Spreadsheet: 6a80d918-9900-46a2-b103-9c0d61189e62
Sheet: Table S4

Table S4: Validation of three CN-LOHs in subset of 208 samples using RT-qPCR and Sequenom genotyping
CN-LOH of 143,751 bp at 17q11.2
Sample_ID | Affymetrix 6_logratio | Affymetrix 6_CN | Affymetrix 6_hetfreq | Affymetrix 6_CN call | qPCR_assay1 | qPCR_assay 2 | qPCR_average_CN | Sequenom_hetfreq | Sequenom+qPCR_CN call | Status
C223 | -0.0652214363217353 | 1.911597205509699 | 0 | CN-LOH | 1.97 | 1.95 | 1.96 | 0 | CN-LOH | BCR
C24 | -0.017943711951375 | 1.975278788671383 | 10 | CN-LOH | 2.05 | 1.99 | 2.02 | 0 | CN-LOH | BCR
C249 | -0.00953740440309047 | 1.986821956917727 | 10 | CN-LOH | 1.83 | 2.03 | 1.93 | 0 | CN-LOH | non-BCR
C34 | 0.0349719449877738 | 2.049073798871424 | 0 | CN-LOH | 1.87 | 1.88 | 1.875 | 0 | CN-LOH | non-BCR
C369 | -0.00929679442197084 | 1.987153343001608 | 0 | CN-LOH | 1.95 | 1.96 | 1.955 | 0 | CN-LOH | non-BCR
C398 | -0.0361601486802101 | 1.95049439327446 | 20 | CN-LOH | 1.96 | 1.85 | 1.905 | 0 | CN-LOH | BCR
C440 | -0.0768253579735755 | 1.896283466461502 | 10 | CN-LOH | 1.86 | 2.05 | 1.955 | 0 | CN-LOH | non-BCR
C534 | -0.139227926731109 | 1.81600990723676 | 0 | CN-LOH | 1.9 | 1.96 | 1.93 | 0 | CN-LOH | non-BCR
C81 | 0.032844565808773 | 2.046054488196703 | 0 | CN-LOH | 2.2 | 2.31 | 2.255 | 0 | CN-LOH | BCR
MT1180 | 0.0263747405260801 | 2.036899416134187 | 10 | CN-LOH | 1.85 | 1.9 | 1.875 | 0 | CN-LOH | BCR
MT209 | -0.0334625393152236 | 1.954144918231622 | 10 | CN-LOH | 1.77 | 1.94 | 1.855 | 0 | CN-LOH | BCR
MT371 | -0.0167551822960376 | 1.976906745138804 | 0 | CN-LOH | 1.93 | 2.07 | 2 | 0 | CN-LOH | BCR
C18 | 0.00416182447224855 | 2.005777843628134 | 0 | CN-LOH | 2.21 | 2.01 | 2.11 | 0.1428571428571429 | CN-LOH | BCR
C49 | -0.0376494117081165 | 1.948481978773345 | 10 | CN-LOH | 2.17 | 2.19 | 2.18 | 0.1428571428571429 | CN-LOH | non-BCR
C56 | -0.0337365120649337 | 1.953773854625565 | 0 | CN-LOH | 2 | 2.1 | 2.05 | 0.1428571428571429 | CN-LOH | BCR
C702 | -0.0208509676158428 | 1.971302301603072 | 0 | CN-LOH | 2.08 | 2.08 | 2.08 | 0.1428571428571429 | CN-LOH | BCR
GT13 | -0.0405694544315338 | 1.944542201922411 | 0 | CN-LOH | 2.21 | 2.28 | 2.245 | 0.1428571428571429 | CN-LOH | non-BCR
MT1213 | -0.0518731623888015 | 1.929365986037265 | 10 | CN-LOH | 2.17 | 2.1 | 2.135 | 0.1428571428571429 | CN-LOH | BCR
[NAME] | 0.0148209575563669 | 2.020652108898524 | 0 | CN-LOH | 2 | 2.12 | 2.06 | 0.1428571428571429 | CN-LOH | BCR
MT452 | 0.0507294833660125 | 2.071577053757092 | 10 | CN-LOH | 2.09 | 2.05 | 2.07 | 0.1428571428571429 | CN-LOH | BCR
MT813 | -0.0885676592588424 | 1.880911984307759 | 10 | CN-LOH | 2.45 | 2.18 | 2.315 | 0.1428571428571429 | CN-LOH | BCR
C135 | -0.0314070992171764 | 1.956931016719365 | 60 | Normal | 1.81 | 1.93 | 1.87 | 0.7142857142857143 | Normal | non-BCR
C209 | 0.00436816969886422 | 2.006064745760387 | 60 | Normal | 1.86 | 1.94 | 1.9 | 0.7142857142857143 | Normal | BCR
C218 | -0.0374981388449668 | 1.948686296313053 | 70 | Normal | 2.08 | 2.02 | 2.05 | 0.7142857142857143 | Normal | non-BCR
