Assessing Consistency Between Versions of Genotype-Calling Algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 Using HapMap Samples

2010 ◽  
pp. 355-360 ◽  
Author(s):  
Huixiao Hong ◽  
Lei Xu ◽  
Weida Tong
Keyword(s):  
Snp Array ◽  
Genotype Calling ◽  
Genome Wide ◽  
Calling Algorithm

scholarly journals RMR-Related MAP2K6 Gene Variation on the Risk of Overweight/Obesity in Children: A 3-Year Panel Study

2021 ◽  
Vol 11 (2) ◽  
pp. 91
Author(s):  
Myoungsook Lee ◽  
Yunkyoung Lee ◽  
Inhae Kang ◽  
Jieun Shin ◽  
Sungbin R. Sorn
Keyword(s):  
Dietary Intake ◽  
Resting Metabolic Rate ◽  
Panel Study ◽  
Snp Array ◽  
Fat Intake ◽  
Nucleotide Polymorphisms ◽  
Korean Children ◽  
Gene Variation ◽  
Genome Wide ◽  
Prevalence Of Obesity

From a pilot GWAS, seven MAP2K6 (MEK6) SNPs were significantly associated with resting metabolic rate (RMR) in obese children aged 8–9 years. The aim of this study was to investigate how RMR-linked MEK6 variation affected obesity in Korean children. With the follow-up students (77.9%) in the 3-year panel study, the changes of the variables associated with obesity (such as anthropometrics, blood biochemistry, and dietary intake) were collected. After the MEK6 SNPs were screened by Affymetrix Genome-Wide Human SNP array 6.0, the genotyping of the seven MEK6 SNPs was performed via SNaPshot assay. As the prevalence of obesity (≥85th percentile) increased from 19.4% to 25.5%, the rates of change of the variables RMR, body mass index (BMI), waist circumference (WC), systolic blood pressure (SBP), and dietary intake (energy and carbohydrate intakes) increased. The rate of overweight/obesity was higher in all mutant alleles of the seven MEK6 SNPs than it was in the matched children without mutant alleles. However, over the 3-year study period, RMRs were only significantly increased by the mutants of two single nucleotide polymorphisms (SNPs), rs996229 and rs756942, mainly related to male overweight/obesity as both WC and SBP levels increased. In the mutants of two of the SNPs, the odds ratio of overweight/obesity risk was six times higher in the highest tercile of fat intake and SBP than those of the lowest tercile. For personalized medicine to prevent pediatric obesity, SBP, WC, and dietary fat intake should be observed, particularly if boys have mutants of MEK6 SNPs, rs9916229, or rs756942.

scholarly journals Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 493
Author(s):  
Salvatore Mastrangelo ◽  
Filippo Cendron ◽  
Gianluca Sottile ◽  
Giovanni Niero ◽  
Baldassare Portolano ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Snp Array ◽  
Fixation Index ◽  
Phenotypic Traits ◽  
Plumage Color ◽  
Phenotypic Marker ◽  
Genome Wide ◽  
A Genome ◽  
The Difference ◽  
Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

scholarly journals Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e48305 ◽  
Author(s):  
Cameron Peace ◽  
Nahla Bassil ◽  
Dorrie Main ◽  
Stephen Ficklin ◽  
Umesh R. Rosyara ◽  
...  
Keyword(s):  
Sweet Cherry ◽  
Snp Array ◽  
Sour Cherry ◽  
Genome Wide ◽  
A Genome

scholarly journals Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

Genomics ◽  
2011 ◽  
Vol 98 (2) ◽  
pp. 79-89 ◽  
Author(s):  
Thomas J. Hoffmann ◽  
Mark N. Kvale ◽  
Stephanie E. Hesselson ◽  
Yiping Zhan ◽  
Christine Aquino ◽  
...  
Keyword(s):  
High Throughput ◽  
Snp Array ◽  
Tool Design ◽  
Genome Wide Association ◽  
Next Generation ◽  
Genome Wide

scholarly journals Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

2018 ◽  
Vol 50 (7) ◽  
pp. 523-531 ◽  
Author(s):  
Bingxing An ◽  
Jiangwei Xia ◽  
Tianpeng Chang ◽  
Xiaoqiao Wang ◽  
Jian Miao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Snp Array ◽  
Genome Wide Association ◽  
Heart Weight ◽  
Spleen Weight ◽  
Internal Organs ◽  
Genome Wide ◽  
A Genome

Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are of economic interest to breeders, but they are intrinsically linked to many valuable traits, such as growth, health, and productivity. Using the Illumina Bovine HD 770K SNP array, we performed a genome-wide association study for heart weight, liver weight, spleen weight, lung weight, and kidney weight in 1,217 Simmental cattle. In our research, 38 significant single nucleotide polymorphisms (SNPs) ( P < 1.49 × 10−6) were identified for five internal organ weight traits. These SNPs are within or near 13 genes, and some of them have been reported previously, including NDUFAF4, LCORL, BT.94996, SLIT2, FAM184B, LAP3, BBS12, MECOM, CD300LF, HSD17B3, TLR4, MXI1, and MB21D2. In addition, we detected four haplotype blocks on BTA6 containing 18 significant SNPs associated with spleen weight. Our results offer worthy insights into understanding the genetic mechanisms of internal organs' development, with potential application in breeding programs of Simmental beef cattle.

scholarly journals AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data

2020 ◽  
Vol 36 (15) ◽  
pp. 4369-4371
Author(s):  
Andrew Whalen ◽  
Gregor Gorjanc ◽  
John M Hickey
Keyword(s):  
Snp Array ◽  
High Accuracy ◽  
Supplementary Information ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Sib Families ◽  
Genotype By Sequencing ◽  
Low Coverage ◽  
Python Package

Abstract Summary AlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at &lt;1x coverage. Availability and implementation AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Identification of Genetic Loci Associated with Plasma Long-chain Polyunsaturated Fatty Acids in Hispanic Children (P08-129-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Ruixue Hou ◽  
Shelley Cole ◽  
Karin Haack ◽  
Sandra Laston ◽  
Nitesh Mehta ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Arachidonic Acid ◽  
Polyunsaturated Fatty Acids ◽  
Plasma Levels ◽  
Transmembrane Protein ◽  
Snp Array ◽  
Chromosome 11 ◽  
Hispanic Children ◽  
Genome Wide ◽  
Long Chain

Abstract Objectives Long-chain polyunsaturated fatty acids (LC-PUFAs) are critical to the functioning of cell membranes as important constituents of phospholipids. They also serve as precursors for prostaglandins, leukotrienes and thromboxanes which affect metabolic processes such as vasodilation, inflammation and cell proliferation. The objective of this study was to identify genes that influence the plasma levels of LC-PUFAs in Hispanic children of the Viva La Familia study. Methods Plasma levels of LC-PUFAs, including eicosapentanoic acid (EPA, 20:5, n-3), docosahexanoic acid (DHA, 22:6, n-3), docosapentanoic acid (DPA, 22:5, n-3), arachidonic acid (20: 4 n-6) and docosapentanoic acid (DPA, 22:5 n-6), were measured as part of metabolomics profiling. Genome-wide single nucleotide polymorphisms (SNP) (array and exome sequence) association analysis (GWAS) were conducted using additive genetic models adjusting for kinships. Results GWAS identified several loci on chromosome 11 with significant evidence of association with LC-PUFAs. These include association of EPA and arachidonic acid with rs174548, rs174545, rs174546, rs174550, 1rs74538 of fatty acid desaturase 1 (FADS1), rs1535, rs174577, rs174568, 174570, 2072114, 2727270 of FADS2, rs174538 of flap structure-specific endonuclease 1 (FEN1), rs174535, rs174528, rs198462, rs174532, rs149803 and rs198464 of myelin regulatory factor (MYRF) and rs102275 and rs102274 of transmembrane protein 258 (TMEM258) (P < 10−12, MAF 5–45%). Other LC-PUFAs showed suggestive evidence of association with the same SNPs. Except for FADS2 SNPs, carriers of minor alleles of all other identified SNPs had lower levels of EPA and arachidonic acid with effect sizes ranging from 5–10%. The analysis of exome variants revealed significant association of EPA with two novel SNPs in syphingomyelin synthase 2 (SGMS2) (P = 1.6 × 10−8) and synaptotagmin 7 (SYT7) (<3 × 10−15, MAF 1.5–33%). The same two loci were associated with arachidonic acid (<6 × 10−9). No significant or suggestive associations were found for other LC-PUFAs. Conclusions In summary, our genome-wide and exome sequencing results replicated the association of EPA and arachidonic acid with FADS and TMEM258 genes and identified novel loci related to neuronal signaling mainly in MYRF, SGMS2 and SYT7. Funding Sources National Institutes of Health (NIH) [DK080457], and the USDA/ARS [Cooperative Agreement 6250-51000-053].

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