Identifying allelic loss and homozygous deletions in pancreatic cancer without matched normals using high-density single-nucleotide polymorphism arrays
Identifying allelic loss and homozygous deletions in pancreatic cancer without matched normals using high-density single-nucleotide polymorphism arrays
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DOI：
10.1158/0008-5472.can-06-0721
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发表时间：
2006-08-15
期刊：
影响因子：
11.2
通讯作者：
Kern, Scott E.
中科院分区：
文献类型：
--
作者：
Calhoun, Eric S.;Hucl, Tomas;Kern, Scott E.
寡核苷酸阵列和全基因组复杂性降低数据分析的最新进展现在允许同时评估数万个单核苷酸多态性，用于等位基因状态的全基因组分析。使用这些阵列，我们创建了26个胰腺癌细胞系的高分辨率等位基因图谱。杂合性的区域隐含地用于揭示等位基因丢失的区域。阵列衍生的地图进行了验证，在一个子集的7个样品中使用的317个微卫星标记的面板，显示杂合调用之间的一致性为97.1%。使用三个匹配的肿瘤/正常对来估计用于鉴定杂合性丢失的假阴性和潜在假阳性率：每个基因组分别为3.6个区域（平均最小丢失区域，720，228 bp）和2.3个区域（平均杂合空位距离，4，434，994 bp）。基因组部分等位基因丢失计算表明，等位基因丢失的累积水平范围广泛，从17.1%到79.9%的单倍体基因组长度。“NoCall”频率的区域性增加与拷贝数损失估计相结合，用于鉴定41个纯合缺失（19个首次报告），暗示胰腺癌中另外13个区域被破坏。出乎意料的是，其中23个发生在两个品系（BxPc 3和MiaPaCa 2）中，表明存在至少两种染色体不稳定性（CIN）模式的亚类，在此通过等位基因丢失和拷贝数变化（原始CIN）和那些也高度富集在纯合缺失的基因组“空穴”中（空穴CIN）来区分。这项研究提供了以前不可用的高分辨率等位基因型和缺失断点地图在广泛共享的胰腺癌细胞系，并有效地消除了需要匹配的正常组织，以确定信息位点。
Recent advances in oligonucleotide arrays and whole-genome complexity reduction data analysis now permit the evaluation of tens of thousands of single-nucleotide polymorphisms simultaneously for a genome-wide analysis of allelic status. Using these arrays, we created high-resolution allelotype maps of 26 pancreatic cancer cell lines. The areas of heterozygosity implicitly served to reveal regions of allelic loss. The array-derived maps were verified by a panel of 317 microsatellite markers used in a subset of seven samples, showing a 97.1% concordance between heterozygous calls. Three matched tumor/normal pairs were used to estimate the false-negative and potential false-positive rates for identifying loss of heterozygosity: 3.6 regions (average minimal region of loss, 720,228 bp) and 2.3 regions (average heterozygous gap distance, 4,434,994 bp) per genome, respectively. Genomic fractional allelic loss calculations showed that cumulative levels of allelic loss ranged widely from 17.1% to 79.9% of the haploid genome length. Regional increases in "NoCall" frequencies combined with copy number loss estimates were used to identify 41 homozygous deletions (19 first reports), implicating an additional 13 regions disrupted in pancreatic cancer. Unexpectedly, 23 of these occurred in just two lines (BxPc3 and MiaPaCa2), suggesting the existence of at least two subclasses of chromosomal instability (CIN) patterns, distinguished here by allelic loss and copy number changes (original CIN) and those also highly enriched in the genomic "holes" of homozygous deletions (holey CIN). This study provides previously unavailable high-resolution allelotype and deletion breakpoint maps in widely shared pancreatic cancer cell lines and effectively eliminates the need for matched normal tissue to define informative loci.