使用存档前列腺组织中的DNA进行高分辨率寡核苷酸比较基因组杂交。
High resolution oligonucleotide CGH using DNA from archived prostate tissue.
作者信息
Paris Pamela L, Sridharan Shivaranjani, Scheffer Alicia, Tsalenko Anya, Bruhn Laurakay, Collins Colin
机构信息
Department of Urology, Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA.
出版信息
Prostate. 2007 Sep 15;67(13):1447-55. doi: 10.1002/pros.20632.
Abstract
BACKGROUND
The current focus on biomarker discovery is a result of an improved understanding of the biological basis for carcinogenesis and advances in technology. Biomarkers can aid in diagnosis, prognosis, treatment selection, and drug development. There is an urgent need for high-resolution tools that perform well using archived tissue for biomarker discovery and tools that can translate into the clinic.
METHODS
Oligonucleotide array comparative genomic hybridization (oCGH) was compared to BAC-based aCGH using unamplified total genomic DNA from formalin fixed paraffin-embedded (FFPE) prostate tissue.
RESULTS
The copy number aberrations detected with the BAC and oligonucleotide arrays were highly correlated in cases where the arrays contained probes in similar genomic locations. The oligonucleotide array platform provided more precise mapping due to the higher density of oligonucleotide probes.
CONCLUSIONS
These results demonstrate the utility of high-resolution oligonucleotide arrays designed to use genomic DNA for CGH measurements using archived tissue samples for discovery and clinic based assays.
摘要
背景
当前对生物标志物发现的关注源于对致癌作用生物学基础理解的加深以及技术的进步。生物标志物有助于诊断、预后评估、治疗选择和药物研发。迫切需要能利用存档组织进行生物标志物发现且性能良好的高分辨率工具以及可转化应用于临床的工具。
方法
使用来自福尔马林固定石蜡包埋（FFPE）前列腺组织的未扩增全基因组DNA，将寡核苷酸阵列比较基因组杂交（oCGH）与基于BAC的aCGH进行比较。
结果
在阵列包含相似基因组位置探针的情况下，用BAC和寡核苷酸阵列检测到的拷贝数畸变高度相关。由于寡核苷酸探针密度更高，寡核苷酸阵列平台提供了更精确的定位。
结论
这些结果证明了高分辨率寡核苷酸阵列的实用性，该阵列设计用于使用基因组DNA通过存档组织样本进行CGH测量，以用于发现和基于临床的检测。
相似文献
1
High resolution oligonucleotide CGH using DNA from archived prostate tissue.使用存档前列腺组织中的DNA进行高分辨率寡核苷酸比较基因组杂交。
Prostate. 2007 Sep 15;67(13):1447-55. doi: 10.1002/pros.20632.
2
Challenges in array comparative genomic hybridization for the analysis of cancer samples.用于癌症样本分析的阵列比较基因组杂交技术面临的挑战。
Genet Med. 2007 Sep;9(9):585-95. doi: 10.1097/gim.0b013e3181461c4a.
3
High-resolution cDNA microarray CGH mapping of genomic imbalances in osteosarcoma using formalin-fixed paraffin-embedded tissue.使用福尔马林固定石蜡包埋组织对骨肉瘤基因组失衡进行高分辨率cDNA微阵列比较基因组杂交定位
Cytogenet Genome Res. 2004;107(1-2):77-82. doi: 10.1159/000079574.
4
High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.使用基因组微阵列比较基因组杂交技术对石蜡包埋和福尔马林固定的前列腺肿瘤进行高分辨率分析。
Am J Pathol. 2003 Mar;162(3):763-70. doi: 10.1016/S0002-9440(10)63873-4.
5
Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.通过定制的 BAC 和寡核苷酸阵列比较基因组杂交对新鲜冷冻和福尔马林固定石蜡包埋的神经胶质瘤进行全基因组比较：有助于分析存档的神经胶质瘤。
Acta Neuropathol. 2011 Apr;121(4):529-43. doi: 10.1007/s00401-010-0773-z. Epub 2010 Nov 16.
6
Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA.使用寡核苷酸微阵列和全基因组DNA的比较基因组杂交
Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. doi: 10.1073/pnas.0407979101. Epub 2004 Dec 10.
7
Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses.用于靶向临床阵列比较基因组杂交分析的细菌人工染色体模拟寡核苷酸阵列
Genet Med. 2008 Apr;10(4):278-89. doi: 10.1097/GIM.0b013e31816b4420.
8
1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.使用针对癌症基因分析优化的BAC克隆集进行的基于阵列的1兆碱基分辨率比较基因组杂交。
Genome Res. 2004 Jan;14(1):179-87. doi: 10.1101/gr.1847304. Epub 2003 Dec 12.
9
Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization.用于比较基因组杂交的全覆盖、高分辨率人类8号染色体q臂基因组微阵列的构建与应用
Cytometry A. 2005;63(1):10-9. doi: 10.1002/cyto.a.20102.
10
Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material.针对存档福尔马林固定石蜡包埋肿瘤材料优化的自动化阵列比较基因组杂交技术。
BMC Cancer. 2007 Mar 7;7:43. doi: 10.1186/1471-2407-7-43.