C22 | -0.0756627395749092 | 1.897812232105562 | 70 | Normal | 2.07 | 1.82 | 1.945 | 0.7142857142857143 | Normal | non-BCR
C371 | 0.112330466508865 | 2.161945966878392 | 70 | Normal | 1.77 | 1.8 | 1.785 | 0.7142857142857143 | Normal | BCR
C388 | -0.0805327445268631 | 1.891416720331953 | 60 | Normal | 1.8 | 1.88 | 1.84 | 0.7142857142857143 | Normal | non-BCR
C448 | 0.0101893693208694 | 2.014175465067408 | 70 | Normal | 2.1 | 1.98 | 2.04 | 0.7142857142857143 | Normal | BCR
C494 | -0.0732751190662384 | 1.900955659440616 | 60 | Normal | 1.78 | 1.81 | 1.795 | 0.7142857142857143 | Normal | BCR
C498 | -0.0976109504699707 | 1.869158679184642 | 70 | Normal | 1.88 | 2.01 | 1.945 | 0.7142857142857143 | Normal | non-BCR
C571 | -0.0237589627504348 | 1.967332811328681 | 70 | Normal | 1.99 | 2.01 | 2 | 0.7142857142857143 | Normal | non-BCR
MT103 | -0.00584785034880042 | 1.991909566081382 | 70 | Normal | 1.91 | 1.84 | 1.875 | 0.7142857142857143 | Normal | non-BCR
MT121 | 0.000614324293565005 | 2.000851815650054 | 70 | Normal | 1.9 | 1.94 | 1.92 | 0.7142857142857143 | Normal | non-BCR
MT196 | -0.0554513521492481 | 1.924586678386958 | 70 | Normal | 1.74 | 1.98 | 1.86 | 0.7142857142857143 | Normal | non-BCR
[NAME] | -0.0253781713545322 | 1.965126014217473 | 70 | Normal | 1.99 | 2.01 | 2 | 0.7142857142857143 | Normal | BCR
MT606 | 0.014184545725584 | 2.019760941135512 | 60 | Normal | 1.86 | 2.05 | 1.955 | 0.7142857142857143 | Normal | non-BCR
MT79 | 0.0487515367567539 | 2.068738850848677 | 60 | Normal | 2 | 2.04 | 2.02 | 0.7142857142857143 | Normal | BCR
MT848 | -0.0107238283380866 | 1.985188732932978 | 70 | Normal | 2.12 | 2.19 | 2.155 | 0.7142857142857143 | Normal | non-BCR
CN-LOH of 57,590 bp at 11q13.1
C81 | 0.0573218017816543 | 2.081064675234512 | 0 | CN-LOH | 2.21 | NA | NA | 0 | CN-LOH | BCR
MT452 | 0.0477819666266441 | 2.067349012046028 | 0 | CN-LOH | 2.04 | NA | NA | 0 | CN-LOH | BCR
MT478 | -0.0125639559701085 | 1.982658279950449 | 0 | CN-LOH | 2 | NA | NA | 0 | CN-LOH | BCR
MT813 | -0.0421931892633438 | 1.942354875658913 | 0 | CN-LOH | 2.3 | NA | NA | 0 | CN-LOH | BCR
MT867 | -0.0178405623883008 | 1.975420021864962 | 0 | CN-LOH | 2.19 | NA | NA | 0 | CN-LOH | BCR
C108 | -0.109087824821472 | 1.854348205009968 | 0 | CN-LOH | 2.13 | NA | NA | 11.11111111111112 | CN-LOH | non-BCR
C144 | -0.0839414596557617 | 1.886953067272606 | 0 | CN-LOH | 1.94 | NA | NA | 11.11111111111112 | CN-LOH | BCR
C209 | 0.019929964095354 | 2.027820516258673 | 0 | CN-LOH | 2 | NA | NA | 11.11111111111112 | CN-LOH | BCR
C60 | -0.104127056896686 | 1.860735434839363 | 8.33333333333333 | CN-LOH | 1.97 | NA | NA | 11.11111111111112 | CN-LOH | BCR
MT689 | -0.0609061755239963 | 1.917323564480008 | 0 | CN-LOH | 2.2 | NA | NA | 11.11111111111112 | CN-LOH | BCR
GT13 | 0.0160833746194839 | 2.022421035821742 | 50 | Normal | 2.24 | NA | NA | 55.55555555555556 | Normal | non-BCR
GT2 | -0.0956237763166427 | 1.871735040065925 | 50 | Normal | 2.01 | NA | NA | 55.55555555555556 | Normal | non-BCR
GT7 | 0.0290672089904546 | 2.040704383970161 | 50 | Normal | 2.09 | NA | NA | 55.55555555555556 | Normal | non-BCR
GT74 | 0.0497021116316318 | 2.070102367815095 | 50 | Normal | 2.14 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT103 | 0.0434155315160751 | 2.061101469473537 | 50 | Normal | 1.84 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT121 | 0.115876615047454 | 2.167266572604329 | 50 | Normal | 1.89 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT209 | 0.0272322054952383 | 2.038110405972489 | 50 | Normal | 1.94 | NA | NA | 55.55555555555556 | Normal | BCR
MT237 | 0.0312682501971721 | 2.043820151618237 | 50 | Normal | 1.74 | NA | NA | 55.55555555555556 | Normal | BCR
MT275 | 0.0309737157076597 | 2.043402936570184 | 50 | Normal | 1.78 | NA | NA | 55.55555555555556 | Normal | BCR
MT289 | 0.123834751546382 | 2.179254595040886 | 50 | Normal | 1.95 | NA | NA | 55.55555555555556 | Normal | BCR
MT290 | 0.141969084739685 | 2.206820190012421 | 50 | Normal | 1.86 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT355 | 0.0786890760064125 | 2.112116006666892 | 50 | Normal | 1.86 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT371 | -0.0826796144247055 | 1.888604202299915 | 50 | Normal | 2.02 | NA | NA | 55.55555555555556 | Normal | BCR
MT379 | 0.0114737385883927 | 2.015969397158438 | 50 | Normal | 1.93 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT49 | -0.0547807365655899 | 1.925481502171737 | 50 | Normal | 1.82 | NA | NA | 55.55555555555556 | Normal | non-BCR
[NAME] | 0.0013495102757588 | 2.001871693748898 | 50 | Normal | 1.99 | NA | NA | 55.55555555555556 | Normal | BCR
MT606 | 0.0680154934525489 | 2.096547466245558 | 50 | Normal | 2.01 | NA | NA | 55.55555555555556 | Normal | non-BCR
MT66 | -0.0235508866608142 | 1.967616574998943 | 50 | Normal | 2.16 | NA | NA | 55.55555555555556 | Normal | BCR
MT94 | -0.131089091300964 | 1.826283717341835 | 50 | Normal | 1.9 | NA | NA | 55.55555555555556 | Normal | BCR
BM01-15 | 0.0597225241363048 | 2.084530562000377 | 50 | Normal | 2.11 | NA | NA | 66.66666666666667 | Normal | non-BCR
C109 | 0.135109156370162 | 2.196351800406064 | 50 | Normal | 2.09 | NA | NA | 66.66666666666667 | Normal | non-BCR
C11 | 0.0755406618118286 | 2.107511731259793 | 50 | Normal | 1.95 | NA | NA | 66.66666666666667 | Normal | BCR
C134 | 0.157393842935562 | 2.230541272309315 | 50 | Normal | 1.91 | NA | NA | 66.66666666666667 | Normal | non-BCR
CN-LOH of 91,670 bp at 6q24.1
C152 | -0.0342520140111446 | 1.953075859362324 | 0 | CN-LOH | 2.06 | NA | NA | 0 | CN-LOH | BCR
C203 | -0.0937665030360221 | 1.874146195567711 | 0 | CN-LOH | 1.95 | NA | NA | 0 | CN-LOH | BCR
C223 | 0.0173087939620018 | 2.024139601851778 | 0 | CN-LOH | 2.02 | NA | NA | 0 | CN-LOH | BCR
C24 | -0.0215633120387792 | 1.970329192569104 | 0 | CN-LOH | 1.89 | NA | NA | 0 | CN-LOH | BCR
C281 | -0.0138135403394699 | 1.980941752133939 | 0 | CN-LOH | 1.87 | NA | NA | 0 | CN-LOH | BCR
C284 | 0.0391138084232807 | 2.054964980306277 | 0 | CN-LOH | 1.95 | NA | NA | 0 | CN-LOH | non-BCR
