`
`0
`
`60
`#reads por !ilOkb
`
`00
`
`100
`
`120
`
`chr17
`12r---~----~----~--~----~--~----.
`
`10
`
`chr coordtnale
`
`X 101
`
`#reads per 500kb
`
`00
`
`100
`
`120
`
`chr1B
`12r---~----~----r---~----~--~~--.
`
`10
`
`8
`
`chr coonfrnate
`
`~20·~----':-0---
`
`#leads pur 500kb
`
`100
`
`120
`
`6 of8
`
`16V
`
`6/16/2008 2:22PM
`
`

`

`lile:///E:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`J5
`
`10
`
`45
`
`35
`
`.::30
`e;25
`'0 ,..
`u
`~20
`a.
`~ 15
`
`10
`
`5
`
`0
`
`3
`chr coord1nate
`
`5
`
`6
`
`x107
`
`#reads por 500kb
`
`100
`
`120
`
`chr20
`12r---~----~----r---~----~----r----,
`
`10
`
`j
`~ 6
`
`..
`
`chr coordmato
`
`X 107
`
`60
`# nuuJs per 500kb
`
`110
`
`100
`
`chr21
`6r---~----~y--r----~--~----~---.
`
`5
`
`chr coord1nate
`
`#reads pur 500kb
`
`100
`
`120
`
`7 of8
`
`16W
`
`6116/2008 2:22 PM
`
`

`

`file://IE:/Down%20Syndrome%20Diagnostics/sequencing/454/P25/ ...
`
`chr22
`
`chr22
`
`chr coordinate
`
`chrX
`
`•10'
`
`6
`8
`chr coordinate
`
`thrY
`
`10
`
`12
`
`u
`
`16
`•10'
`
`6
`
`j
`
`0
`-20
`
`0
`
`60
`#reads per 500kb
`
`80
`
`100
`
`120
`
`thrX
`
`60
`#I Tl!t::ldO per SCNlkb
`
`80
`
`100
`
`120
`
`thrY
`
`25
`
`20
`
`j
`i
`..
`
`10
`
`9
`
`j 6
`i 5
`..
`
`0
`
`3
`chr coordmale
`
`5
`
`X 107
`
`9li
`
`20
`
`40
`60
`If! roads p11 500kb
`
`80
`
`100
`
`120
`
`-:;
`~30
`'0
`~25
`il-20
`l!
`
`15
`
`10
`
`5
`
`0
`-1
`
`45
`
`~ 11
`i25
`[20
`;:.
`,g
`
`15
`
`10
`
`40
`
`35
`
`3:1
`
`]25
`I!
`'0 g-20
`~ i 15
`
`10
`
`5
`
`0
`-1
`
`8 of8
`
`16X
`
`6/16/2008 2:22 PM
`
`

