Biology subjects

Shin, J. H.

Publications and source records attributed to Shin, J. H..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Context-aware single-cell multiome approach identified cell-type specific lung cancer susceptibility genes

Genome-wide association studies (GWAS) identified over fifty loci associated with lung cancer risk. However, the genetic mechanisms and target genes underlying these loci are largely unknown, as most risk-associated-variants might regulate gene expression in a context-specific manner. Here, we generated a barcode-shared transcriptome and chromatin accessibility map of 117,911 human lung cells from age/sex-matched ever- and never-smokers to profile context-specific gene regulation. Accessible chromatin peak detection identified cell-type-specific candidate cis-regulatory elements (cCREs) from each lung cell type. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs prioritized the variants for 68% of the GWAS loci, a subset of which was also supported by transcription factor abundance and footprinting. cCRE colocalization and single-cell based trait relevance score nominated epithelial and immune cells as the main cell groups contributing to lung cancer susceptibility. Notably, cCREs of rare proliferating epithelial cell types, such as AT2-proliferating (0.13%) and basal cells (1.8%), overlapped with CCVs, including those in TERT. A multi-level cCRE-gene linking system identified candidate susceptibility genes from 57% of lung cancer loci, including those not detected in tissue- or cell-line-based approaches. cCRE-gene linkage uncovered that adjacent genes expressed in different cell types are correlated with distinct subsets of coinherited CCVs, including JAML and MPZL3 at the 11q23.3 locus. Our data revealed the cell types and contexts where the lung cancer susceptibility genes are functional.

genomics↗

bioRxiv2023

Dopamine and schizophrenia from bench to bedside: Discovery of a striatal co-expression risk gene set that predicts in vivo measures of striatal function.

Schizophrenia (SCZ) is characterized by a polygenic risk architecture implicating diverse molecular pathways important for synaptic function. However, how polygenic risk funnels through these pathways to translate into syndromic illness is unanswered. To evaluate biologically meaningful pathways of risk, we used tensor decomposition to characterize gene co-expression in post-mortem brain (of neurotypicals: N=154; patients with SCZ: N=84; and GTEX samples N=120) from caudate nucleus (CN), hippocampus (HP), and dorsolateral prefrontal cortex (DLPFC). We identified a CN-predominant gene set showing dopaminergic selectivity that was enriched for genes associated with clinical state and for genes associated with SCZ risk. Parsing polygenic risk score for SCZ based on this specific gene set (parsed-PRS), we found that greater pathway-specific SCZ risk predicted greater in vivo striatal dopamine synthesis capacity measured by [18F]-FDOPA PET in three independent cohorts of neurotypicals and patients (total N=235) and greater fMRI striatal activation during reward anticipation in two additional independent neurotypical cohorts (total N=141). These results reveal a bench to bedside translation of dopamine-linked genetic risk variation in driving in vivo striatal neurochemical and hemodynamic phenotypes that have long been implicated in the pathophysiology of SCZ.

neuroscience↗

bioRxiv2023

Differential expression of tension-sensitive HOX genes in fibroblasts is associated with different scar types

A scar is considered a natural consequence of the wound-healing process. However, the mechanism by which scars form remains unclear. Here, we suggest a new mechanism of wound healing and scar formation that involves the mechanosensitive regulation of HOX genes. RNA-sequencing of fibroblasts from different types of scars revealed differential HOX gene expression. Computational simulations predicted injury-induced tension loss in the skin, and in vitro experiments revealed a negative correlation between tension and fibroblast proliferation. Remarkably, exogenous tensile stress in fibroblasts has been shown to alter HOX gene expression levels in different scar types. Overall, we propose a model for normal wound healing and scar formation and show that successful wound healing requires tensional homeostasis in the skin tissue, which is regulated by tension-sensitive HOX genes.

