Genotyping Technologies for Genetic Research

被引：141

作者：

Ragoussis, Jiannis ^{[1
]}

机构：

[1] Univ Oxford, Genom Lab, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

来源：

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS | 2009年 / 10卷

关键词：

whole-genome association; GeneChip; Beadchip; P CNV; molecular haplotyping; GENOME-WIDE ASSOCIATION; COPY NUMBER VARIATION; SINGLE-NUCLEOTIDE POLYMORPHISMS; HIDDEN-MARKOV MODEL; STRUCTURAL VARIATION; SEQUENCE VARIANT; COST EFFICIENCY; HAPLOTYPE MAP; RISK LOCI; SNP ARRAY;

D O I：

10.1146/annurev-genom-082908-150116

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The past few years have seen enormous advances in genotyping technology, including chips that accommodate in excess of 1 million SNP assays. In addition, the cost per genotype has been driven down to levels unimagined only a few years ago. These developments have resulted in an explosion of positive whole-genome association studies and the identification of many new genes for common diseases. Here 1 review high-throughput genotyping platforms as well as other approaches for lower numbers of assays but high sample throughput, which play an important role in genotype validation and study replication. Further, the utility of SNP arrays for detecting structural variation through the development of genotyping algorithms is reviewed and methods for long-range haplotyping are presented. It is anticipated that in the future, sample throughput and cost savings will be increased further through the combination of automation, microfluidics, and nanotechnologies.

引用

页码：117 / 133

页数：17

共 104 条

[11] Advances in sequencing technology [J].

Chan, EY .

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS, 2005, 573 (1-2) :13-40

[12] Replicating genotype-phenotype associations [J].

Chanock, Stephen J. ;

Manolio, Teri ;

Boehnke, Michael ;

Boerwinkle, Eric ;

Hunter, David J. ;

Thomas, Gilles ;

Hirschhorn, Joel N. ;

Abecasis, Goncalo ;

Altshuler, David ;

Bailey-Wilson, Joan E. ;

Brooks, Lisa D. ;

Cardon, Lon R. ;

Daly, Mark ;

Donnelly, Peter ;

Fraumeni, Joseph F., Jr. ;

Freimer, Nelson B. ;

Gerhard, Daniela S. ;

Gunter, Chris ;

Guttmacher, Alan E. ;

Guyer, Mark S. ;

Harris, Emily L. ;

Hoh, Josephine ;

Hoover, Robert ;

Kong, C. Augustine ;

Merikangas, Kathleen R. ;

Morton, Cynthia C. ;

Palmer, Lyle J. ;

Phimister, Elizabeth G. ;

Rice, John P. ;

Roberts, Jerry ;

Rotimi, Charles ;

Tucker, Margaret A. ;

Vogan, Kyle J. ;

Wacholder, Sholom ;

Wijsman, Ellen M. ;

Winn, Deborah M. ;

Collins, Francis S. .

NATURE, 2007, 447 (7145) :655-660

[13] QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data [J].

Colella, Stefano ;

Yau, Christopher ;

Taylor, Jennifer M. ;

Mirza, Ghazala ;

Butler, Helen ;

Clouston, Penny ;

Bassett, Anne S. ;

Seller, Anneke ;

Holmes, Christopher C. ;

Ragoussis, Jiannis .

NUCLEIC ACIDS RESEARCH, 2007, 35 (06) :2013-2025

[14] Systematic assessment of copy number variant detection via genome-wide SNP genotyping [J].

Cooper, Gregory M. ;

Zerr, Troy ;

Kidd, Jeffrey M. ;

Eichler, Evan E. ;

Nickerson, Deborah A. .

NATURE GENETICS, 2008, 40 (10) :1199-1203

[15] SNP-specific extraction of haplotype-resolved targeted genomic regions [J].

Dapprich, Johannes ;

Ferriola, Deborah ;

Magira, Eleni E. ;

Kunkel, Mark ;

Monos, Dimitri .

NUCLEIC ACIDS RESEARCH, 2008, 36 (15)

[16] Unsupervised segmentation of continuous genomic data [J].

Day, Nathan ;

Hemmaplardh, Andrew ;

Thurman, Robert E. ;

Stamatoyannopoulos, John A. ;

Noble, William S. .

BIOINFORMATICS, 2007, 23 (11) :1424-1426

[17] Assessment of two flexible and compatible SNP genotyping platforms:: TaqMan® SNP genotyping assays and the SNPlex™ genotyping system [J].

De La Vega, FA ;

Lazaruk, KD ;

Rhodes, MD ;

Wenz, MH .

MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS, 2005, 573 (1-2) :111-135

[18] High-throughput multiplex single-nucleotide polymorphism analysis for red cell and platelet antigen genotypes [J].

Denomme, GA ;

Van Oene, M .

TRANSFUSION, 2005, 45 (05) :660-666

[19] A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia [J].

Di Bernardo, Maria Chiara ;

Crowther-Swanepoel, Dalemari ;

Broderick, Peter ;

Webb, Emily ;

Sellick, Gabrielle ;

Wild, Ruth ;

Sullivan, Kate ;

Vijayakrishnan, Jayaram ;

Wang, Yufei ;

Pittman, Alan M. ;

Sunter, Nicola J. ;

Hall, Andrew G. ;

Dyer, Martin J. S. ;

Matutes, Estella ;

Dearden, Claire ;

Mainou-Fowler, Tryfonia ;

Jackson, Graham H. ;

Summerfield, Geoffrey ;

Harris, Robert J. ;

Pettitt, Andrew R. ;

Hillmen, Peter ;

Allsup, David J. ;

Bailey, James R. ;

Pratt, Guy ;

Pepper, Chris ;

Fegan, Chris ;

Allan, James M. ;

Catovsky, Daniel ;

Houlston, Richard S. .

NATURE GENETICS, 2008, 40 (10) :1204-1210

[20] Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays [J].

Di, XJ ;

Matsuzaki, H ;

Webster, TA ;

Hubbell, E ;

Liu, GY ;

Dong, SL ;

Bartell, D ;

Huang, J ;

Chiles, R ;

Yang, G ;

Shen, MM ;

Kulp, D ;

Kennedy, GC ;

Mei, R ;

Jones, KW ;

Cawley, S .

BIOINFORMATICS, 2005, 21 (09) :1958-1963

← 1 2 3 4 5 6 7 8 9 10 →