Dataset Information

Preparation and validation of the first WHO international genetic reference panel for Fragile X syndrome.

ABSTRACT: Fragile X syndrome is the most common inherited form of mental retardation. It is caused by expansion of a trinucleotide (CGG)n repeat sequence in the 5' untranslated region of the FMR1 gene, resulting in promoter hypermethylation and suppression of FMR1 transcription. Additionally, pre-mutation alleles in carrier males and females may result in Fragile X tremor ataxia syndrome and primary ovarian insufficiency, respectively. Fragile X is one of the most commonly requested molecular genetic tests worldwide. Quality assessment schemes have identified a wide disparity in allele sizing between laboratories. It is therefore important that clinical laboratories have access to characterized reference materials (RMs) to aid accurate allele sizing and diagnosis. With this in mind, a panel of genotyping RMs for Fragile X syndrome has been developed, which should be stable over many years and available to all diagnostic laboratories. Immortalized cell lines were produced by Epstein-Barr virus transformation of lymphocytes from consenting patients. Genomic DNA was extracted in bulk and RM aliquots were freeze-dried in glass ampoules. Twenty-one laboratories from seventeen countries participated in a collaborative study to assess their suitability. Participants evaluated the samples (blinded, in triplicate) in their routine methods alongside in-house and commercial controls. The panel of five genomic DNA samples was endorsed by the European Society of Human Genetics and approved as an International Standard by the Expert Committee on Biological Standardization at the World Health Organization.

SUBMITTER: Hawkins M

PROVIDER: S-EPMC3039502 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Preparation and validation of the first WHO international genetic reference panel for Fragile X syndrome.

Hawkins Malcolm M Boyle Jennifer J Wright Kathleen E KE Elles Rob R Ramsden Simon C SC O'Grady Anna A Sweeney Michael M Barton David E DE Burgess Trent T Moore Melanie M Burns Chris C Stacey Glyn G Gray Elaine E Metcalfe Paul P Hawkins J Ross JR

European journal of human genetics : EJHG 20100825 1

Fragile X syndrome is the most common inherited form of mental retardation. It is caused by expansion of a trinucleotide (CGG)n repeat sequence in the 5' untranslated region of the FMR1 gene, resulting in promoter hypermethylation and suppression of FMR1 transcription. Additionally, pre-mutation alleles in carrier males and females may result in Fragile X tremor ataxia syndrome and primary ovarian insufficiency, respectively. Fragile X is one of the most commonly requested molecular genetic test ...[more]

PMID: 20736975

Similar Datasets

Project description:Immunomodulatory therapeutics such as monoclonal antibodies (mAb) carry an inherent risk of undesired immune reactions. One such risk is cytokine release syndrome (CRS), a rapid systemic inflammatory response characterized by the secretion of pro-inflammatory cytokines from immune cells. It is crucial for patient safety to correctly identify potential risk of CRS prior to first-in-human dose administration. For this purpose, a variety of in vitro cytokine release assays (CRA) are routinely used as part of the preclinical safety assessment of novel therapeutic mAbs. One of the challenges for the development and comparison of CRA performance is the lack of availability of standard positive and negative control mAbs for use in assay qualification. To address this issue, the National Institute for Biological Standards and Control (NIBSC) developed a reference panel of lyophilised mAbs known to induce CRS in the clinic: human anti-CD52, mouse anti-CD3 and human superagonistic (SA) anti-CD28 mAb manufactured according to the respective published sequences of Campath-1H® (alemtuzumab, IgG1) , Orthoclone OKT-3® (muromonab, IgG2a) and TGN1412 (theralizumab, IgG4), as well as three isotype matched negative controls (human IgG1, mouse IgG2a and human IgG4, respectively). The relative capacity of these control mAbs to stimulate the release of IFN-?, IL-2, TNF-? and IL-6 in vitro was evaluated in eleven laboratories in an international collaborative study mediated through the HESI Immuno-safety Technical Committee Cytokine Release Assay Working Group. Participants tested the NIBSC mAbs in a variety of CRA platforms established at each institution. This paper presents the results from the centralised cytokine quantification on all the plasma/supernatants corresponding to the stimulation of immune cells in the different CRA platforms by a single concentration of each mAb. Each positive control mAb induced significant cytokine release in most of the tested CRA platforms. There was a high inter-laboratory variability in the levels of cytokines produced, but similar patterns of response were observed across laboratories that replicated the cytokine release patterns previously published for the respective clinical therapeutic mAbs. Therefore, the positive and negative mAbs are suitable as a reference panel for the qualification and validation of CRAs, comparison of different CRA platforms (e.g. solid vs aqueous phase), and intra- and inter-laboratory comparison of CRA performance. Thus, the use of this panel of positive and negative control mAbs will increase the confidence in the robustness of a CRA platform to identify a potential CRS risk for novel immunomodulatory therapeutic candidates.

Project description:BackgroundGenotype imputation is a cost-effective method to generate sequence-level genotypes for a large number of animals. Its application can improve the power of genomic studies, provided that the accuracy of imputation is sufficiently high. The purpose of this study was to develop an optimal strategy for genotype imputation from genotyping array data to sequence level in German warmblood horses, and to investigate the effect of different factors on the accuracy of imputation. Publicly available whole-genome sequence data from 317 horses of 46 breeds was used to conduct the analyses.ResultsDepending on the size and composition of the reference panel, the accuracy of imputation from medium marker density (60K) to sequence level using the software Beagle 5.1 ranged from 0.64 to 0.70 for horse chromosome 3. Generally, imputation accuracy increased as the size of the reference panel increased, but if genetically distant individuals were included in the panel, the accuracy dropped. Imputation was most precise when using a reference panel of multiple but related breeds and the software Beagle 5.1, which outperformed the other two tested computer programs, Impute 5 and Minimac 4. Genome-wide imputation for this scenario resulted in a mean accuracy of 0.66. Stepwise imputation from 60K to 670K markers and subsequently to sequence level did not improve the accuracy of imputation. However, imputation from higher density (670K) was considerably more accurate (about 0.90) than from medium density. Likewise, imputation in genomic regions with a low marker coverage resulted in a reduced accuracy of imputation.ConclusionsThe accuracy of imputation in horses was influenced by the size and composition of the reference panel, the marker density of the genotyping array, and the imputation software. Genotype imputation can be used to extend the limited amount of available sequence-level data from horses in order to boost the power of downstream analyses, such as genome-wide association studies, or the detection of embryonic lethal variants.

Dataset Information

Preparation and validation of the first WHO international genetic reference panel for Fragile X syndrome.

Publications

Preparation and validation of the first WHO international genetic reference panel for Fragile X syndrome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets