Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5′ splice‐site disruption
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383 citations
Cites background from "Extensive in silico analysis of NF1..."
...According to Wimmer et al. (2007), splicing mutations can be briefly divided into five categories: (1) splicing mutations within the canonical splice sites leading to whole exon skipping, (2) deep intronic variants creating new splice sites resulting in the inclusion of cryptic exons, (3) exonic…...
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...According to Wimmer et al. (2007), splicing mutations can be briefly divided into five categories that are further briefly discussed (Fig....
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...Second, the presence of exonic changes that cause the disruption of exonic splicing enhancers may also lead to the entire exon skipping (so-called type V splicing mutation) (Wimmer et al. 2007)....
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284 citations
Cites background from "Extensive in silico analysis of NF1..."
...Famous examples are the neurofibromatosis type 1 gene and the ataxia telangiectasia mutated gene, where a significant number of mutations lead to exon skipping (Teraoka et al. 1999; Ars et al. 2000; Wimmer et al. 2007)....
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228 citations
Cites background or methods from "Extensive in silico analysis of NF1..."
...One million cells were suspended in 10 ml, treated with puromycin (10 mg/ml) for 5 h the following day [Dehainault et al., 2007; Wimmer et al., 2007]; (3) RNA was extracted from PAXgene blood RNA tubes (allowing RNA stabilization at collection) using the dedicated kit and according to the manufacturer’s protocols (Preanalytix, Qiagen, Hombreachtikon, Switzerland); and (4) RNA was extracted from stimulated T lymphocytes (see supplementary data) and RNA was analyzed as described in the supplementary section....
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...This absence of interpretation guidelines can be explained by the small-scale series published to date [Holla et al., 2009; Houdayer et al., 2008; Thery et al., 2011; Vreeswijk et al., 2009; Whiley et al., 2011; Wimmer et al., 2007]....
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...One million cells were suspended in 10 ml, treated with puromycin (10 mg/ml) for 5 h the following day [Dehainault et al., 2007; Wimmer et al., 2007]; (3) RNA was extracted from PAXgene blood RNA tubes (allowing RNA stabilization at collection) using the dedicated kit and according to the…...
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184 citations
Cites result from "Extensive in silico analysis of NF1..."
...Predicting the precise consequence of the mutation is far more difficult, although recent analyses have shown some progress (Wimmer et al. 2007; Divina et al. 2009)....
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161 citations
References
83,420 citations
"Extensive in silico analysis of NF1..." refers methods in this paper
...To detect putative false positives due to multiple testing, the false discovery rate (FDR) controlling procedure [Benjamini and Hochberg, 1995] was applied on the P-values obtained from three test groups, separately....
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5,209 citations
"Extensive in silico analysis of NF1..." refers background in this paper
..., 2005] and mutations 1466A4G and 57491332A4G, found so far 11 and five times, respectively, may result from spontaneous adenine deamination [Lindahl, 1993] that leads to the formation of hypoxanthine, which mispairs with cytosine, and hence represents a premutagenic lesion for A4G/T4C transitions....
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...A possible explanation for the recurrence of these two A4G mutations is a high susceptibility to spontaneous adenosine deamination [Lindahl, 1993]....
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4,101 citations
2,235 citations
"Extensive in silico analysis of NF1..." refers methods in this paper
...The position-weight matrices developed by Shapiro and Senapathy (S&S) [Senapathy et al., 1990; Shapiro and Senapathy, 1987] evaluate concordance of a sequence to the splice-site consensus motifs....
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1,667 citations