cell biology↗

bioRxiv2023

TrkB-dependent regulation of molecular signaling across septal cell types

The lateral septum (LS), a GABAergic structure located in the basal forebrain, is implicated in social behavior, learning and memory. We previously demonstrated that expression of tropomyosin kinase receptor B (TrkB) in LS neurons is required for social novelty recognition. To better understand molecular mechanisms by which TrkB signaling controls behavior, we locally knocked down TrkB in LS and used bulk RNA-sequencing to identify changes in gene expression downstream of TrkB. TrkB knockdown induces upregulation of genes associated with inflammation and immune responses, and downregulation of genes associated with synaptic signaling and plasticity. Next, we generated one of the first atlases of molecular profiles for LS cell types using single nucleus RNA-sequencing (snRNA-seq). We identified markers for the septum broadly, and the LS specifically, as well as for all neuronal cell types. We then investigated whether the differentially expressed genes (DEGs) induced by TrkB knockdown map to specific LS cell types. Enrichment testing identified that downregulated DEGs are broadly expressed across neuronal clusters. Enrichment analyses of these DEGs demonstrated that downregulated genes are uniquely expressed in the LS, and associated with either synaptic plasticity or neurodevelopmental disorders. Upregulated genes are enriched in LS microglia, associated with immune response and inflammation, and linked to both neurodegenerative disease and neuropsychiatric disorders. In addition, many of these genes are implicated in regulating social behaviors. In summary, the findings implicate TrkB signaling in the LS as a critical regulator of gene networks associated with psychiatric disorders that display social deficits, including schizophrenia and autism, and with neurodegenerative diseases, including Alzheimers.

neuroscience↗

bioRxiv2023

Genetic and environmental contributions to ancestry differences in gene expression in the human brain

Ancestral differences in genomic variation are determining factors in gene regulation; however, most gene expression studies have been limited to European ancestry samples or adjusted for ancestry to identify ancestry-independent associations. We instead examined the impact of genetic ancestry on gene expression and DNA methylation (DNAm) in admixed African/Black American neurotypical individuals to untangle effects of genetic and environmental factors. Ancestry-associated differentially expressed genes (DEGs), transcripts, and gene networks, while notably not implicating neurons, are enriched for genes related to immune response and vascular tissue and explain up to 26% of heritability for ischemic stroke, 27% of heritability for Parkinsons disease, and 30% of heritability for Alzhemiers disease. Ancestry-associated DEGs also show general enrichment for heritability of diverse immune-related traits but depletion for psychiatric-related traits. The cell-type enrichments and direction of effects vary by brain region. These DEGs are less evolutionarily constrained and are largely explained by genetic variations; roughly 15% are predicted by DNAm variation implicating environmental exposures. We also compared Black and White Americans, confirming most of these ancestry-associated DEGs. Our results highlight how environment and genetic background affect genetic ancestry differences in gene expression in the human brain and affect risk for brain illness. SummaryWe examine the impact of genetic ancestry on gene expression and DNA methylation of admixed African/Black Americans, highlighting how genetic and environmental background affect risk for brain illness.

genetics↗

bioRxiv2023

The fingering patterns in the epithelial layer control the gap closure rate via curvature-mediated force

Closing gaps in cellular monolayers is a fundamental aspect of both morphogenesis and wound healing. This closure can be achieved through leader cell crawling or actomyosin-based contraction, depending on the size of the gap. Here, we focus on wounds whose closure is driven by interfacial instabilities, featuring both leader cell-driven fingers and actin-mediated contraction. Our proposed model predicts a positive correlation between the frequency of fingering and the overall speed of boundary closure. This fingering frequency is precisely regulated through the orchestration of cell density-driven pressure, cell-cell repulsions, and the initial curvature of the wound boundary. Our findings demonstrate an inverse correlation between fingering frequency and boundary curvatures, indicating a "self-control" mechanism for closure rates independent of the initial curvatures of the wound periphery. Notably, changes in curvature caused by fingering formation generate force that aids in the healing process.

