GRR: Graphical Representation of Relationship Errors

Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7RZ, UK.
Bioinformatics (Impact Factor: 4.98). 09/2001; 17(8):742-3. DOI: 10.1093/bioinformatics/17.8.742
Source: PubMed


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

Contact: goncalo{at};

Download full-text


Available from: Stacey Cherny
  • Source
    • "All sequence variants presented herein are named according to LGI1 gene transcript variant NM 005097.2. Upon identification of a de novo variant in LGI1, the relevant trio was analysed for relationship specification using the application Graphical Representation of Relationships (Abecasis et al., 2001) after whole genome genotyping with the GeneChip Mapping 250 K Nsp Array (Affymetrix Inc., Santa Clara, Calif., USA). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Autosomal dominant lateral temporal lobe epilepsy (ADLTE) is an autosomal dominant epileptic syndrome characterized by focal seizures with auditory or aphasic symptoms. The same phenotype is also observed in a sporadic form of lateral temporal lobe epilepsy (LTLE), namely idiopathic partial epilepsy with auditory features (IPEAF). Heterozygous mutations in LGI1 account for up to 50% of ADLTE families and only rarely observed in IPEAF cases. In this study, we analysed a cohort of 26 individuals with LTLE diagnosed according to the following criteria: focal epilepsy with auditory aura and absence of cerebral lesions on brain MRI. All patients underwent clinical, neuroradiological and electroencephalography examinations and afterwards they were screened for mutations in LGI1 gene. The single LGI1 mutation identified in this study is a novel missense variant (NM_005097.2: c.1013T>C; p.Phe338Ser) observed de novo in a sporadic patient. This is the first study involving clinical analysis of a LTLE cohort from Turkey and genetic contribution of LGI1 to ADLTE phenotype. Identification of rare LGI1 gene mutations in sporadic cases supports diagnosis as ADTLE and draws attention to potential familial clustering of ADTLE in suggestive generations, which is especially important for genetic counselling.
    Full-text · Article · Jan 2016 · Epilepsy research
  • Source
    • "The class 2 isoform, which has no N-terminal domain, is also present in the human inner ear (Liang et al., 1999). Myosin XVa plays a crucial role in the graded elongation of stereocilia (Abecasis et al., 2001; Belyantseva et al., 2003; Krendel and Mooseker, 2005) and actin-organization in inner ear hair cells (Berg et al., 2001; Wang et al., 1998), which are vital for sound transduction. Myosin XVa is therefore an essential component of normal auditory function. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Mutations of MYO15A are generally known to cause severe to profound hearing loss throughout all frequencies. Here, we found two novel MYO15A mutations, c.3871C>T (p.L1291F) and c.5835T>G (p.Y1945X) in an affected individual carrying congenital profound sensorineural hearing loss (SNHL) through targeted resequencing of 134 known deafness genes. The variant, p.L1291F and p.Y1945X, resided in the myosin motor and IQ2 domains, respectively. The p.L1291F variant was predicted to affect the structure of the actin-binding site from three-dimensional protein modeling, thereby interfering with the correct interaction between actin and myosin. From the literature analysis, mutations in the N-terminal domain were more frequently associated with residual hearing at low frequencies than were mutations in the other regions of this gene. Therefore we suggest a hypothetical genotype-phenotype correlation whereby MYO15A mutations that affect domains other than the N-terminal domain, lead to profound SNHL throughout all frequencies and mutations that affect the N-terminal domain, result in residual hearing at low frequencies. This genotype-phenotype correlation suggests that preservation of residual hearing during auditory rehabilitation like cochlear implantation should be intended for those who carry mutations in the N-terminal domain and that individuals with mutations elsewhere in MYO15A require early cochlear implantation to timely initiate speech development.
    Full-text · Article · Aug 2015 · Moleculer Cells
  • Source
    • "We verified sample genders by counting heterozygous SNPs on the X chromosome. Relationship errors were evaluated with the help of the program Graphical Relationship Representation (Abecasis et al. 2001). The program PedCheck was applied to detect Mendelian errors (O'Connell and Weeks 1998) and data for SNPs with such errors were removed from the data set. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Seckel syndrome is a heterogeneous, autosomal recessive disorder marked by prenatal proportionate short stature, severe microcephaly, intellectual disability, and characteristic facial features. Here, we describe the novel homozygous splice-site mutations c.383+1G>C and c.4005-9A>G in CDK5RAP2 in two consanguineous families with Seckel syndrome. CDK5RAP2 (CEP215) encodes a centrosomal protein which is known to be essential for centrosomal cohesion and proper spindle formation and has been shown to be causally involved in autosomal recessive primary microcephaly. We establish CDK5RAP2 as a disease-causing gene for Seckel syndrome and show that loss of functional CDK5RAP2 leads to severe defects in mitosis and spindle organization, resulting in cells with abnormal nuclei and centrosomal pattern, which underlines the important role of centrosomal and mitotic proteins in the pathogenesis of the disease. Additionally, we present an intriguing case of possible digenic inheritance in Seckel syndrome: A severely affected child of nonconsanguineous German parents was found to carry heterozygous mutations in CDK5RAP2 and CEP152. This finding points toward a potential additive genetic effect of mutations in CDK5RAP2 and CEP152.
    Full-text · Article · May 2015
Show more