Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing
ABSTRACT It was previously demonstrated that splicing elements are positional dependent. We exploited this relationship between location and function by comparing positional distributions between all possible 4096 hexamers around a database of human splice sites. The distance measure used in this study found point mutations that produced higher distances disrupted splicing, whereas point mutations with smaller distances generally had no effect on splicing. Reasoning the idea that functional splicing elements have signature positional distributions around constitutively spliced exons, we introduce Spliceman-an online tool that predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation included the analyses of 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
Freely available on the web at http://fairbrother.biomed.brown.edu/spliceman/
Full-textDOI: · Available from: Eric KH Lim, Apr 28, 2014
- SourceAvailable from: Maria teresa Sanseverino
[Show abstract] [Hide abstract]
- "Primer sequences and PCR conditions are available upon request. The Spliceman web server (Lim and Fairbrother, 2012) was used to estimate the pathogenicity of the splice-site mutation identified in patient 3. "
ABSTRACT: Campomelic dysplasia (CD) is an autosomal, dominantly inherited, skeletal abnormality belonging to the subgroup of bent bone dysplasias. In addition to bowed lower limbs, CD typically includes the following: disproportionate short stature, flat face, micrognathia, cleft palate, bell-shaped thorax, and club feet. Up to three quarters of 46, XY individuals may be sex-reversed. Radiological signs include scapular and pubic hypoplasia, narrow iliac wings, spaced ischia, and bowed femora and tibiae. Lethal CD is usually due to heterozygous mutations in SOX9, a major regulator of chondrocytic development. We present a detailed clinical and molecular characterization of nine Brazilian CD patients. Infants were either stillborn (n = 2) or died shortly after birth and presented similar phenotypes. Sex-reversal was observed in one of three chromosomally male patients. Sequencing of SOX9 revealed new heterozygous mutations in seven individuals. Six patients had mutations that resulted in premature transcriptional termination, while one infant had a single-nucleotide substitution at the conserved splice-site acceptor of intron 1. No clear genotype-phenotype correlations were observed. This study highlights the diversity of SOX9 mutations leading to lethal CD, and expands the group of known genetic alterations associated with this skeletal dysplasia.Genetics and Molecular Biology 03/2015; 38(1):14-20. DOI:10.1590/S1415-475738120140147 · 0.88 Impact Factor
[Show abstract] [Hide abstract]
- "The effect of noncoding variants on splicing and positioning and strength of exonic splice enhancers was evaluated using different in silico prediction programs integrated in Alamut Software (Interactive Software). These predictions were complemented by the ASSEDA tool (http://splice.uwo.ca) and Spliceman algorithm (http://fairbrother.biomed.brown.edu/spliceman/index.cgi) [Lim and Fairbrother, 2012; Mucaki et al., 2013]. In addition, the localization of the variant in candidate regulatory regions was evaluated with RegulomeDb and datasets from the ENCODE project, and conservation was taken into account (Supp. "
ABSTRACT: Autosomal recessive Stargardt disease (STGD1) is hallmarked by a large proportion of patients with a single heterozygous causative variant in the disease gene ABCA4. Braun et al. (2013) reported deep intronic variants of ABCA4 in STGD1 patients with one coding variant, prompting us to perform an augmented screen in 131 Belgian STGD1 patients with one or no ABCA4 variant to uncover deep intronic causal ABCA4 variants. This revealed a second variant in 28.6% of cases. Twenty-six percent of these carry the same causal variant c.4539+2001G>A (V4). Haplotyping in V4 carriers showed a common region of 63 kb, suggestive of a founder mutation. Genotype-phenotype correlations suggest a moderate-to-severe impact of V4 on the STGD1 phenotype. In conclusion, V4 occurs in a high fraction of Belgian STGD1 patients and represents the first deep intronic founder mutation in ABCA4. This emphasizes the importance of augmented molecular genetic testing of ABCA4 in Belgian STGD1.This article is protected by copyright. All rights reservedHuman Mutation 01/2015; 36(1). DOI:10.1002/humu.22716 · 5.05 Impact Factor
[Show abstract] [Hide abstract]
- "Use of splice prediction tools is particularly important, as approximately 14% to 15% of all hereditary disease alleles are annotated as splicing mutations . Groups that utilized a suite of splice prediction tools, such as the maximum entropy model MAXENT , ExonScan  or positional distribution analysis [64,65], were more likely to have identified potentially pathogenic mutations, particularly in the TTN gene in Family 1. "
ABSTRACT: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data was donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.Genome biology 03/2014; 15(3):R53. DOI:10.1186/gb-2014-15-3-r53 · 10.47 Impact Factor