使用基因组表征的遗传分析。
Genetic analysis using genomic representations.
作者信息
Lucito R, Nakimura M, West J A, Han Y, Chin K, Jensen K, McCombie R, Gray J W, Wigler M
机构信息
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
出版信息
Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4487-92. doi: 10.1073/pnas.95.8.4487.
Abstract
Analysis of the genetic changes in human tumors is often problematical because of the presence of normal stroma and the limited availability of pure tumor DNA. However, large amounts of highly reproducible "representations" of tumor and normal genomes can be made by PCR from nanogram amounts of restriction endonuclease cleaved DNA that has been ligated to oligonucleotide adaptors. We show here that representations are useful for many types of genetic analyses, including measuring relative gene copy number, loss of heterozygosity, and comparative genomic hybridization. Representations may be prepared even from sorted nuclei from fixed and archived tumor biopsies.
摘要
由于正常基质的存在以及纯肿瘤DNA的可得性有限，对人类肿瘤中的基因变化进行分析往往存在问题。然而，通过聚合酶链反应（PCR），可以从纳克量的经限制性内切酶切割并连接到寡核苷酸接头的DNA中，制备出大量高度可重复的肿瘤和正常基因组“代表性片段”。我们在此表明，这些代表性片段可用于多种类型的基因分析，包括测量相对基因拷贝数、杂合性缺失以及比较基因组杂交。甚至可以从固定存档的肿瘤活检组织中分拣出的细胞核制备代表性片段。
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本文引用的文献
1
Comparative genomic hybridization.比较基因组杂交
Curr Protoc Hum Genet. 2001 May;Chapter 4:Unit4.6. doi: 10.1002/0471142905.hg0406s06.
2
[A novel quantitative PCR with fluorogenic probe].一种新型的荧光探针定量聚合酶链反应
Rinsho Byori. 1997 Mar;45(3):218-23.
3
Development of DNA libraries specific for Chinese hamster chromosomes 3, 4, 9, 10, X, and Y by DOP-PCR.通过引物介导的PCR技术构建中国仓鼠3号、4号、9号、10号、X染色体和Y染色体特异性DNA文库。
Cytogenet Cell Genet. 1996;75(1):57-62. doi: 10.1159/000134457.
4
A novel method for real time quantitative RT-PCR.一种用于实时定量逆转录聚合酶链反应的新方法。
Genome Res. 1996 Oct;6(10):995-1001. doi: 10.1101/gr.6.10.995.
5
Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.平行人类基因组分析：基于微阵列的1000个基因的表达监测
Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10614-9. doi: 10.1073/pnas.93.20.10614.
6
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization.一种用于通过双色荧光探针杂交分析复杂DNA样本的DNA微阵列系统。
Genome Res. 1996 Jul;6(7):639-45. doi: 10.1101/gr.6.7.639.
7
[Comparative genomic hybridization in pathology. A new molecular cytogenetic method].
Pathologe. 1996 May;17(3):189-94. doi: 10.1007/s002920050154.
8
9
Genome analysis with gene expression microarrays.使用基因表达微阵列进行基因组分析。
Bioessays. 1996 May;18(5):427-31. doi: 10.1002/bies.950180513.
10
Comparative genomic hybridization: a new tool in cancer pathology.
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