Whole‐Genome Genotyping

Gunderson, Kevin L.; Steemers, Frank J.; Ren, Hongi; Ng, Pauline C.; Zhou, Lixin; Tsan, Chan; Chang, Weijie; Bullis, Dave; Musmacker, Joe; King, Christine; Lebruska, Lori L.; Barker, David; Oliphant, Arnold; Kuhn, Kenneth M.; Shen, Richard

doi:10.1016/s0076-6879(06)10017-8

Cited by 115 publications

(82 citation statements)

References 22 publications

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“…For sunflower, a randomly selected pair of elite alleles is expected to differ at 1 out of every 106 nucleotides (i.e., 1/0.0094 ¼ 106.4), whereas corn is expected to differ at 1 out of every 105 nucleotides (Tenaillon et al 2001), and soybean is expected to differ at 1 out of every 1,030 nucleotides . Hence, SNP frequencies seem to be sufficient in the modern sunflower cultivars for the development of SNP genotyping assays for most loci and for very high density genetic mapping using highly parallel SNP genotyping methods (Borevitz et al 2003;Hazen and Kay 2003;Winzeler et al 2003;Werner et al 2005;Gunderson et al 2006;Syvanen 2001Syvanen , 2005.…”

Section: Discussionmentioning

confidence: 99%

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Kolkman

Berry²,

Leόn³

et al. 2007

Genetics

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Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression -the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/ 62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (u ¼ 0.0094) than wild populations (u ¼ 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome ($3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

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Section: Discussionmentioning

confidence: 99%

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Kolkman

Berry²,

Leόn³

et al. 2007

Genetics

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“…Study samples, including 49 study duplicates, were plated and genotyped together with 135 HapMap controls (86 CEU; 49 YRI). Genotyping was performed using Illumina Human1Mv1_C BeadChips and the Illumina Infinium II assay protocol (39). Allele cluster definitions for each SNP were determined using Illumina BeadStudio Genotyping Module version 3.1.14 and the combined intensity data from the samples.…”

Section: Methodsmentioning

confidence: 99%

A genome-wide association study of alcohol dependence

Bierut

Agrawal

Bucholz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

410

465

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Excessive alcohol consumption is one of the leading causes of preventable death in the United States. Approximately 14% of those who use alcohol meet criteria during their lifetime for alcohol dependence, which is characterized by tolerance, withdrawal, inability to stop drinking, and continued drinking despite serious psychological or physiological problems. We explored genetic influences on alcohol dependence among 1,897 European-American and African-American subjects with alcohol dependence compared with 1,932 unrelated, alcohol-exposed, nondependent controls. Constitutional DNA of each subject was genotyped using the Illumina 1M beadchip. Fifteen SNPs yielded P < 10 −5 , but in two independent replication series, no SNP passed a replication threshold of P < 0.05. Candidate gene GABRA2 , which encodes the GABA receptor α2 subunit, was evaluated independently. Five SNPs at GABRA2 yielded nominal (uncorrected) P < 0.05, with odds ratios between 1.11 and 1.16. Further dissection of the alcoholism phenotype, to disentangle the influence of comorbid substance-use disorders, will be a next step in identifying genetic variants associated with alcohol dependence.

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“…Recalling is an extremely important step-badly called genotypes create biases that severely impair the quality control and analysis of data. The complexities of genotyping and recalling are beyond the scope of this protocol, but guidance is available from array manufacturers and as referenced in the online protocol [13].…”

Section: Pre-analytical Procedures: Genotyping Calling and Recallingmentioning

confidence: 99%

Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray

Coleman¹,

Euesden²,

Patel³

et al. 2015

Briefings in Functional Genomics

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The decreasing cost of performing genome-wide association studies has made genomics widely accessible. However, there is a paucity of guidance for best practice in conducting such analyses. For the results of a study to be valid and replicable, multiple biases must be addressed in the course of data preparation and analysis. In addition, standardizing methods across small, independent studies would increase comparability and the potential for effective meta-analysis. This article provides a discussion of important aspects of quality control, imputation and analysis of genome-wide data from a lowcoverage microarray, as well as a straight-forward guide to performing a genome-wide association study. A detailed protocol is provided online, with example scripts available at https://github.com/JoniColeman/gwas_scripts.

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Whole‐Genome Genotyping

Cited by 115 publications

References 22 publications

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

A genome-wide association study of alcohol dependence

Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray

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