Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Generation of an induced pluripotent stem cell (iPSC) line from a patient with developmental and epileptic encephalopathy carrying a KCNA2 (p.Leu328Val) mutation

Mutations in the KCNA2 gene, coding for the voltage-gated K+ channel Kv1.2, can cause developmental and epileptic encephalopathies. Kv1.2 channels play an important role in the repolarization phase of an action potential in nerve cells. Here, we reprogrammed human skin fibroblasts from a 13-year-old male patient with developmental and epileptic encephalopathy carrying a point mutation (c.982T>G, p.Leu328Val) in KCNA2 to human induced pluripotent stem cells (iPSCs) (HIHDNEi001-A). The cells maintained a normal karyotype and their pluripotency state was verified by the expression and staining of several pluripotency markers and capability to differentiate into all three germ layers

Generation of an induced pluripotent stem cell (iPSC) line from a patient with GEFS+ carrying a STX1B (p.Lys45delinsArgMetCysIleGlu and p.Leu46Met) mutation

The STX1B gene encodes the presynaptic protein syntaxin-1B, which plays a major role in regulating fusion of synaptic vesicles. Mutations in STX1B are known to cause epilepsy syndromes, such as genetic epilepsies with febrile seizures plus (GEFS+). Here, we reprogrammed skin fibroblasts from a female patient affected by GEFS+ to human induced pluripotent stem cells (iPSCs). The patient carries an InDel mutation (c.133_134insGGATGTGCATTG; p.Lys45delinsArgMetCysIleGlu and c.135_136AC > GA; p.Leu46Met), located in the regulatory Habc-domain of STX1B. Successful reprogramming of cells was confirmed by a normal karyotype, expression of several pluripotency markers and the potential to differentiate into all three germ layers

Reconstructions of GFP labeled and Biocytin filled neurons and spine details of the analyzed cells

The data is organized as follows: 1) reconstruction: this folder contains two overview gallery pictures and subfolders for each GFP labeled and each Biocytin filled neurons with the original image file and the reconstruction image + a SWC file that can be used to produce a 3D image of the cells 2) spines: This folder contains two exel sheets with the values for spine length, spine density and spine head diameter of the analyzed cells 3) summary files: This exel sheets contain overview information about the reconstructed neurons (apical, basal and total dendrite length

Data from: Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease

Most of our knowledge on human CNS circuitry and related disorders originates from model organisms. How well such data translate to the human CNS remains largely to be determined. Human brain slice cultures derived from neurosurgical resections may offer novel avenues to approach this translational gap. We now demonstrate robust preservation of the complex neuronal cytoarchitecture and electrophysiological properties of human pyramidal neurons in long-term brain slice cultures. Further experiments delineate the optimal conditions for efficient viral transduction of cultures, enabling "high throughput" fluorescence mediated 3D reconstruction of genetically targeted neurons at comparable quality to state-of-the-art biocytin fillings, and demonstrate feasibility of long term live cell imaging of human cells in vitro. This model system has implications toward a broad spectrum of translational studies, regarding the validation of data obtained in non-human model systems, for therapeutic screening and genetic dissection of human CNS circuitry

Long-term adult human brain slice cultures as a model system to study human CNS circuitry and disease

Most of our knowledge on human CNS circuitry and related disorders originates from model organisms. How well such data translate to the human CNS remains largely to be determined. Human brain slice cultures derived from neurosurgical resections may offer novel avenues to approach this translational gap. We now demonstrate robust preservation of the complex neuronal cytoarchitecture and electrophysiological properties of human pyramidal neurons in long-term brain slice cultures. Further experiments delineate the optimal conditions for efficient viral transduction of cultures, enabling "high throughput" fluorescence mediated 3D reconstruction of genetically targeted neurons at comparable quality to state-of-the-art biocytin fillings, and demonstrate feasibility of long term live cell imaging of human cells in vitro. This model system has implications toward a broad spectrum of translational studies, regarding the validation of data obtained in non-human model systems, for therapeutic screening and genetic dissection of human CNS circuitry