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BackgroundThe clinical severity of sickle cell disease (SCD) is strongly influenced by the level of fetal haemoglobin (HbF) persistent in each patient. Three major HbF loci (BCL11A,HBS1L-MYB, andXmn1-HBG2) have been reported, but a considerable hidden heritability remains.AimBuilding on the power of a large and genetically diverse patient pool present in Nigeria, we conducted a genome-wide association study for HbF levels in patients from three regions of the country with a diverse ethnic make-up.MethodsWe analysed genome-wide trait association in 1006 Nigerian patients with SCD (HbSS/HbSβ0), followed by a replication and meta-analysis exercise in four independent SCD cohorts (3,582 patients). To dissect association signals at the major loci, we performed stepwise conditional analysis, haplotype association analysis and included public functional annotation data (fGCTA).ResultsAssociation signals were detected forBCL11A(lead SNP rs6706648, β=- 0.39,P=4.96 x 10-34) andHBS1L-MYB(lead SNP rs61028892, β=0.73,P=1.18 x 10-9), whereas the variant allele forXmn1-HBG2was found to be very rare. Genetically dissecting the two major loci, we defined trait-boosting haplotypes containing suspected or so-far unidentified causal variants. AtBCL11A, one such haplotype (trait increaseP< 0.0001) contains the putative functional variant rs1427407-‘T’ and a second haplotype (P< 0.0001) is tagged by the rs7565301-‘A’ allele, with no obvious candidate causal variant. AtHBS1L- MYB, one haplotype (trait increaseP< 0.0001) contains the likely functional rs66650371 (Δ3-bp), and a second (P< 0.0001) is tagged by the ‘C’ allele of rs6102889. Together, variants atBCL11AandHBS1L-MYBSNPs explained 24.1% of the trait variance.We detected three novel association signals:SLC28A3on chromosome 9 (rs115555854: β=- 0.73,P=2.52 x 10-8),TICRRon chromosome 15 (rs140496989: β=-0.43,P=3.34 x 10-8), andPIEZO2on chromosome 18 (rs58817161: β= −0.63,P= 8.04 x 10-8). These appeared to be restricted to the Nigerian patient cohort and were not confirmed in the replication cohorts.ConclusionsStudying a diverse cohort of Nigerian patients with sickle cell disease, we genetically dissected the known fetal-haemoglobin lociBCL11AandHBS1L-MYBand detected putative new trait-associated regions.

The Mood Disorder Questionnaire (MDQ) is a common screening tool for bipolar disorder that assesses manic symptoms. Its utility for genetic studies of mania or bipolar traits has not been fully examined. We psychometrically compared the MDQ to self-reported bipolar disorder in participants from the United Kingdom National Institute of Health and Care Research Mental Health BioResource. We conducted genome-wide association studies of manic symptom quantitative traits and symptom subgroups, derived from the MDQ items (N = 11,568–19,859). We calculated genetic correlations with bipolar disorder and other psychiatric and behavioral traits. The MDQ screener showed low positive predictive value (0.29) for self-reported bipolar disorder. Neither concurrent nor lifetime manic symptoms were genetically correlated with bipolar disorder. Lifetime manic symptoms had a highest genetic correlation (rg = 1.0) with posttraumatic stress disorder although this was not confirmed by within-cohort phenotypic correlations (rp = 0.41). Other significant genetic correlations included attention deficit hyperactivity disorder (rg = 0.69), insomnia (rg = 0.55), and major depressive disorder (rg = 0.42). Our study adds to existing literature questioning the MDQ's validity and suggests it may capture symptoms of general distress or psychopathology, rather than hypomania/mania specifically, in at-risk populations.

BackgroundAnxiety and depressive disorders often co-occur and the order of their emergence may be associated with different clinical outcomes. However, minimal research has been conducted on anxiety-anxiety comorbidity. This study examined factors associated with anxiety comorbidity and anxiety-MDD temporal sequence.MethodsOnline, self-report data were collected from the UK-based GLAD and COPING NBR cohorts (N = 38,775). Logistic regression analyses compared differences in sociodemographic, trauma, and clinical factors between single anxiety, anxiety-anxiety comorbidity, anxiety-MDD (major depressive disorder) comorbidity, and MDD-only. Additionally, anxiety-first and MDD-first anxiety-MDD were compared. Differences in familial risk were assessed in those participants with self-reported family history or genotype data.ResultsAnxiety-anxiety and anxiety-MDD had higher rates of self-reported anxiety or depressive disorder diagnoses, younger age of onset, and higher recurrence than single anxiety. Anxiety-MDD displayed greater clinical severity/complexity than MDD only. Anxiety-anxiety had more severe current anxiety symptoms, less severe current depressive symptoms, and reduced likelihood of self-reporting an anxiety/depressive disorder diagnosis than anxiety-MDD. Anxiety-first anxiety-MDD had a younger age of onset, more severe anxiety symptoms, and less likelihood of self-reporting a diagnosis than MDD-first. Minimal differences in familial risk were found.LimitationsSelf-report, retrospective measures may introduce recall bias. The familial risk analyses were likely underpowered.ConclusionsAnxiety-anxiety comorbidity displayed a similarly severe and complex profile of symptoms as anxiety-MDD but distinct features. For anxiety-MDD, first-onset anxiety had an earlier age of onset and greater severity than MDD-first. Anxiety disorders and comorbidity warrant further investigation and attention in research and practice.

