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maf-minor-allele-frequency

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Data handling, quality checks, and exclusions during MR. *MAGIC and DIAGRAM...
Published: 28 August 2017
Figure 2 Data handling, quality checks, and exclusions during MR. *MAGIC and DIAGRAM sets are imputed based on HapMap2 and therefore do not include indels. MAF, minor allele frequency; T2DM, type 2 diabetes. Figure 2. Data handling, quality checks, and exclusions during MR. *MAGIC and DIAGRAM se... More
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Contribution and <span class="search-highlight">frequency</span> of risk <span class="search-highlight">alleles</span> dictate mapping strategies. Link...
Published: 01 July 2010
FIG. 1. Contribution and frequency of risk alleles dictate mapping strategies. Linkage studies have demonstrated that multifactorial disorders, including type 1 diabetes, cannot be explained by a limited number of rare variants with large effects, and GWA studies have shown that they cannot be exp... More
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Structure of the <em>GHSR</em> 1a isoform and position of the 10 se...
Published: 01 January 2005
FIG. 1. Structure of the GHSR 1a isoform and position of the 10 selected SNPs covering the GHSR gene region including general SNP characteristics as given in the dbSNP database and the Golden Path Genome Browser (July 2003 release). There is no publicly available SNP in exon 2. *SNPs are shown as rs numbers from the dbSNP database. †MAF, minor allele frequency. FIG. 1. Structure of the GHSR 1a isoform and position of the 10 selected SNPs covering the GHSR gene region including general SNP characteristics as given in the dbSNP database and the Golden Path Genome Browser (July 2003 release). There is no publicly available SNP in exon 2. *SNPs are shown as rs numbers from the dbSNP database. †MAF, minor allele frequency. More
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Genetic structure of the <em>ATGL</em> gene, including the genotype...
Published: 01 May 2006
FIG. 1. Genetic structure of the ATGL gene, including the genotyped polymorphism. A: Schematic of the ATGL gene with the sequenced region (shown as thick line with two gaps) as well as the SNP locations. The SNPs are provided with position names as well as rs numbers. SNPs marked with an asterisk are causing a nonsynonymous amino acid exchange: SNP 4 = L219F, SNP 7 = N252K, and SNP 10 = P481L. MAF, minor allele frequency. B: The shade of the diamonds represents the pairwise r2 between the two SNPs defined by the top left and the top right sides of the diamond. Shading represents magnitude and significance of the pairwise r2, with black reflecting high r2 (>0.8), dark gray indicating r2 between 0.8 and 0.6, moderate gray an r2 between 0.6 and 0.4, light gray an r2 between 0.4 and 0.2, and white reflecting low r2 (<0.2). FIG. 1. Genetic structure of the ATGL gene, including the genotyped polymorphism. A: Schematic of the ATGL gene with the sequenced region (shown as thick line with two gaps) as well as the SNP locations. The SNPs are provided with position names as well as rs numbers. SNPs marked with an asterisk are causing a nonsynonymous amino acid exchange: SNP 4 = L219F, SNP 7 = N252K, and SNP 10 = P481L. MAF, minor allele frequency. B: The shade of the diamonds represents the pairwise r2 between the two SNPs defined by the top left and the top right sides of the diamond. Shading represents magnitude and significance of the pairwise r2, with black reflecting high r2 (>0.8), dark gray indicating r2 between 0.8 and 0.6, moderate gray an r2 between 0.6 and 0.4, light gray an r2 between 0.4 and 0.2, and white reflecting low r2 (<0.2). More
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Linkage disequilibrium statistics (D′, <em>r</em><sup>2</sup>) amon...
Published: 01 July 2006
FIG. 1. Linkage disequilibrium statistics (D′, r2) among the SNPs and the minor allele frequency (MAF) of SNPs of PPARD. SNPs are coded by National Center for Biotechnology Information’s dbSNP accession numbers. FIG. 1. Linkage disequilibrium statistics (D′, r2) among the SNPs and the minor allele frequency (MAF) of SNPs of PPARD. SNPs are coded by National Center for Biotechnology Information’s dbSNP accession numbers. More
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The statistical power of this study to detect genetic associations with dif...
