4004 results for "*geneti*"

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• Genetic analysis of nevus spilus-type congenital melanocytic nevus

  We performed whole-exome sequencing (WES) of lesional dermis and SNP array of peripheral blood, lesional epidermis, lesional dermis, and/or cultured melanocytes from individuals with nevus spilus-type congenital melanocytic nevus.

  Study JGAS000929

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• WES of serrated polyposis syndrome

  Samples were obtained from patients diagnosed with serrated polyposis syndrome (SPS). To provide further detail, the dataset comprises two whole-exome sequencing samples from patients within the same family, uploaded in BAM file format with IDs 449758 and 449549. Exomic regions were sequenced using HiSeq2000 Platform (Illumina, San Diego, USA) and Sure SelectXT All Exon v5 kit (Agilent, Santa Clara, CA, USA) for exon enrichment. Only those potentially pathogenic germline genetic variants shared by both individuals were considered.

  Dataset EGAD50000001126

• Characterization of cell types, positional codes, and enhancers contributing to human facial individuality and pathology

  Human genetic diversity generates an astonishing variety of facial shapes, and craniofacial anomalies rank among the most common birth defects. This study generated a multimodal atlas of human embryonic craniofacial development across embryonic weeks 6–11, including single-cell transcriptomics, chromatin accessibility, and spatial transcriptomics. The dataset characterizes cell states, mesenchymal subtypes, and their gene-enhancer cis-regulatory landscapes in space and time. These data provide a resource for studying normal human facial development, craniofacial abnormalities, and the genetic mechanisms underlying facial individuality.

  Study EGAS50000002001

• Long read whole genome sequencing data from brain postmortem tissue

  Chart genetic variation in the human brain in healthy controls and Parkinson’s disease (PD) patients.

  Study EGAS50000001452

• scATAC Gene scores

  Gene score matrices generated with ArchR based on chromatin profiles

  Study EGAS50000001993

• Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus

  SMART-PTA single-cell whole-genome and full transcriptome sequencing form normal esophagus samples

  Dataset EGAD50000002573

• GLASS-NL DNA-Methylation

  Study EGAS00001007546

• Chromosomal mutational signatures of DNA damaging agents at single cell resolution

  The chromosomal scale mutational spectrum of small molecules that interact with DNA has been hard to study at scale, as mutational events are distributed in location and occur in parallel in different cells. Here, we present a framework that pairs phylogenetic ancestry reconstruction with mutational signature decomposition to characterise recent, cell-private CNA mutational processes at single-cell resolution. We used this framework to characterize the cell-wise “foreground” of contemporaneous CNAs induced by strand-break inducing chemotherapeutic drugs of different mechanisms. We demonstrate that platinum salts, G-quadruplex stabilizers and topoisomerase II inhibitors, although mechanistically distinct, converge on a mutational signature dominated by telomere-bounded copy-number gain and losses. This signature is observed in different genetic backgrounds and in vivo, in drug treated patient derived-xenograft tumours. We also observe a high rate of endogenous telomere-bounded mutational foreground in BRCA1 deficient cells. We show that the single cell genome derived signature exposures are drug dose-dependent, and use this to identify the decay of mutational load after drug withdrawal. We observe that both cisplatin and a G4 binder molecule (CX5461) exhibit foreground mutational signature persistence up to 3 weeks after drug withdrawal, suggesting that residual effects of exposure may last longer than anticipated. Finally, extending the framework to serially drug-treated patient-derived xenograft (PDX) models, we show that telomere-bounded CNA signature exposure is associated with tumour response across and resistance states exhibit only background levels of mutational signatures. This is consistent with loss of mutational activity on the genome, as opposed to acquired tolerance to chromosomal mutations as a mechanism for some forms of chemotherapeutic drug resistance. Together our results show that scWGS can identify contemporaneous chromosomal mutation patterns induced by small molecules in human tissues.

  Study EGAS50000002035

• Multi-faceted metastasis decoding: clonal fitness, site pressure, and transcriptional modulation

  The dynamics of unique pressures that evolve metastasis fitness due to genetic and non-genetic components in relationship to primary versus metastatic site has remained difficult to decipher due to the highly complex and intertwined relationship of these features to the heterogeneous clonal structures within tumors. To simplify this problem, we generated serially passaged patient-derived xenografts (PDX) that developed reproducible metastasis and examined them for robust clonal selection using DLP+ single cell genome sequencing. This clonal composition analysis identified a simpler PDX model of metastases that displayed very high intra-PDX clonal competitive fitness, marked with dominant and differential clonal sweeps at metastatic and primary sites by different clones. Further testing this fitness using the different combinations of clones’ transplantation, re-confirmed this high clonal selectivity of a metastatically fit clone at metastatic sites compared to the primary site, hence revealing copy number aberration (CNA) clonal state dependent fixed metastasis fitness. Overall, by testing 9 PDX lines we found two lines with reproducible metastasis which identified a model that simplified the complexities of tumor evolution during metastasis and revealed the dominant role of favorable CNA clonal structure in fixating fitness.

  Study EGAS50000001515