biophysics↗

bioRxiv2023

Shear-induced phenotypic transformation of microglia in vitro

Brain cells are influenced by continuous fluid shear stress driven by varying hydrostatic and osmotic pressure conditions, depending on the brains pathophysiological conditions. While all brain cells are sensitive to the subtle changes in various physicochemical factors in the microenvironment, microglia, the resident brain immune cells, exhibit the most dramatic morphodynamic transformation. However, little is known about the phenotypic alterations in microglia in response to the changes in fluid shear stress. In this study, we first established a flow-controlled microenvironment to investigate the effects of shear flow on microglial phenotypes, including morphology, motility, and activation states. Microglia exhibited two distinct morphologies with different migratory phenotypes in a static condition: bipolar cells that oscillate along their long axis and unipolar cells that migrate persistently. When exposed to flow, a significant fraction of bipolar cells showed unstable oscillation with an increased amplitude of oscillation and a decreased frequency, which consequently led to the phenotypic transformation of oscillating cells into migrating cells. Interestingly, the level of pro-inflammatory genes increased in response to shear stress, while there were no significant changes in the level of anti-inflammatory genes. Our findings suggest that an interstitial fluid-level stimulus can cause a dramatic phenotypic shift in microglia toward pro-inflammatory states, shedding light on pathological outbreaks of severe brain diseases. Given that the fluidic environment in the brain can be locally disrupted in pathological circumstances, the mechanical stimulus by a fluid flow should also be considered a crucial element in regulating the immune activities of the microglia in brain diseases. Statement of SignificanceCellular morphology and motility are important factors that encompass the alterations in protein and gene-level expressions within cells. In pathological conditions, microglia, the resident brain immune cells, are known to undergo morphodynamic transformations in response to various physicochemical stimuli. Besides the commonly known soluble biochemical factors in the microenvironment, the differential flow characteristics of ISF have been linked to several neurological diseases, such as Alzheimers, Parkinsons, and brain tumors. Microglial cells, which are extremely sensitive to subtle changes in extracellular stimuli, have been identified as key players in these pathological conditions. Despite its importance, however, it has been challenging to study the sole effect of a shear flow on microglia. We investigated the morphodynamic features of microglia in response to precisely controlled interstitial-level fluid flow conditions using a microfluidic system in which isolated microglia are monitored in real-time while the undesirable effects from other extracellular factors are minimized.

bioengineering↗

bioRxiv2023

High-resolution assessment of multidimensional cellular mechanics using label-free refractive-index traction force microscopy

A critical requirement for studying cell mechanics is three-dimensional (3D) assessment of cellular shapes and forces with high spatiotemporal resolution. Traction force microscopy (TFM) with fluorescence imaging enables the measurement of cellular forces, but it is limited by photobleaching and a slow 3D acquisition speed. Here, we present refractive-index traction force microscopy (RI-TFM), a high-speed volumetric technique that simultaneously quantifies the 3D morphology and traction force of cells. RI-TFM reconstructs a 3D tomogram of single cells on a planar hydrogel elastomer using a high-speed illumination scheme with 0.5-Hz temporal resolution. This allows for quantitative analyses of 3D dry-mass distributions and shear (in-plane) and normal (out-of-plane) tractions of single cells on the extracellular matrix without labelling. When combined with a constrained total variation-based deconvolution algorithm, the proposed method provides 0.55-Pa shear (in-plane) and 1.59-Pa normal (out-of-plane) traction sensitivity for a 1-kPa hydrogel substrate. We demonstrate the utility of RI-TFM by assessing the effects of compromised intracellular stress due to actin disruption or low temperature and capturing the rapid dynamics of cellular junction formation in the spatiotemporal changes in non-planar traction components.

biophysics↗

bioRxiv2022

Dissecting the energetic architecture within an RNA tertiary structural motif via high-throughput thermodynamic measurements

