The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.

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Esteban Gonzalez Burchard and colleagues explore how making medical research more diverse would aid not only social justice but scientific quality and clinical effectiveness, too.

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Fragile X syndrome is caused by the transcriptional silencing of the FMR1 gene due to a trinucleotide repeat expansion. The encoded protein, Fmrp, has been found to be a nucleocytoplasmic RNA-binding protein containing both KH domains and RGG boxes that associates with polyribosomes as a ribonucleoprotein particle. RNA binding has previously been demonstrated with in vitro-translated Fmrp; however, it remained uncertain whether the selective RNA binding observed was an intrinsic property of Fmrp or required an associated protein(s). Here, baculovirus-expressed and affinity-purified FLAG-tagged murine Fmrp was shown to bind directly to both ribonucleotide homopolymers and human brain mRNA. FLAG-Fmrp exhibited selectivity for binding poly(G) > poly(U) > > poly(C) or poly(A). Moreover, purified FLAG-Fmrp bound to only a subset of brain mRNA, including the 3 untranslated regions of myelin basic protein message and its own message. Recombinant isoform 4, lacking the RGG boxes but maintaining both KH domains, was also purified and was found to only weakly interact with RNA. FLAG-purified I304N Fmrp, harboring the mutation of severe fragile X syndrome, demonstrated RNA binding, in contrast to previous suggestions. These data demonstrate the intrinsic property of Fmrp to selectively bind RNA and show FLAG-Fmrp as a suitable reagent for structural characterization and identification of cognate RNA ligands.Fragile X syndrome, a common mental retardation syndrome, results from an unstable CGG repeat expansion in the 5Ј-untranslated region of the FMR1 gene, leading to transcriptional silencing and the absence of Fmrp protein (1-4). Characterization of in vitro-translated Fmrp has shown it to be an RNA-associated protein with selectivity for homopolymer RNA and some human brain transcripts (5, 6). Fmrp contains nuclear localization and export sequences (7), as well as RGG box and KH domain motifs found in many RNA-binding proteins. The RGG box has been found in hnRNP 1 U, hnRNP A1, nucleolin, and fibrillarin and has been shown to autonomously bind homopolymeric RNA (8). However, the amino acid context surrounding the RGG box may influence the specificity and avidity of the RNA-nucleic acid interaction (8, 9). The KH domain is highly conserved in hnRNP K, yeast MER-1 splicing regulator, Sam68, and chicken vigillin, among other RNA-binding proteins (10).Fmrp expression is widespread but not ubiquitous. The majority of Fmrp is associated with polyribosomes and has been found to form an mRNP, which can be stripped from ribosomes by EDTA or RNase treatment (11)(12)(13)(14). A prevailing model suggests that Fmrp directly binds specific mRNAs in the nucleus as part of a hnRNP particle and then mediates its transport to the cytoplasm and delivery of the mRNP to the ribosome (4, 7).Homopolymer binding assays performed with in vitro-translated Fmrp and carboxyl-terminal truncated Fmrp proteins suggested a role for both the KH domain and RGG box in RNA binding (15). However, whether the observed RNA binding by Fmrp is mediated directly...

Toronto 2009 Data Release Workshop AuthorsOpen discussion of ideas and full disclosure of supporting facts provide the bedrock for scientific discourse and new developments. Traditionally, this has been formally accomplished through published papers, in which both the salient ideas and the supporting facts are combined in a single discrete 'package'. With the advent of methods for large-scale and high-throughput analyses, the generation and transmission of the underlying factual information -the data -are being transformed in an electronic process that involves submitting and retrieving information to and from scientific databases.

Summary Points Health disparities persist across race/ethnicity for the majority of Healthy People 2010 health indicators. Most physicians and scientists are informed by research extrapolated from a largely homogenous population, usually White and male. A growing proportion of Americans are not fully benefiting from clinical and biomedical advances since racial and ethnic minorities make up nearly 40% of the U.S. population. Ignoring the racial/ethnic diversity of the U.S. population is a missed scientific opportunity to fully understand the factors that lead to disease or health. U.S. biomedical research and study populations must better reflect the country's changing demographics. Adequate representation of diverse populations in scientific research is imperative as a matter of social justice, economics, and science.

In at least 98% of fragile X syndrome cases, the disease results from expansion of the CGG repeat in the 5' end of FMR1. The use of microsatellite markers in the FMR1 region has revealed a disparity of risk between haplotypes for CGG repeat expansion. Although instability appears to depend on both the haplotype and the AGG interspersion pattern of the repeat, these factors alone do not completely describe the molecular basis for the linkage disequilibrium between normal and fragile X chromosomes, in part due to instability of the marker loci themselves. In an effort to better understand the mechanism of dynamic mutagenesis, we have searched for and discovered a single nucleotide polymorphism in intron 1 of FMR1 and characterized this marker, called ATL1, in 564 normal and 152 fragile X chromosomes. The G allele of this marker is found in 40% of normal chromosomes, in contrast to 83% of fragile X chromosomes. Not only is the G allele exclusively linked to haplotypes over-represented in fragile X syndrome, but G allele chromosomes also appear to transition to instability at a higher rate on haplotypes negatively associated with risk of expansion. The two alleles of ATL1 also reveal a highly significant linkage disequilibrium between unstable chromosomes and the 5' end of the CGG repeat itself, specifically the position of the first AGG interruption. The data expand the number of haplotypes associated with FMR1 and specifically allow discrimination, by ATL1 alleles, of single haplotypes with differing predispositions to expansion. Such haplotypes should prove useful in further defining the mechanism of dynamic mutagenesis.