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1
Diversity of human copy number variation and multicopy genes.人类拷贝数变异和多拷贝基因的多样性。
Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.
2
Exome sequencing: the sweet spot before whole genomes.外显子组测序：全基因组测序前的甜蜜点。
Hum Mol Genet. 2010 Oct 15;19(R2):R145-51. doi: 10.1093/hmg/ddq333. Epub 2010 Aug 12.
3
Massively parallel sequencing of exons on the X chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate.对 X 染色体外显子进行大规模平行测序，确定 RBM10 是导致综合征型腭裂的致病基因。
Am J Hum Genet. 2010 May 14;86(5):743-8. doi: 10.1016/j.ajhg.2010.04.007. Epub 2010 May 6.
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Copy number variation and human genome maps.拷贝数变异与人类基因组图谱。
Nat Genet. 2010 May;42(5):365-6. doi: 10.1038/ng0510-365.
5
Mutation spectrum revealed by breakpoint sequencing of human germline CNVs.人类种系 CNV 断点测序揭示的突变谱。
Nat Genet. 2010 May;42(5):385-91. doi: 10.1038/ng.564. Epub 2010 Apr 4.
6
Next generation sequencing in research and diagnostics of ocular birth defects.下一代测序在眼部出生缺陷的研究和诊断中的应用。
Mol Genet Metab. 2010 Jun;100(2):184-92. doi: 10.1016/j.ymgme.2010.03.004. Epub 2010 Mar 15.
7
Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79.靶向捕获和下一代测序鉴定出 C9orf75，其编码蛋白为 taperin，是常染色体隐性遗传非综合征型耳聋 DFNB79 的致病基因。
Am J Hum Genet. 2010 Mar 12;86(3):378-88. doi: 10.1016/j.ajhg.2010.01.030. Epub 2010 Feb 18.
8
Massively parallel sequencing of ataxia genes after array-based enrichment.基于微阵列富集的共济失调基因的大规模平行测序。
Hum Mutat. 2010 Apr;31(4):494-9. doi: 10.1002/humu.21221.
9
U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line.U87MG 解码：一条染色体结构异常的人类癌细胞系的基因组序列。
PLoS Genet. 2010 Jan 29;6(1):e1000832. doi: 10.1371/journal.pgen.1000832.
10
Structural variation in the human genome and its role in disease.人类基因组中的结构变异及其在疾病中的作用。
Annu Rev Med. 2010;61:437-55. doi: 10.1146/annurev-med-100708-204735.

基于外显子组测序的拷贝数变异和杂合性丢失检测：ExomeCNV。

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.

机构信息

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

出版信息

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.

DOI:10.1093/bioinformatics/btr462
PMID:21828086
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3179661/
Abstract

MOTIVATION

The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.

RESULTS

We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design.

AVAILABILITY

CRAN package 'ExomeCNV'.

CONTACT

fsathira@fas.harvard.edu; snelson@ucla.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

从外显子测序数据中检测拷贝数变异 (CNV) 和杂合性丢失 (LOH) 的能力扩展了这种强大方法的实用性，该方法主要用于点突变或小插入/缺失检测。

结果

我们提出了 ExomeCNV，这是一种使用覆盖深度和 B 等位基因频率从映射的短序列读取中检测 CNV 和 LOH 的统计方法，我们评估了该方法的功效和混杂变量的影响。我们将我们的方法应用于癌症外显子重测序数据集。正如预期的那样，准确性和分辨率取决于覆盖深度和捕获探针设计。

可用性

CRAN 软件包“ExomeCNV”。

联系人

fsathira@fas.harvard.edu; snelson@ucla.edu

补充信息

补充数据可在 Bioinformatics 在线获得。