High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains.
High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains.
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DOI：
10.1534/g3.111.000885
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发表时间：
2011-12
期刊：
影响因子：
--
通讯作者：
Berman J
中科院分区：
文献类型：
--
作者：
Abbey D;Hickman M;Gresham D;Berman J
表型多样性可通过杂合性丢失（洛）或通过获得跨越整个染色体或较短的连续染色体片段的拷贝数变异（CNV）而迅速产生。白色念珠菌是一种杂合二倍体酵母病原体，减数分裂周期未知，纯合和非整倍体改变临床特征，包括耐药性。在这里，我们开发了一种高分辨率的微阵列，可以同时检测139，000个单核苷酸多态性（SNP）等位基因和120，000个拷贝数变异位点。白色念珠菌基因组。阵列分析的一个重要特征是基于染色体拷贝数确定SNP等位基因比率的计算管道。使用阵列和分析工具，我们构建了菌株SC 5314的单倍型图（hapmap），将SNP等位基因分配给特定的同源物，并使用它来跟踪一系列衍生实验室菌株中杂合性缺失（洛）和拷贝数变化的获得。这种高分辨率SNP/CGH微阵列和相关的hapmap促进了实验室菌株中等位基因的定相，并揭示了在实验室菌株的分子操作期间经常出现的有害基因组变化。此外，它提供了一个有用的工具，快速，高分辨率和成本效益的特点，在等位基因多样性的变化，以及在新的C染色体拷贝数的变化。白色念珠菌分离株。
Phenotypic diversity can arise rapidly through loss of heterozygosity (LOH) or by the acquisition of copy number variations (CNV) spanning whole chromosomes or shorter contiguous chromosome segments. In Candida albicans, a heterozygous diploid yeast pathogen with no known meiotic cycle, homozygosis and aneuploidy alter clinical characteristics, including drug resistance. Here, we developed a high-resolution microarray that simultaneously detects ∼39,000 single nucleotide polymorphism (SNP) alleles and ∼20,000 copy number variation loci across the C. albicans genome. An important feature of the array analysis is a computational pipeline that determines SNP allele ratios based upon chromosome copy number. Using the array and analysis tools, we constructed a haplotype map (hapmap) of strain SC5314 to assign SNP alleles to specific homologs, and we used it to follow the acquisition of loss of heterozygosity (LOH) and copy number changes in a series of derived laboratory strains. This high-resolution SNP/CGH microarray and the associated hapmap facilitated the phasing of alleles in lab strains and revealed detrimental genome changes that arose frequently during molecular manipulations of laboratory strains. Furthermore, it provided a useful tool for rapid, high-resolution, and cost-effective characterization of changes in allele diversity as well as changes in chromosome copy number in new C. albicans isolates.
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压力改变白色念珠菌中杂合性丧失的速率和类型。
影响因子：
6.4
作者：
Forche A;Abbey D;Pisithkul T;Weinzierl MA;Ringstrom T;Bruck D;Petersen K;Berman J
通讯作者：
Berman J
影响因子：
4.9
作者：
Arendrup, Maiken Cavling;Garcia-Effron, Guillermo;Bruun, Brita
通讯作者：
Bruun, Brita
DOI：
10.1073/pnas.0913883107
发表时间：
2010-01-26
影响因子：
11.1
作者：
Gresham, David;Curry, Bo;Botstein, David
通讯作者：
Botstein, David
影响因子：
9.8
作者：
Forche A;Alby K;Schaefer D;Johnson AD;Berman J;Bennett RJ
通讯作者：
Bennett RJ
影响因子：
3.3
作者：
Forche, Anja;Magee, P. T.;May, Georgiana
通讯作者：
May, Georgiana