Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

被引：850

作者：

Aird, Daniel ^{[1
]}

Ross, Michael G. ^{[1
]}

Chen, Wei-Sheng ^{[2
]}

Danielsson, Maxwell ^{[2
]}

Fennell, Timothy

Russ, Carsten ^{[1
]}

Jaffe, David B. ^{[1
]}

Nusbaum, Chad ^{[1
]}

Gnirke, Andreas ^{[1
]}

机构：

[1] Broad Inst MIT & Harvard, Genome Sequencing & Anal Program, Cambridge, MA 02141 USA

[2] Cambridge Rindge & Latin Sch, Cambridge, MA 02138 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 02期

关键词：

HUMAN GENOME; HIGH-DENSITY; SHORT-READ; DISCOVERY;

D O I：

10.1186/gb-2011-12-2-r18

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.

引用

页数：14

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