Structured RNAs and RNA/protein complexes perform critical cellular functions. They often contain structurally conserved tertiary contact "motifs," whose occurrence simplifies the RNA folding landscape. Prior studies have focused on the conformational and energetic modularity of intact motifs. Here we turn to the dissection of one common motif, the 11nt receptor (11ntR), using quantitative analysis of RNA on a massively parallel array (RNA-MaP) to measure the binding of all single and double 11ntR mutants to GAAA and GUAA tetraloops, thereby probing the energetic architecture of the motif. While the 11ntR behaves as a motif, its cooperativity is not absolute. Instead, we uncovered a gradient from high cooperativity amongst base paired and neighboring residues to additivity between distant residues. As expected, substitutions at residues in direct contact with the GAAA tetraloop resulted in the largest decreases to binding, and energetic penalties of mutations were substantially smaller for binding to the alternate GUAA tetraloop, which lacks tertiary contacts present with the canonical GAAA tetraloop. However, we found that the energetic consequences of base partner substitutions are not, in general, simply described by base pair type or isostericity. We also found exceptions to the previously established stability-abundance relationship for 11ntR sequence variants. These findings of "exceptions to the rule" highlight the power of systematic high-throughput approaches to uncover novel variants for future study in addition to providing an energetic map of a functional RNA. Significance StatementProperly folded RNAs perform essential biological processes. Many RNAs contain tertiary contact "motifs" whose structural and energetic properties are conserved across different RNAs. This study delves into the nature of an RNA motif. We determined the effects of mutations on the energetic properties of a common tertiary contact motif, referred to as the 11-nucleotide receptor. As deep study of the energetic architecture of this and other RNAs requires thermodynamic measurements for many sequence variants, we used RNA-MaP, a quantitative, high-throughput method, to obtain binding free energies for all single and double mutants of the motif. Our results revealed the energetic architecture of this motif and identified rare variants with unexpected properties.

biophysics↗

bioRxiv2022

Selection and adaptive introgression guided the complex evolutionary history of European common bean

Domesticated crops have been disseminated by humans over vast geographic areas. After 1492, the common bean (Phaseolus vulgaris L.) was introduced in Europe. Here, we combine whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, and we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarros expedition to northern Peru in 1529. We show that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

genomics↗

bioRxiv2022

A new transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer in adults. When ccRCC is localized to the kidney, surgical resection or ablation of the tumor is often curative. However, in the metastatic setting, ccRCC remains a highly lethal disease. Here we take advantage of fresh patient samples that include treatment-naive primary tumor tissue, matched adjacent normal kidney tissue, as well as tumor samples collected from patients with bone metastases. Single-cell transcriptomic analysis of tumor cells from the primary tumors revealed a distinct transcriptional signature that was predictive of metastatic potential and patient survival. Analysis of supporting stromal cells within the tumor environment demonstrated vascular remodeling within the endothelial cells and a proliferative signature within the fibroblasts that was associated with poor survival. An in silico cell-to-cell interaction analysis highlighted the CXCL9/CXCL10-CXCR3 axis and the CD70-CD27 axis as potential therapeutic targets. Our findings provide biological insights into the interplay between tumor cells and the ccRCC microenvironment.

cancer biology↗

bioRxiv2021

Vimentin Intermediate Filaments and Filamentous Actin Form Unexpected Interpenetrating Networks That Redefine the Cell Cortex

Vimentin intermediate filaments (VIFs) and F-actin are filamentous cytoskeletal proteins generally thought to form completely independent networks that have vastly different properties and functions. Here, we show that, unexpectedly, there exist both extensive structural and functional interactions between VIFs and F-actin. We show that VIFs and F-actin form an interpenetrating network (IPN) within the cell cortex and interact synergistically at multiple length scales. This IPN structure has important functional consequences in cells: The IPN results in enhanced contractile forces in the cell. In addition, VIFs influence the diffusive behavior of actin monomers, suggesting specific associations between actin and vimentin proteins in the cytoplasm; this facilitates formation of the IPN and has downstream effects on other actin-driven processes. The results suggest that contributions of VIFs and F-actin are strongly correlated. Such interactions counter generally accepted behavior and are broadly significant given the wide range of processes currently attributed to F-actin alone.

cell biology↗

bioRxiv2021

Investigating trait variability of gene co-expression network architecture in brain by manipulating genomic signatures of schizophrenia risk