引用本文的文献
1
Single nucleus DNA sequencing of flow sorted archived frozen and formalin fixed paraffin embedded solid tumors.对经流式分选的存档冷冻和福尔马林固定石蜡包埋实体瘤进行单细胞 DNA 测序。
BMC Genomics. 2024 Oct 8;25(1):943. doi: 10.1186/s12864-024-10850-w.
2
Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?连续性进行性白斑和口腔癌中反复出现的基因组改变：口腔肿瘤发生的驱动因素？
Hum Mol Genet. 2014 May 15;23(10):2618-28. doi: 10.1093/hmg/ddt657. Epub 2014 Jan 8.
3
Deep clonal profiling of formalin fixed paraffin embedded clinical samples.对福尔马林固定石蜡包埋临床样本进行深度克隆分析。
PLoS One. 2012;7(11):e50586. doi: 10.1371/journal.pone.0050586. Epub 2012 Nov 30.
4
DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.DNA 碎片化模拟方法 (FSM) 和片段大小匹配可提高 FFPE 组织的 aCGH 性能。
PLoS One. 2012;7(6):e38881. doi: 10.1371/journal.pone.0038881. Epub 2012 Jun 15.
5
The zinc finger transcription factor ZKSCAN3 promotes prostate cancer cell migration.锌指转录因子 ZKSCAN3 促进前列腺癌细胞迁移。
Int J Biochem Cell Biol. 2012 Jul;44(7):1166-73. doi: 10.1016/j.biocel.2012.04.005. Epub 2012 Apr 16.
6
Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.原子弹幸存者乳腺癌中基因组不稳定性的意义：基于微阵列比较基因组杂交的分析。
Radiat Oncol. 2011 Dec 7;6:168. doi: 10.1186/1748-717X-6-168.
7
Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens.原发性中枢神经系统淋巴瘤：基于阵列的比较基因组杂交技术在福尔马林固定石蜡包埋肿瘤标本中的验证研究。
Clin Cancer Res. 2011 Jul 1;17(13):4245-53. doi: 10.1158/1078-0432.CCR-11-0395. Epub 2011 May 11.
8
Genome structural variation discovery and genotyping.基因组结构变异发现与基因分型。
Nat Rev Genet. 2011 May;12(5):363-76. doi: 10.1038/nrg2958. Epub 2011 Mar 1.
9
Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.通过定制的 BAC 和寡核苷酸阵列比较基因组杂交对新鲜冷冻和福尔马林固定石蜡包埋的神经胶质瘤进行全基因组比较：有助于分析存档的神经胶质瘤。
Acta Neuropathol. 2011 Apr;121(4):529-43. doi: 10.1007/s00401-010-0773-z. Epub 2010 Nov 16.
10
Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.随机 DNA 碎片化允许通过寡核苷酸阵列 CGH 在临床 FFPE 样本中检测单拷贝、单外显子拷贝数改变。
Nucleic Acids Res. 2010 Jan;38(2):e9. doi: 10.1093/nar/gkp881. Epub 2009 Oct 29.
本文引用的文献
1
Genomic profiling of hormone-naïve lymph node metastases in patients with prostate cancer.前列腺癌患者初治淋巴结转移灶的基因组分析
Neoplasia. 2006 Dec;8(12):1083-9. doi: 10.1593/neo.06421.
2
The effectiveness of screening for prostate cancer: a nested case-control study.前列腺癌筛查的有效性：一项巢式病例对照研究。
Arch Intern Med. 2006 Jan 9;166(1):38-43. doi: 10.1001/archinte.166.1.38.
3
Human and mouse oligonucleotide-based array CGH.基于寡核苷酸的人类和小鼠比较基因组杂交技术
Nucleic Acids Res. 2005 Dec 16;33(22):e192. doi: 10.1093/nar/gni191.
4
The changing face of prostate cancer.前列腺癌不断变化的面貌。
J Clin Oncol. 2005 Nov 10;23(32):8146-51. doi: 10.1200/JCO.2005.02.9751.
5
Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA.使用寡核苷酸微阵列和全基因组DNA的比较基因组杂交
Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17765-70. doi: 10.1073/pnas.0407979101. Epub 2004 Dec 10.
6
High-resolution global profiling of genomic alterations with long oligonucleotide microarray.利用长寡核苷酸微阵列对基因组改变进行高分辨率全球分析。
Cancer Res. 2004 Jul 15;64(14):4744-8. doi: 10.1158/0008-5472.CAN-04-1241.
7
High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides.使用点阵寡核苷酸的高分辨率微阵列比较基因组杂交分析
J Clin Pathol. 2004 Jun;57(6):644-6. doi: 10.1136/jcp.2003.013029.
8
Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.全基因组扫描可识别与前列腺肿瘤复发和转移相关的基因型。
Hum Mol Genet. 2004 Jul 1;13(13):1303-13. doi: 10.1093/hmg/ddh155. Epub 2004 May 11.
9
A tiling resolution DNA microarray with complete coverage of the human genome.一种具有人类基因组完全覆盖度的平铺式分辨率DNA微阵列。
Nat Genet. 2004 Mar;36(3):299-303. doi: 10.1038/ng1307. Epub 2004 Feb 15.
10
High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.使用基因组微阵列比较基因组杂交技术对石蜡包埋和福尔马林固定的前列腺肿瘤进行高分辨率分析。
Am J Pathol. 2003 Mar;162(3):763-70. doi: 10.1016/S0002-9440(10)63873-4.
Zotero 插件