C285 | 0.0282815191894769 | 2.039593321645082 | 0 | CN-LOH | 1.91 | NA | NA | 0 | CN-LOH | non-BCR
C293 | -0.0146695524454116 | 1.97976672407597 | 0 | CN-LOH | 1.83 | NA | NA | 0 | CN-LOH | non-BCR
C341 | -0.0175261497497558 | 1.975850580429159 | 0 | CN-LOH | 1.78 | NA | NA | 0 | CN-LOH | non-BCR
C423 | -0.0100588705390691 | 1.986103944365871 | 0 | CN-LOH | 2.01 | NA | NA | 0 | CN-LOH | BCR
C482 | -0.012781735509634 | 1.982359013780425 | 0 | CN-LOH | 2.04 | NA | NA | 0 | CN-LOH | non-BCR
C515 | -0.0883124843239784 | 1.881244697756056 | 0 | CN-LOH | 1.96 | NA | NA | 0 | CN-LOH | non-BCR
C524 | -0.0123470602557063 | 1.982956376498214 | 0 | CN-LOH | 2.07 | NA | NA | 0 | CN-LOH | BCR
C702 | -0.0123126171529293 | 1.983003718440649 | 0 | CN-LOH | 1.97 | NA | NA | 0 | CN-LOH | BCR
C81 | -0.0638230219483375 | 1.91345102834084 | 0 | CN-LOH | 2.13 | NA | NA | 0 | CN-LOH | BCR
MT101 | 0.0109535614028573 | 2.015242651569227 | 0 | CN-LOH | 1.89 | NA | NA | 0 | CN-LOH | BCR
MT155 | -0.0378194823861122 | 1.94825229744057 | 0 | CN-LOH | 1.79 | NA | NA | 0 | CN-LOH | non-BCR
MT196 | -0.0186119899153709 | 1.974364021817024 | 0 | CN-LOH | 1.85 | NA | NA | 0 | CN-LOH | non-BCR
MT289 | -0.0256753508001565 | 1.964721261377296 | 0 | CN-LOH | 2.08 | NA | NA | 0 | CN-LOH | BCR
MT370 | -0.03634013235569 | 1.950251074178762 | 0 | CN-LOH | 2.2 | NA | NA | 0 | CN-LOH | non-BCR
MT38 | 0.048755295574665 | 2.068744240776941 | 0 | CN-LOH | 1.88 | NA | NA | 0 | CN-LOH | BCR
MT380 | 0.0265573021024465 | 2.037157185854534 | 0 | CN-LOH | 1.88 | NA | NA | 0 | CN-LOH | BCR
[NAME] | -0.0490643382072448 | 1.933125982817155 | 0 | CN-LOH | 2.06 | NA | NA | 0 | CN-LOH | BCR
[NAME] | -0.0496448911726474 | 1.93234823269512 | 0 | CN-LOH | 1.92 | NA | NA | 0 | CN-LOH | BCR
MT79 | 0.0343095585703849 | 2.048133220941037 | 0 | CN-LOH | 2.05 | NA | NA | 0 | CN-LOH | BCR
MT87 | 0.0448957085609436 | 2.063217204649244 | 0 | CN-LOH | 2.22 | NA | NA | 0 | CN-LOH | BCR
C250 | -0.0914171412587165 | 1.877200641821341 | 0 | CN-LOH | 1.96 | NA | NA | 12.5 | CN-LOH | non-BCR
C339 | 0.0632107481360435 | 2.089576747711595 | 0 | CN-LOH | 1.82 | NA | NA | 12.5 | CN-LOH | BCR
PK70 | 0.020658791065216 | 2.028845198271776 | 0 | CN-LOH | 2.09 | NA | NA | 12.5 | CN-LOH | non-BCR
BM01-15 | 0.00720742251724004 | 2.010016608871259 | 60 | Normal | 2.09 | NA | NA | 62.5 | Normal | non-BCR
BM01-28 | 0.00751931266859173 | 2.010451192851505 | 60 | Normal | 2.01 | NA | NA | 62.5 | Normal | non-BCR
BM01-4 | 0.0829248055815696 | 2.11832625763304 | 60 | Normal | 2.45 | NA | NA | 62.5 | Normal | non-BCR
C11 | -0.0143169099465012 | 1.980250703848195 | 60 | Normal | 2 | NA | NA | 62.5 | Normal | BCR
C134 | -0.00828264746814966 | 1.988550709691736 | 60 | Normal | 2.15 | NA | NA | 62.5 | Normal | non-BCR
C138 | -0.0544280931353569 | 1.925952212457412 | 60 | Normal | 2.11 | NA | NA | 62.5 | Normal | non-BCR
C139 | 0.00556711386889219 | 2.007732568299458 | 50 | Normal | 1.86 | NA | NA | 62.5 | Normal | non-BCR