ObjectiveThe Eating Disorders Genetics Initiative United Kingdom (EDGI UK), part of the National Institute for Health and Care Research (NIHR) Mental Health BioResource, aims to deepen our understanding of the environmental and genetic aetiology of eating disorders. EDGI UK launched in February 2020 and is partnered with the UK eating disorders charity, Beat. There are multiple EDGI branches worldwide.MethodEDGI UK recruits via media and clinical services. Anyone living in England, at least 16 years old, with a lifetime probable or clinical eating disorder is eligible to sign up online:edgiuk.org. Participants complete online questionnaires, donate a saliva sample for genetic analysis, and consent to medical record linkage and recontact for future studies.ResultsAs of September 2022, EDGI UK has recruited 8,397 survey participants: 98% female, 93% white, 97.7% cisgender, 67% heterosexual, and 52% have a university degree. Half (51.7%) of participants have returned their saliva kit. The most common diagnoses are anorexia nervosa (42.7%), atypical anorexia nervosa (31.4%), bulimia nervosa (33.2%), binge-eating disorder (14.6%), and purging disorder (33.5%).ConclusionEDGI UK is the largest UK eating disorders study but needs to increase its diversity, and efforts are underway to do so. It also offers a unique opportunity to accelerate eating disorder research, and collaboration between researchers and participants with lived experience, with unparalleled sample size.

The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses that rely on various software, different programming languages, and numerous dependencies to be installed and configured correctly. The entire process can be time-consuming, can lead to reproducibility errors, and can be a daunting task for bioinformaticians. To address this, we introduce the COPILOT protocol, which has been successfully used to transform raw Illumina genotype intensity data into high-quality analysis-ready data on tens of thousands of human patient samples that have been genotyped on a variety of Illumina genotyping arrays. This includes processing both mainstream and custom content genotyping chips with over 4 million markers per sample. The COPILOT QC protocol consists of two distinct tandem procedures to process raw Illumina genotyping data. The first protocol is an up-to-date process to systematically QC raw Illumina microarray genotyping data using the Illumina-specific GenomeStudio software. The second protocol takes the output from the first protocol and further processes the data through the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) containerized QC pipeline, to automate an array of complex bioinformatics analyses to improve data quality through a secondary clustering algorithm and to automatically identify typical Genome-Wide Association Study (GWAS) data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers, through ancestry estimation. The data is returned to the user in analysis-ready PLINK binary format and is accompanied by a comprehensive and interactive HTML summary report file which quickly helps the user understand the data and guides the user for further data analyses. The COPILOT protocol and containerized pipeline are also available at https://khp-informatics.github.io/COPILOT/index.html. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing raw Illumina genotyping data using GenomeStudio Basic Protocol 2: COPILOT: A containerised workflow for processing Illumina genotyping data.

BackgroundThe Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses. This process can be time-consuming, lead to reproducibility errors, and be a daunting task for novice bioinformaticians.ResultsHere we introduce the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) protocol, which provides an in-depth and clear guide to process raw Illumina genotype data in GenomeStudio, followed by a containerised workflow to automate an array of complex bioinformatics analyses involved in a GWAS quality control (QC). The COPILOT protocol was applied to two independent cohorts consisting of 2791 and 479 samples genotyped on the Infinium Global Screening (GSA) array with Multi-disease (MD) drop-in (~750,000 markers) and the Infinium H3Africa consortium array (~2,200,000 markers) respectively. Following the COPILOT protocol, an average sample quality improvement of 1.24% was observed across sample call rates, with notable improvement for low-quality samples. For example, from the 3270 samples processed, 141 samples had an initial sample call rate below 98%, averaging 96.6% (95% CI 95.6-97.7%), which is considered below the acceptable sample call rate threshold for a typical GWAS analysis. However, following the COPILOT protocol, all 141 samples had a call rate above 98% after QC and averaged 99.6% (95% CI 99.5-99.7%). In addition, the COPILOT pipeline automatically identified potential data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers through ancestry estimation.ConclusionsThe COPILOT protocol makes processing Illumina genotyping data transparent, effortless and reproducible. The container is deployable on multiple platforms, improves data quality, and the end product is analysis-ready PLINK formatted data, with a comprehensive and interactive summary report to guide the user for further data analyses.