Published: 01 July 2008
FIG. 1. The statistical power of this study to detect genetic associations with different minor allele frequencies (MAFs) at α = 0.05 level. The PPARG SNP rs2197423 has an MAF = 0.116; the CDKN2A/B SNP rs2383208 has an MAF = 0.176; the SLC30A8 SNP rs13266634 and the CDKAL1 SNP rs7756992 have similar MAFs, average 0.294; the other nine SNPs, rs4402960, rs4712523, rs5215, rs10012946, rs7923837, rs1412829, rs1111875, rs7501939, and rs8050136, have similar MAFs, average 0.364. x-axis, OR value; y-axis, statistical power. FIG. 1. The statistical power of this study to detect genetic associations with different minor allele frequencies (MAFs) at α = 0.05 level. The PPARG SNP rs2197423 has an MAF = 0.116; the CDKN2A/B SNP rs2383208 has an MAF = 0.176; the SLC30A8 SNP rs13266634 and the CDKAL1 SNP rs7756992 have similar MAFs, average 0.294; the other nine SNPs, rs4402960, rs4712523, rs5215, rs10012946, rs7923837, rs1412829, rs1111875, rs7501939, and rs8050136, have similar MAFs, average 0.364. x-axis, OR value; y-axis, statistical power. More
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Schematic map of the 83.7-kb genomic region showing the approximate locatio...
Published: 01 April 2007
FIG. 1. Schematic map of the 83.7-kb genomic region showing the approximate location of 11 SNPs genotyped in PPARA. A: PPARA messenger RNA. Arrows indicate the start and finish sites of translation (modified from 18 ). B: LD statistics (r2) among the SNPs of PPARA and the minor allele frequency (MAF). SNPs are coded by National Centre for Biotechnology Information dbSNP accession numbers. FIG. 1. Schematic map of the 83.7-kb genomic region showing the approximate location of 11 SNPs genotyped in PPARA. A: PPARA messenger RNA. Arrows indicate the start and finish sites of translation (modified from 18). B: LD statistics (r2) among the SNPs of PPARA and the minor allele frequency (MAF). SNPs are coded by National Centre for Biotechnology Information dbSNP accession numbers. More
Journal Articles
Journal: Diabetes
Diabetes 2004;53(11):3013–3019
Published: 01 November 2004
..., minor allele frequency. TABLE 2 Association analysis of PTPN1 SNPs with fasting glucose (milligrams per deciliter) SNP Alleles MAF Phenotypic mean ± SD P 1/1 1/2 2/2 rs2904268 G/C 0.18 93.72 ± 9.85 92.96 ± 9.42 91.37 ± 9.17 0.719 rs803742 C/T 0.32...
Includes: Supplementary data
Meeting Abstracts
Journal: Diabetes
Diabetes 2020;69(Supplement_1):242-OR
Published: 01 June 2020
... variants with allele count > 5 by minor allele frequency (MAF): rare variants [MAF<0.1%], and annotation: all non-coding variants, and non-coding variants in pancreatic islets regulatory regions. We further partitioned variants by linkage disequilibrium properties to reduce estimate bias. One...
Journal Articles
Journal: Diabetes
Diabetes 2020;69(4):784–795
Published: 31 January 2020
... Richards Most replicated genetic determinants for type 1 diabetes are common (minor allele frequency [MAF] >5%). We aimed to identify novel rare or low-frequency (MAF <5%) single nucleotide polymorphisms with large effects on risk of type 1 diabetes. We undertook deep imputation of genotyped data...