While the role of genomic risk for schizophrenia on brain gene co-expression networks has been described, the patterns of its manifestations are varied and complex. To acquire a deeper understanding of this issue, we implemented a novel approach to network construction by manipulating the RNA-Seq expression input to "integrate" or "remove" the "modulatory" effects of genomic risk for schizophrenia. We created co-expression networks in DLPFC from the adjusted expression input and compared them in terms of gene overlap and connectivity. We used linear regression models to remove variance explained by RNA quality, cell type proportion, age, sex and genetic ancestry. We also created co-expression networks based on the genomic profile of a normative trait, height, as a "negative control"; we also applied the same analytical approach in two independent samples: LIBD Human Brain Repository (HBR) (N=78 brains, European ancestry) and Common Mind Consortium (CMC) (N=116 brains, European ancestry). In addition to direct comparisons, we explored the biological plausibility of the differential gene clusters between co-expression networks by testing them for enrichment in relevant gene ontologies and gene sets of interest (PGC2-CLOZUK GWAS significant loci genes, height GWAS significant loci genes, genes in synaptic ontologies-SynGO and genes of the "druggable genome"). We identify several key aspects of the role of genomic risk for schizophrenia in brain co-expression networks: 1) Variability of co-expression modules with "integration" or "removal" of genomic profiles of complex traits (normal or pathological); 2) Biological plausibility of gene sets represented in the differential co-expression contrasts and potential relevance for illness etiopathogenesis; 3) Non-preferential mapping of schizophrenia GWAS loci genes to network areas apparently influenced by the genomic risk score. Overall, our study supports the notion that genomic risk for schizophrenia has an extensive and non-linear effect on brain gene co-expression networks that possibly manifests as a molecular background for gene-gene, gene-environment interactions that affect various biological pathways.

genomics↗

bioRxiv2021

Mapping origins of variation in neural trajectories of human pluripotent stem cells

Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. We identified differences in the early lineage emergence across hPSC lines that mapped on the antero-posterior axis of embryonic development. RNA-seq analysis revealed dynamic transcriptomic patterns that defined the emergence of mesendodermal versus neuroectodermal lineages conserved across hPSC lines and cell line-specific transcriptional signatures that were invariant across differentiation. The stable cell line-specific transcriptomic patterns predicted the retinoic acid (RA) response of the cell lines, resulting in distinct bias towards fore-versus hind-brain fates. Replicate hPSC lines and paired adult donor tissue demonstrated that cells from individual humans expressed unique and long-lasting transcriptomic signatures associated with evolutionarily recent genes. In addition to this genetic contribution, we found that replicate lines from a single donor showed divergent brain regional fates linked to distinct chromatin states, indicating that epigenetic mechanisms also contribute to neural fate differences. This variation in lineage bias and its correlation with RA responsive gene expression was also observed in a large collection of hPSC lines. These results define transcriptomic differences in hPSCs that initiate a critical early step specifying anterior or posterior neural fates.

neuroscience↗

bioRxiv2021

Decoding shared versus divergent transcriptomic signatures across cortico-amygdala circuitry in PTSD and depressive disorders

Post-traumatic stress disorder (PTSD) is a debilitating neuropsychiatric disease with a projected lifetime risk of 8.7%. PTSD is highly comorbid with depressive disorders including major depressive disorder (MDD) and bipolar disorder (BD). It is hypothesized that the overlap in symptoms stems from partially shared underlying neurobiological mechanisms. To better understand shared and unique transcriptional patterns of PTSD and MDD we performed RNA-sequencing in the postmortem brain of two prefrontal cortex (PFC) regions and two amygdala (AMY) regions, from neurotypical donors (N=109) as well as donors with diagnoses of PTSD (N=107) or MDD (N=109) across 1285 RNA-seq samples. We identified a small number of differentially expressed genes (DEGs) specific to PTSD, mostly in the cortex compared to amygdala. PTSD-specific DEGs were preferentially enriched in cortistatin-expressing cells, a subpopulation of somatostatin interneurons. These PTSD DEGs also showed strong enrichment for gene sets associated with immune-related pathways and microglia, largely driven by decreased expression of these genes in PTSD donors. While we identified a greater number of DEGs for MDD, there were only a few that were specific to MDD as they showed high overlap with PTSD DEGs. Finally, we used weighted gene co-expression network analysis (WGCNA) as an orthogonal approach to confirm the observed cellular and molecular associations. These findings highlight the sub-population of cortistatin-expressing interneurons as having potential functional significance in PTSD and provide supporting evidence for dysregulated neuroinflammation and immune signaling in MDD and PTSD pathophysiology.

