Biology subjects

Layer, R.

Publications and source records attributed to Layer, R..

4 recordsLinked to original sources

bioRxiv2024

Rapid, Reliable, and Interpretable CNV Curation Visualizations for Diagnostic Settings with SeeNV

Copy number variants (CNVs), structural alterations in the genome involving duplication or deletion of DNA segments, are implicated in various health conditions. Despite their clinical significance, accurate identification and interpretation of CNVs remain challenging, especially in the context of whole exome sequencing (WES), which is commonly used in clinical diagnostic laboratories. While WES offers economic advantages over whole genome sequencing (WGS), it struggles with CNV detection due to technical noise introduced by laboratory and analytic processes. Manual curation of CNV calls generated by these tools is labor-intensive and error-prone. To address this, we introduce SeeNV, a command-line tool designed to aid manual curation of CNVs at scale. SeeNV is one solution to these issues developed in collaboration with and used by the Precision Diagnostics Laboratory at Childrens Hospital Colorado. SeeNV generates static infographics for each CNV, incorporating sample and cohort sequencing coverage statistics, CNV population frequency, and more, facilitating rapid and precise assessment. Using CNVs calls identified in publicly available WES and WGS samples, we show users can rapidly and reliably curate CNV calls, needing only 4.3 seconds to curate a call, achieving 0.93 precision and 0.72 recall. SeeNV is freely available for download on GitHub: https://github.com/MSBradshaw/SeeNV.

genomics↗

bioRxiv2024

Implications of noncoding regulatory functions in the development of insulinomas

Insulinomas are rare neuroendocrine tumours arising from the pancreatic {beta}-cells. While retaining the ability to produce insulin, insulinomas feature aberrant proliferation and altered hormone secretion resulting in failure to maintain glucose homeostasis. With the aim of uncovering the role of noncoding regulatory regions and their aberrations to the development of these tumors, we coupled epigenetic and gene expression profiling with whole-genome sequencing. As a result, we mapped H3K27ac sites in the tumoral tissue and unraveled overlapping somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development and epigenetic modifying genes, including key components of the polycomb complex. Chromatin remodeling is apparent as insulinoma-selective regions are mostly clustered in regulatory domains, shared across patients and containing a specific set of regulatory sequences dominated by the binding motif of the transcription factor SOX17. Moreover, a large fraction of these regions are H3K27me3-repressed in unaffected {beta}-cells, suggesting that tumoral transition is coupled with derepression of {beta}-cell polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements and transcription factors that alter {beta}-cell function and fate in their progression to pancreatic neuroendocrine tumors and a framework to identify coding and noncoding driver mutations.

genomics↗

bioRxiv2021

A complete reference genome improves analysis of human genetic variation

Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 Mbp of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome to clinical and functional study. Here we demonstrate how the new reference universally improves read mapping and variant calling for 3,202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of novel variants per sample--a new frontier for evolutionary and biomedical discovery. Simultaneously, the new reference eliminates tens of thousands of spurious variants per sample, including up to 12-fold reduction of false positives in 269 medically relevant genes. The vast improvement in variant discovery coupled with population and functional genomic resources position T2T-CHM13 to replace GRCh38 as the prevailing reference for human genetics. One Sentence SummaryThe T2T-CHM13 reference genome universally improves the analysis of human genetic variation.

genomics↗

bioRxiv2021

The M1 aminopeptidase NPEPPS is a novel regulator of cisplatin sensitivity

There is an unmet need to improve efficacy of platinum-based cancer chemotherapy. Using multi-omic assessment of cisplatin-responsive and -resistant human bladder cancer cell lines and whole-genome CRISPR screens, we identified Puromycin-Sensitive Aminopeptidase, NPEPPS, as a novel driver of cisplatin resistance. NPEPPS depletion sensitizes resistant bladder cancer cells to cisplatin in vitro and in vivo. Conversely, overexpression of NPEPPS in sensitive cells increased cisplatin resistance. We show that NPEPPS affects treatment response by regulating intracellular cisplatin concentrations. Patient-derived organoids (PDOs) generated from bladder cancer samples before and after cisplatin-based treatment, and from patients who did not receive cisplatin, were evaluated for sensitivity to cisplatin and they were found to be concordant with clinical response. In PDOs, shRNA depletion or pharmacologic inhibition of NPEPPS led to increased cisplatin sensitivity, while NPEPPS overexpression had the opposite effect. Our data present NPEPPS as a novel and druggable driver of cisplatin resistance by regulating intracellular cisplatin concentrations, along with providing the preclinical data to support clinical trials combining NPEPPS inhibition with cisplatin.

cancer biology↗