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基于 CGH 微阵列的无参考偏倚拷贝数变异分析。

Reference-unbiased copy number variant analysis using CGH microarrays.

机构信息

Genomic Medicine Institute, Medical Research Center, Seoul National University, Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Korea.

出版信息

Nucleic Acids Res. 2010 Nov;38(20):e190. doi: 10.1093/nar/gkq730. Epub 2010 Aug 27.

DOI:10.1093/nar/gkq730
PMID:20802225
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2978381/
Abstract

Comparative genomic hybridization (CGH) microarrays have been used to determine copy number variations (CNVs) and their effects on complex diseases. Detection of absolute CNVs independent of genomic variants of an arbitrary reference sample has been a critical issue in CGH array experiments. Whole genome analysis using massively parallel sequencing with multiple ultra-high resolution CGH arrays provides an opportunity to catalog highly accurate genomic variants of the reference DNA (NA10851). Using information on variants, we developed a new method, the CGH array reference-free algorithm (CARA), which can determine reference-unbiased absolute CNVs from any CGH array platform. The algorithm enables the removal and rescue of false positive and false negative CNVs, respectively, which appear due to the effects of genomic variants of the reference sample in raw CGH array experiments. We found that the CARA remarkably enhanced the accuracy of CGH array in determining absolute CNVs. Our method thus provides a new approach to interpret CGH array data for personalized medicine.

摘要

比较基因组杂交 (CGH) 微阵列已被用于确定拷贝数变异 (CNVs) 及其对复杂疾病的影响。在 CGH 阵列实验中，独立于任意参考样本的基因组变异检测绝对 CNV 一直是一个关键问题。使用具有多个超高分辨率 CGH 阵列的大规模并行测序进行全基因组分析为目录高度准确的参考 DNA (NA10851) 基因组变异提供了机会。利用变异信息，我们开发了一种新方法，即 CGH 阵列无参考算法 (CARA)，它可以从任何 CGH 阵列平台确定参考无偏的绝对 CNV。该算法能够分别去除和挽救由于参考样本的基因组变异在原始 CGH 阵列实验中的影响而出现的假阳性和假阴性 CNV。我们发现，CARA 显著提高了 CGH 阵列确定绝对 CNV 的准确性。因此，我们的方法为个性化医疗提供了一种解释 CGH 阵列数据的新方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/6b1b35281489/gkq730f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/eb7dfa485fc2/gkq730f1a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/6d402b42f817/gkq730f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/b81495570a15/gkq730f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/6b1b35281489/gkq730f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/eb7dfa485fc2/gkq730f1a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/6d402b42f817/gkq730f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/b81495570a15/gkq730f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6e99/2978381/6b1b35281489/gkq730f4.jpg

相似文献

[1]
Reference-unbiased copy number variant analysis using CGH microarrays.

Nucleic Acids Res. 2010-8-27

[2]
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[3]
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[4]
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[5]
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[7]
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[8]
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[9]
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[10]
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引用本文的文献

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Stem Cell Rev Rep. 2022-1

[2]
Detection of False-Positive Deletions from the Database of Genomic Variants.

Biomed Res Int. 2019-4-4

[3]
Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children.

Biomed Res Int. 2017-3-27

[4]
Family-Based Benchmarking of Copy Number Variation Detection Software.

PLoS One. 2015-7-21

[5]
CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis.

Hum Mol Genet. 2015-3-15

[6]
tRNA gene copy number variation in humans.

Gene. 2013-12-14

[7]
Copy number variation in transcriptionally active regions of sexual and apomictic Boechera demonstrates independently derived apomictic lineages.

Plant Cell. 2013-10-29

[8]
TIARA genome database: update 2013.

Database (Oxford). 2013-3-20

[9]
Increased genome instability in human DNA segments with self-chains: homology-induced structural variations via replicative mechanisms.

Hum Mol Genet. 2013-3-7

[10]
Increased de novo copy number variants in the offspring of older males.

Transl Psychiatry. 2011-8-30

本文引用的文献

[1]
Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

Nat Genet. 2010-4-4

[2]
Fast and SNP-tolerant detection of complex variants and splicing in short reads.

Bioinformatics. 2010-2-10

[3]
Origins and functional impact of copy number variation in the human genome.

Nature. 2009-10-7

[4]
Personalized copy number and segmental duplication maps using next-generation sequencing.

Nat Genet. 2009-10

[5]
Copy number variation in human health, disease, and evolution.

Annu Rev Genomics Hum Genet. 2009

[6]
Sensitive and accurate detection of copy number variants using read depth of coverage.

Genome Res. 2009-9

[7]
A highly annotated whole-genome sequence of a Korean individual.

Nature. 2009-8-20

[8]
High-resolution mapping of copy-number alterations with massively parallel sequencing.

Nat Methods. 2009-1

[9]
The diploid genome sequence of an Asian individual.

Nature. 2008-11-6

[10]
Accurate whole human genome sequencing using reversible terminator chemistry.

Nature. 2008-11-6

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