Polymorphism ratio sequencing: A new approach for single nucleotide polymorphism discovery and genotyping

被引:26
作者
Blazej, RG
Paegel, BM
Mathies, RA
机构
[1] Univ Calif Berkeley Univ Calif San Francisco, San Francisco Joint Bioengn Grad Grp, Berkeley, CA 94720 USA
[2] Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA
关键词
D O I
10.1101/gr.396203
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Polymorphism ratio sequencing (PRS) combines the advantages of high-throughput DNA sequencing with new labeling and pooling schemes to produce a powerful assay for sensitive single nucleotide polymorphism (SNP) discovery, rapid genotyping, and accurate, multiplexed allele frequency determination. In the PRS method, dideoxy-terminator extension ladders generated from a sample and reference template are labeled with different energy-transfer fluorescent dyes and coinjected into a separation capillary for comparison of relative signal intensities. We demonstrate the PRS method by screening two human mitochondrial genomes for sequence variations using a microfabricated capillary array electrophoresis device. A titration of multiplexed DNA samples places the limit of minor allele frequency detection at 5%. PRS is a sensitive and robust polymorphism detection method for the analysis of individual or multiplexed samples that is compatible with any four-color fluorescence DNA sequencer.
引用
收藏
页码:287 / 293
页数:7
相关论文
共 33 条
[1]   SEQUENCE AND ORGANIZATION OF THE HUMAN MITOCHONDRIAL GENOME [J].
ANDERSON, S ;
BANKIER, AT ;
BARRELL, BG ;
DEBRUIJN, MHL ;
COULSON, AR ;
DROUIN, J ;
EPERON, IC ;
NIERLICH, DP ;
ROE, BA ;
SANGER, F ;
SCHREIER, PH ;
SMITH, AJH ;
STADEN, R ;
YOUNG, IG .
NATURE, 1981, 290 (5806) :457-465
[2]   Association mapping of disease loci, by use of a pooled DNA genomic screen [J].
Barcellos, LF ;
Klitz, W ;
Field, LL ;
Tobias, R ;
Bowcock, AM ;
Wilson, R ;
Nelson, MP ;
Nagatomi, J ;
Thomson, G .
AMERICAN JOURNAL OF HUMAN GENETICS, 1997, 61 (03) :734-747
[3]   Energy transfer cassettes for facile labeling of sequencing and PCR primers [J].
Berti, L ;
Xie, J ;
Medintz, IL ;
Glazer, AN ;
Mathies, RA .
ANALYTICAL BIOCHEMISTRY, 2001, 292 (02) :188-197
[4]  
BROWN MD, 1992, GENETICS, V130, P163
[5]   Accessing genetic information with high-density DNA arrays [J].
Chee, M ;
Yang, R ;
Hubbell, E ;
Berno, A ;
Huang, XC ;
Stern, D ;
Winkler, J ;
Lockhart, DJ ;
Morris, MS ;
Fodor, SPA .
SCIENCE, 1996, 274 (5287) :610-614
[6]   Parameters for reliable results in genetic association studies in common disease [J].
Dahlman, I ;
Eaves, IA ;
Kosoy, R ;
Morrison, VA ;
Heward, J ;
Gough, SCL ;
Allahabadia, A ;
Franklyn, JA ;
Tuomilehto, J ;
Tuomilehto-Wolf, E ;
Cucca, F ;
Guja, C ;
Ionescu-Tirgoviste, C ;
Stevens, H ;
Carr, P ;
Nutland, S ;
McKinney, P ;
Shield, JP ;
Wang, W ;
Cordell, HJ ;
Walker, N ;
Todd, JA ;
Concannon, P .
NATURE GENETICS, 2002, 30 (02) :149-150
[7]   Facile detection of mitochondrial DNA mutations in tumors and bodily fluids [J].
Fliss, MS ;
Usadel, H ;
Cabellero, OL ;
Wu, L ;
Buta, MR ;
Eleff, SM ;
Jen, J ;
Sidransky, D .
SCIENCE, 2000, 287 (5460) :2017-2019
[8]   High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR [J].
Germer, S ;
Holland, MJ ;
Higuchi, R .
GENOME RESEARCH, 2000, 10 (02) :258-266
[9]   A software system for data analysis in automated DNA sequencing [J].
Giddings, MC ;
Severin, J ;
Westphall, M ;
Wu, JZ ;
Smith, LM .
GENOME RESEARCH, 1998, 8 (06) :644-665
[10]   Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography [J].
Giordano, M ;
Mellai, M ;
Hoogendoorn, B ;
Momigliano-Richiardi, P .
JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS, 2001, 47 (1-2) :101-110