Includes: Supplementary data
Meeting Abstracts
Journal: Diabetes
Diabetes 2021;70(Supplement_1):245-OR
Published: 01 June 2021
... analysis includes 18,294 individuals (7,556 cases and 10,738 controls) with genotyping array and whole-exome sequencing data. We were able to impute 38M high-quality variants (rsq>0.8) with TOPMed (5M with minor allele frequency [MAF] 0.001-0.0005) compared to 16M with 1000G Phase 3 panel (1.6M...
Meeting Abstracts
Journal: Diabetes
Diabetes 2019;68(Supplement_1):2116-P
Published: 01 June 2019
... in this cohort, those that were exonic or splicing, have minor allele frequency (MAF) ≤0.05, predicted to be damaging (CADD score ≥15), and located in genes expressed in hypothalamus were selected for analysis. These selection criteria resulted in 94,444 SNVs, and odds ratios were calculated for them...
Meeting Abstracts
Journal: Diabetes
Diabetes 2018;67(Supplement_1):1712-P
Published: 01 July 2018
... Heart Study and Amish; 2562 African ancestry (AA): Jackson Heart Study] using age and sex-adjusted linear mixed-effect regression, and meta-analyzed cohort-specific results. We used Cochran heterogeneity and Fisher’s exact tests to assess ancestral differences in effect and Minor Allele Frequency (MAF...
Journal Articles
Journal: Diabetes
Diabetes 2011;60(2):662–668
Published: 21 January 2011
...-quality score (rsq-hat ≥0.3) using the software MACH (www.sph.umich.edu/csg/abecasis) ( 24 ). The imputed most likely genotypes were then used for subsequent association tests. Four common SNPs identified from direct sequence analysis had minor allele frequencies (MAF) ≥0.05 and failed assay design...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2019;68(12):2327–2336
Published: 19 September 2019
... between the natural logarithm–transformed insulin concentrations of the postprandial state at 30 min after a meal challenge and the fasting state (Δinsulin). After Bonferroni correction, rs505922 (β: −6.5% [minor allele frequency (MAF) 0.32, P = 3.3 × 10−8]) located in the ABO...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2007;56(5):1460–1467
Published: 01 May 2007
..., and the third was found be associated with type 2 diabetes in further samples. MAF, minor allele frequency. TABLE 4 Association of NPY2R SNPs to BMI analyzed as a continuous trait FHS men Scandinavian men Unrelated men combined Scandinavian trios MAF P * β...
Includes: Supplementary data
Meeting Abstracts
Journal: Diabetes
Diabetes 2020;69(Supplement_1):239-OR
Published: 01 June 2020
... to variants with minor allele frequency (MAF) >1%. GWAS were conducted in 72,244 participants (22,045 cases) of European ancestry [EUR] and 24,162 (10,441 cases) of African ancestry [AFR]), adjusted for age at MVP enrollment, sex, and 10 genetic principal components. We identified a single locus associated...
Meeting Abstracts
Journal: Diabetes
Diabetes 2020;69(Supplement_1):198-LB
Published: 01 June 2020
..., and HbA1c. rs200812701 is rare (minor allele frequency [MAF]<0.1%) in all populations except Native Hawaiians (MAF=25%) and Asians (MAF=8%). Many of these loci are known for one trait, but the identification of shared genetic susceptibility for these loci is novel. For example, the PEPD locus...
Journal Articles
Journal: Diabetes
Diabetes 2010;59(3):741–746
Published: 12 December 2009
... in the cumulative frequency of 82 rare (minor allele frequency [MAF] <0.01) nonsynonymous variants between type 2 diabetic case and control subjects (P = 0.79). Two intermediate frequency (MAF 0.01–0.05) nonsynonymous changes also showed no statistical association with type 2 diabetes. CONCLUSIONS...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2022;71(2):359–364
Published: 09 November 2021
... near GCK (rs3757840, βmeta = 0.0062; minor allele frequency [MAF] = 0.49; Pmeta = 3.66 × 10−8) and confirmed the association near RCN3 (rs113886122, βmeta = 0.0134; MAF = 0.17; Pmeta = 5.71 × 10−18...