GRR: Graphical Representation of Relationship Errors
ABSTRACT A graphical tool for verifying assumed relationships between individuals in genetic studies is described. GRR can detect many common errors using genotypes from many markers. AVAILABILITY: GRR is available at http://bioinformatics.well.ox.ac.uk/GRR.
Full-textDOI: · Available from: Stacey Cherny, Sep 28, 2015
- SourceAvailable from: Joseph H Lee
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- "The genotype data included ∼2.3 million SNPs from the Illumina Omni chip. Quality control was performed before imputation by checking pedigree relationships using GRR (Abecasis et al., 2001) and Loki (Heath, 1997) approaches. Single-nucleotide polymorphism (SNPs) were eliminated if presented Mendelian errors, coded allele frequency <1% or >99%, deviations from Hardy-Weinberg equilibrium (p < 1.0 × 10 −6 ), and/or low call rate (98%). "
ABSTRACT: The plasma levels of high-density lipoprotein cholesterol (HDL) have an inverse relationship to the risks of atherosclerosis and cardiovascular disease, and have also been associated with longevity. We sought to identify novel loci for HDL that could potentially provide new insights into biological regulation of HDL metabolism in healthy-longevous subjects. We performed a genome-wide association scan on HDL using a mixed model approach to account for family structure using kinship coefficients. A total of 4,114 subjects of European descent (480 families) were genotyped at ~2.3 million SNPs and ~38 million SNPs were imputed using the 1000 Genome Cosmopolitan reference panel in MACH. We identified novel variants near-NLRP1 (17p13) associated with an increase of HDL levels at genome-wide significant level (p< 5.0E-08). Additionally, several CETP (16q21) and ZNF259-APOA5-A4-C3-A1 (11q23.3) variants associated with HDL were found, replicating those previously reported in the literature. A possible regulatory variant upstream of NLRP1 that is associated with HDL in these elderly LLFS subjects may also contribute to their longevity and health. Our NLRP1 intergenic SNPs show a potential regulatory function in ENCODE; however, it is not clear whether they regulate NLRP1 or other more remote gene. NLRP1 plays an important role in the induction of apoptosis, and its inflammasome is critical for mediating innate immune responses. Nlrp1a (a mouse ortholog of human NLRP1) interacts with SREBP-1a (17p11) which has a fundamental role in lipid concentration and composition, and is involved in innate immune response in macrophages. The NLRP1 region is conserved in mammals, but also has evolved adaptively showing signals of positive selection in European populations that might confer an advantage. NLRP1 intergenic SNPs have also been associated with immunity/inflammasome disorders which highlights the biological importance of this chromosomal region.Frontiers in Genetics 06/2014; 5:159. DOI:10.3389/fgene.2014.00159
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- "Samples from the indicated individuals were subjected to a whole genome scan, using the Affymetrix GeneChip Human Mapping 250K Nsp Array. Relationship errors were evaluated with the help of the program Graphical Relationship Representation . The program PedCheck was applied to detect Mendelian errors . "
ABSTRACT: Cone-rod dystrophies (CORDs) represent a heterogeneous group of monogenic diseases leading to early impairment of vision. The majority of CORD entities show autosomal modes of inheritance and X-linked traits are comparably rare. So far, three X-chromosomal entities were reported (CORDX1, -X2 and -X3). In this study, we analysed a large family of German origin with solely affected males over three generations showing a CORDX-like phenotype. Due to the heterogeneity of cone-rod dystrophies, we performed a combined linkage and X-exome sequencing approach and identified a novel large intragenic in-frame deletion encompassing exons 18 to 26 within the CACNA1F gene. CACNA1F is described causative for CORDX3 in a single family originating from Finland and alterations in this gene have not yet been reported in other CORDX pedigrees. Our data independently confirm CACNA1F as the causative gene for CORDX3-like phenotypes and detailed clinical characterization of the family expands the knowledge about the phenotypic spectrum of deleterious CACNA1F alterations.PLoS ONE 10/2013; 8(10):e76414. DOI:10.1371/journal.pone.0076414 · 3.23 Impact Factor
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- "Because genotyping errors can lead to incorrect inferences about gene flow in pedigrees and may reduce the effectiveness of linkage analysis, strict quality controls (QC) were performed in our data. First of all, the software Graphical Representation of Relationship Errors (GRR) was used to identify errors in the structure of the pedigrees and to eliminate duplicate samples, monozygotic twins, and unrelated subjects . In one family GRR detected an inconsistency involving a mother and her two children. "
ABSTRACT: Background Congenital heart defects (CHD) is the most common cause of death from a congenital structure abnormality in newborns and is often associated with fetal loss. There are many types of CHD. Human genetic studies have identified genes that are responsible for the inheritance of a particular type of CHD and for some types of CHD previously thought to be sporadic. However, occasionally different members of the same family might have anatomically distinct defects — for instance, one member with atrial septal defect, one with tetralogy of Fallot, and one with ventricular septal defect. Our objective is to identify susceptibility loci for CHD in families affected by distinct defects. The occurrence of these apparently discordant clinical phenotypes within one family might hint at a genetic framework common to most types of CHD. Results We performed a genome-wide linkage analysis using MOD score analysis in families with diverse CHD. Significant linkage was obtained in two regions, at chromosome 15 (15q26.3, Pempirical = 0.0004) and at chromosome 18 (18q21.2, Pempirical = 0.0005). Conclusions In these two novel regions four candidate genes are located: SELS, SNRPA1, and PCSK6 on 15q26.3, and TCF4 on 18q21.2. The new loci reported here have not previously been described in connection with CHD. Although further studies in other cohorts are needed to confirm these findings, the results presented here together with recent insight into how the heart normally develops will improve the understanding of CHD.BMC Genetics 05/2013; 14(1):44. DOI:10.1186/1471-2156-14-44 · 2.40 Impact Factor