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New developments in high-throughput resequencing and variation detection using high density microarrays

lijanan33 添加于 2015-5-23 21:49 | 1591 次阅读 | 0 个评论

作者
Warrington JA, Shah NA, Chen X, Janis M, Liu C, Kondapalli S, Reyes V, Savage MP, Zhang Z, Watts R, DeGuzman M, Berno A, Snyder J, Baid J
摘要
We developed a high-throughput method for resequencing for single nucleotide polymorphism (SNP) discovery using high-density microarrays. Over the two-year course of this study a number of improvements in sample preparation methods, hybridization assay, array handling, and analysis method were developed and implemented. DNA from 40 unrelated individuals of three different ethnic origins was amplified, labeled, and hybridized to arrays designed with probes representing genomic, coding, and regulatory regions. Protocol improvements including the use of long PCR and semi-automation reduced labeling and fragmentation costs by 33%. Automation improvements include the development of a scanner autoloader for arrays, a faster array wash station, and a linked laboratory tracking and data management system. Validation of a smaller feature size, 20 x 24 microns, allowed the simultaneous screening of 30-kb sense and 30-kb antisense DNA on each microarray, increasing throughput to 1.4 Mb per day per two laboratory personnel. More than 15,000 SNPs were identified in 8.3 Mb of the human genome using high-density resequencing and variation detection arrays (microarrays).
详细资料
- 关键词: Automation; Base Sequence; Continental Population Groups/genetics; Female; Gene Frequency; Genetic Variation/*genetics; Genome, Human; Humans; Male; Oligonucleotide Array Sequence Analysis/*instrumentation/*methods; Polymorphism, Single Nucleotide/*genetics; RNA, Messenger/analysis/genetics; Sequence Analysis, DNA/*instrumentation/*methods; Software
- 文献种类: Journal Article
- 期刊名称: Human Mutation
- 期刊缩写: Hum Mutat
- 期卷页: 2002年第19卷第4期 402-409页
- 地址: Affymetrix, Inc., Santa Clara, California, USA. Janet_Warrington@affymetrix.com
- ISBN: 1059-7794
学科领域生物医药 » 基础医学
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