`

`file:///C:/Documents%20and%20SettingsNann!MyD/o20Docurnents ...
`
`1'>1
`
`~~
`User: Shared
`Data File:C:\ Documents and Settings\ Yann\ My Documents\ Down Syndrome
`Diagnostics\ Real-Time PCR\ 20080417 _P25piasmadna.tad
`lXI
`Active Dye: AU Dyes
`~
`C{T) Threshold: 0 002133
`Threshold has been set via signal to noise.
`[)(
`
`..A
`
`:H ~n·
`'A
`(::.
`
`["il i Z 3 415 16l7lal9•n
`~
`II!
`lc
`.
`fD ' ~
`l! ~
`IF XI
`I ~ XX g.~
`IH
`
`"""
`
`(')(
`!'roo~
`
`Quantltation Graph
`
`C(T) Control Graph y = -3.319x + 37.01 ; rA2 = 0.989
`
`o.ozs
`
`~ 35
`
`30
`
`25
`
`\
`
`\
`
`zs
`lcyclel
`~ -- ~,..,
`flfM: ~>ys 1/f - B 1
`
`Note
`
`0
`
`l
`
`2
`IL09 Ouanthy I
`
`3
`
`4
`
`Set
`
`[
`
`cl~ "f :
`J40Ml
`~
`Pi
`~
`MM-6\Iltt.
`~rlc';lf
`1.\~"b~rt? ;
`IO"'W.S
`nU\v.~tA
`~ ~,lg.~
`flo,-(' ~.
`
`(CO..w't'l)
`
`I of 1
`
`Dye Type Efficiency C(t) copies Avg
`C(t)
`N/A N/A
`N/A
`HEX Replicate N/A
`NTC
`N/A
`FAM Replicate N/A
`N/A NIA
`NTC
`P25 original HEX Replicate 4418 33.62 10.55 33.67
`35.94
`31 .59 35.95 NIA
`P25 original FAM Replicate
`cleanup HEX Replicate N/A
`P25
`cleanup FAM Replicate N/A
`P25
`2465 24.38 0.11
`24.53 7212 24.53
`HEX Replicate 47.71
`dil1
`22.81
`012
`22.91
`FAM Replicate 47.25 22.91 N/A
`23.08
`drl1
`26 91
`26.78 0.06
`26.84 721
`2684
`HEX Replicate 56.21
`dil2
`25.21
`24.82
`FAM Replicate 39.33 25.03 N/A
`016
`25.03
`dil2
`31.49
`30.65 0.35
`HEX Replicate 42.23 31.13 72
`31 .13
`dli3
`29.49
`29.03 0.21
`FAM Replicate 40.02 29.34 N/A 2934
`di13
`35.40
`34.26
`34.78
`0.47
`HEX Replicate 41.58 34.75 7.2
`dil4
`33.12
`32.85 0.11
`FAM Replicate 47.89 32.97 N/A 3297
`dil4
`37.73 3512 1.31
`HEX Replicate 49.25 36.99 0.72 36.43
`dil5
`36.51
`FAM Replicate 31 .06 36.49 N/A
`36.75
`36.37
`0.17
`dll 5
`~
`l..uQ cf ~NA f'D r p@..
`lO ~i)c
`+"~ll'(rute'
`0:~
`FAM \ ~n~ .:"[
`o.~
`ftObG
`([OA.AM) \.
`o.~
`~G>C { pn~"k
`o. ~
`o.~
`p,M,,.
`().}
`I
`~p(Ct~4
`--L
`t-ho
`~
`
`Max
`C(t)
`N/A
`N/A
`34.22
`36.27
`
`Min
`C(t)
`N/A
`N/A
`33.21
`35.62
`
`N/A NIA
`
`N/A
`
`N/A
`
`N/A
`
`C(t)
`so
`N/A
`NIA
`0.42
`0.27
`
`N/A
`
`N/A N/A
`
`NIA
`
`N/A
`
`N/A
`
`N/A
`
`Avg
`copies
`N/A
`N/A
`o.iO.&
`NIA
`
`Max
`copies
`N/A
`N/A
`13.93
`NIA
`
`N/A
`
`N/A
`
`N/A
`
`7212
`N/A
`721
`NIA
`72
`N/A
`72
`N/A
`0.72
`N/A
`
`N/A
`
`7212
`NIA
`721
`NIA
`72
`NIA
`72
`NIA
`0.72
`N/A
`
`Min
`copies
`N/A
`N/A
`6.926
`N/A
`
`N/A
`
`NIA
`
`7212
`NIA
`721
`N/A
`72
`NIA
`7.2
`N/A
`0.72
`N/A
`
`copies
`SD
`N/A
`N/A
`2.87
`NIA
`
`N/A
`
`N/A
`
`0
`NIA
`0
`NIA
`0
`N/A
`0
`N/A
`0
`N/A
`
`fJ.S
`1 t0. b c.o\'~Q s I A.L€
`~~ o~ rbod
`i.:e. lbq~ copie.s
`} ~ ·
`5": .b n~
`if. qo ll~ fbr %'f. (r'L.~ M ·
`
`l
`
`