neuroscience↗

bioRxiv2021

Prime editing enables precise genome editing in mouse liver and retina

Prime editing can induce any small-sized genetic change without donor DNA or double strand breaks. However, it has not been investigated whether prime editing is possible in postnatal animals. Here we delivered prime editors 2 and 3 into a mouse model of hereditary tyrosinemia, a genetic liver disease, using hydrodynamic injection, which corrected the disease-causing mutation and rescued the phenotype. We also achieved prime editing in the retina and retina pigment epithelium in wild-type mice by delivering prime editor 3 using trans-splicing adeno-associated virus. Deep sequencing showed that unintended edits at or near the target site or off-target effects were not detectable except for low levels (0% to 1.2%) of indels when PE3, but not PE2, was used. Our study suggests that precise, prime editor-mediated genome editing is possible in somatic cells of adult animals.

bioengineering↗

bioRxiv2020

Enriching neural stem cell and pro-healing glial phenotypes with electrical stimulation after traumatic brain injury in male rats

Traumatic Brain Injury (TBI) by an external physical impact results in compromised brain function via undesired neuronal death. Following the injury, resident and peripheral immune cells, astrocytes, and neural stem cells (NSCs) cooperatively contribute to the recovery of the neuronal function after TBI. However, excessive pro-inflammatory responses of immune cells, and the disappearance of endogenous NSCs at the injury site during the acute phase of TBI, can exacerbate TBI progression leading to incomplete healing. Therefore, positive outcomes may depend on early interventions to control the injury-associated cellular milieu in the early phase of injury. Here, we explore electrical stimulation (ES) of the injury site in a rodent model (male Sprague-Dawley rats) to investigate its overall effect on the constituent brain cell phenotype and composition during the acute phase of TBI. Our data showed that a brief ES for 1h on day 2 of TBI promoted pro-healing phenotypes of microglia as assessed by CD206 expression and increased the population of NSCs and Nestin+ astrocytes at 7 days post-TBI. Also, ES effectively increased the number of viable neurons when compared to the unstimulated control group. Given the salience of microglia and neural stem cells for healing after TBI, our results strongly support the potential benefit of the therapeutic use of ES during the acute phase of TBI to regulate neuroinflammation and to enhance neuroregeneration. Significance StatementTraumatic brain injury (TBI) occurs when a head injury leads to a disruption of normal function in the brain and is a major cause of death and disability, worldwide. The authors used electrical stimulation during the acute phase of TBI, which promoted pro-healing phenotypes of microglia and increased the number of neural stem cells and Nestin+ astrocytes, thereby enhancing neuronal viability. These findings support further study of electrical stimulation to regulate neuroinflammation and to enhance neuroregeneration after TBI. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/372979v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1bdc466org.highwire.dtl.DTLVardef@1a912c4org.highwire.dtl.DTLVardef@10f269dorg.highwire.dtl.DTLVardef@1b02487_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO C_FIG

bioengineering↗

bioRxiv2020

Comprehensive identification of somatic nucleotide variants in human brain tissue

Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. Here, the Brain Somatic Mosaicism Network conducted a coordinated, multi-institutional study to: (i) examine the ability of existing methods to detect simulated somatic single nucleotide variants (SNVs) in DNA mixing experiments; (ii) generate multiple replicates of whole genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual; (iii) devise strategies to discover somatic SNVs; and (iv) apply various approaches to validate somatic SNVs. These efforts led to the identification of 43 bona fide somatic SNVs that ranged in variant allele fractions from ~0.005 to ~0.28. Guided by these results, we devised best practices for calling mosaic SNVs from 250X whole genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrated that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. Thus, this study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

genomics↗