0000000000460032
AUTHOR
Bernt Popp
showing 5 related works from this author
High-speed and accurate color-space short-read alignment with CUSHAW2
2013
Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real color-space mate-paired reads to the human genome. The results show that CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and BFAST at an order-of-magnitude faster speed and significantly smaller peak resident memory size. Availability: CUSHAW2 and all simulated datasets are avail…
CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
2014
The majority of next-generation sequencing short-reads can be properly aligned by leading aligners at high speed. However, the alignment quality can still be further improved, since usually not all reads can be correctly aligned to large genomes, such as the human genome, even for simulated data. Moreover, even slight improvements in this area are important but challenging, and usually require significantly more computational endeavor. In this paper, we present CUSHAW3, an open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. In this aligner, we have investigated a hybrid seeding approach to improve alignment quality, which incorp…
Expanding the Phenotype Associated with NAA10-Related N-Terminal Acetylation Deficiency
2016
International audience; N-terminal acetylation is a common protein modification in eukaryotes associated with numerous cellular processes. Inherited mutations in NAA10, encoding the catalytic subunit of the major N-terminal acetylation complex NatA have been associated with diverse, syndromic X-linked recessive disorders, whereas de novo missense mutations have been reported in one male and one female individual with severe intellectual disability but otherwise unspecific phenotypes. Thus, the full genetic and clinical spectrum of NAA10 deficiency is yet to be delineated. We identified three different novel and one known missense mutation in NAA10, de novo in 11 females, and due to maternal…
DLG4-related synaptopathy: a new rare brain disorder
2021
Contains fulltext : 245031.pdf (Publisher’s version ) (Closed access) PURPOSE: Postsynaptic density protein-95 (PSD-95), encoded by DLG4, regulates excitatory synaptic function in the brain. Here we present the clinical and genetic features of 53 patients (42 previously unpublished) with DLG4 variants. METHODS: The clinical and genetic information were collected through GeneMatcher collaboration. All the individuals were investigated by local clinicians and the gene variants were identified by clinical exome/genome sequencing. RESULTS: The clinical picture was predominated by early onset global developmental delay, intellectual disability, autism spectrum disorder, and attention deficit-hyp…
New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated acti…
2021
International audience; Purpose: A few de novo missense variants in the cytoplasmic FMRP-interacting protein 2 (CYFIP2) gene have recently been described as a novel cause of severe intellectual disability, seizures, and hypotonia in 18 individuals, with p.Arg87 substitutions in the majority.Methods: We assembled data from 19 newly identified and all 18 previously published individuals with CYFIP2 variants. By structural modeling and investigation of WAVE-regulatory complex (WRC)-mediated actin polymerization in six patient fibroblast lines we assessed the impact of CYFIP2 variants on the WRC.Results: Sixteen of 19 individuals harbor two previously described and 11 novel (likely) disease-ass…