Computational Method for Estimating DNA Copy Numbers in Normal Samples, Cancer Cell Lines, and Solid Tumors Using Array Comparative Genomic Hybridization

<div class="floats-full-page floats-full-page-other"><h2>Table 4</h2><div class="floats-full-page-caption">Frequent amplifications with CN <svg height="11.0625" id="M206" style="vertical-align:-0.30096pt" version="1.1" viewbox="0 0 22.987499 11.0625" width="22.987499" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.25,0,0,-1.25,0,11.0625)">
<g transform="translate(72,-63.15)">
<text transform="matrix(1,0,0,-1,-71.95,63.5)">
<tspan style="font-size: 12.50px; " x="0" y="0">&gt;</tspan>
<tspan style="font-size: 12.50px; " x="12.027886" y="0">9</tspan>
</text>
</g>
</g>
</svg> observed in 178 cancer cell lines. Chromosomal positions are based on March 2006 version of the UCSC Human Genome Browser. </div><div class="floats-full-page-content"><table class="table-group" id="tab4"><tr><td><table class="table"><tr><td class="thead-hr" colspan="3"><hr /></td></tr><tr class="thead"><td align="left">Region</td><td align="center">Number of observations</td><td align="center">Likely oncogene</td></tr><tr><td class="thead-hr" colspan="3"><hr /></td></tr><tr><td align="left">chr8:81240524-81974370</td><td align="center">5</td><td align="center">TPD52</td></tr><tr><td align="left">chr8:113091665-114742342</td><td align="center">10*</td><td align="center"></td></tr><tr><td align="left">chr8:128756816-128849113</td><td align="center">17</td><td align="center">MYC</td></tr><tr><td align="left">chr8:142078709-142107781</td><td align="center">7**</td><td align="center">PTK2</td></tr><tr><td align="left">chr11:68619900-69985448</td><td align="center">11</td><td align="center">CTTN, FGF4, FGF3, FGF19, ORAOV1, CCND1, MYEOV</td></tr><tr><td align="left">chr17:34999505-35264341</td><td align="center">14</td><td align="center">ERBB2</td></tr><tr><td align="left">chr17:43477124-44795465</td><td align="center">10</td><td align="center"></td></tr><tr><td align="left">chr17:55677511-61149311</td><td align="center">6</td><td align="center">APPBP2, PPM1D, BCAS3</td></tr><tr><td align="left">chr20:45554593-46054338</td><td align="center">5</td><td align="center">NCOA3</td></tr><tr><td align="left">chr20:55503756-56241375</td><td align="center">5</td><td align="center"></td></tr><tr><td align="left">chr20:57622421-58603945</td><td align="center">6</td><td align="center"></td></tr><tr><td align="left">chr22:19057363-20130955</td><td align="center">5</td><td align="center">CRKL</td></tr><tr class="table-tr"><td colspan="3"><hr class="tbody-hr" /></td></tr></table></td></tr><tr class="table-fn"><td><svg height="11.525" id="M207" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 6.4749999 11.525" width="6.4749999" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.25,0,0,-1.25,0,11.525)">
<g transform="translate(72,-62.78)">
<text transform="matrix(1,0,0,-1,-71.95,67.83)">
<tspan style="font-size: 8.75px; " x="0" y="0">∗</tspan>
</text>
</g>
</g>
</svg>One of these amplifications also involves MYC. <br /><svg height="11.525" id="M208" style="vertical-align:-0.0pt" version="1.1" viewbox="0 0 12.1875 11.525" width="12.1875" xmlns="http://www.w3.org/2000/svg">
<g transform="matrix(1.25,0,0,-1.25,0,11.525)">
<g transform="translate(72,-62.78)">
<text transform="matrix(1,0,0,-1,-71.95,67.83)">
<tspan style="font-size: 8.75px; " x="0" y="0">∗</tspan>
<tspan style="font-size: 8.75px; " x="4.5772958" y="0">∗</tspan>
</text>
</g>
</g>
</svg>Two of these amplifications also involve MYC.<br /></td></tr></table></div></div>

Table 4 | Computational Method for Estimating DNA Copy Numbers in Normal Samples, Cancer Cell Lines, and Solid Tumors Using Array Comparative Genomic Hybridization

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Table 4: Computational Method for Estimating DNA Copy Numbers in Normal Samples, Cancer Cell Lines, and Solid Tumors Using Array Comparative Genomic Hybridization

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Table 4

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