Candida species are a dominant constituent of the human mycobiome and a better understanding of their metabolism from a fungal perspective can provide key insights into their ability to cause pathogenesis. Here, we have developed the BioFung database – a fungal specific tool for functional annotation using the KEGG database that provides an efficient method for annotation of protein-encoding gene. Analysis of carbohydrate-active enzyme (CAZymes) and BioFung, uncovered core and accessory features across Candida species demonstrating plasticity, adaptation to the environment and acquired features. Integerative functional analysis revealed that all Candida species can employ amino acid metabolism. However, metabolomics revealed that only a specific cluster of species (AGAu species - C. albicans, C. glabrata and C. auris) utilised amino acid metabolism. We identified critical metabolic pathways in the AGAu clusters with biomarkers and anti-fungal target potential in the CAZyme profile, polyamine, choline and fatty acid biosynthesis pathways. This study, combining genomic analysis, metabolomics and gene expression validation, highlights the metabolic diversity within AGAu species that underlies their remarkable ability to dominate the mycobiome and cause disease.

Changes in microbial metabolism have been used as the main approach to assess function and elucidate environmental and host-microbiome interactions. This can be hampered by uncharacterised metagenome species and lack of metabolic annotation. To address this, we present a comprehensive computational platform for population stratification based on microbiome composition, the underlying metabolic potential and generation of metagenome species and community level metabolic models. We revisit the concepts of enterotype and microbiome richness introducing the reactobiome as a stratification method to unravel the metabolic features of the human gut microbiome. The reactobiome encapsulates resilience and microbiome dysbiosis at a functional level. We describe five reactotypes in healthy populations from 16 countries, with specific amino acid, carbohydrate and xenobiotic metabolic features. The validity of the approach was tested to unravel host-microbiome and environmental interactions by applying the reactobiome analysis on a one-year Swedish longitudinal cohort, integrating gut metagenomics, plasma metabolomics and clinical data.

Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 x 10(-8), OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency amp;lt; 0.01) via gene-wide aggregation testing (IFIH1: p(burden) = 2.53 x 10(-7), OR = 0.707; TYK2: p(burden) = 6.17 x 10(-4), OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted. Funding Agencies|Medical Research Council (MRC) Stratified Medicine award [MR/L011808/1]; Psoriasis Association [RG2/10]; MRC Clinical Training Fellowship [MR/L001543/1]; NIHR Biomedical Research Centre based at Guys and St Thomas NHS Foundation Trust; Kings College London; NIHR Biomedical Research Centre at South London; Maudsley NHS Foundation Trust; Maudsley Charity [980]; Guys and St Thomass Charity [STR130505]; MRC grant [G0000934]; Wellcome Trust grant [068545/Z/02]; German Federal Ministry of Education and Research (BMBF) [01ZX1306A]; PopGen Biobank (Kiel, Germany) [01EY1103]; Helmholtz Zentrum Munchen - German Research Center for Environmental Health; BMBF; State of Bavaria; Munich Center of Health Sciences (MC Health); Ludwig-Maximilians-Universitat, of LMUinnovativ; BMBF [01ZZ9603, 01ZZ0103, 01ZZ0403, 03152061A, 03Z1CN22]; Ministry of Cultural Affairs; Social Ministry of the Federal State of Mecklenburg -West Pomerania; network Greifswald Approach to Individualized Medicine (GANI MED); Federal State of Mecklenburg West Pomerania; BMBF Metarthros grant [01EC1407A]; National Institutes of Health [R01AR042742, R01AR050511, R01AR054966, R01AR063611, R01AR065183]; GAIN award from the Foundation for the National Institutes of Health; Ann Arbor Veterans Affairs Hospital; Taubman Medical Research Institute; International Psoriasis Council

Individuals with intact cognition and neuropathology consistent with Alzheimer's disease (AD) are referred to as asymptomatic AD (AsymAD). These individuals are highly likely to develop AD, yet transcriptomic changes in the brain which might reveal mechanisms for their AD vulnerability are currently unknown. Entorhinal cortex, frontal cortex, temporal cortex and cerebellum tissue from 27 control, 33 AsymAD and 52 AD human brains were microarray expression profiled. Differential expression analysis identified a significant increase of transcriptomic activity in the frontal cortex of AsymAD subjects, suggesting fundamental changes in AD may initially begin within the frontal cortex region prior to AD diagnosis. Co-expression analysis identified an overactivation of the brain "glutamate-glutamine cycle", and disturbances in the brain energy pathways in both AsymAD and AD subjects, while the connectivity of key hub genes in this network indicates a shift from an already increased cell proliferation in AsymAD subjects to stress response and removal of amyloidogenic proteins in AD subjects. This study provides new insight into the earliest biological changes occurring in the brain prior to the manifestation of clinical AD symptoms and provides new potential therapeutic targets for early disease intervention.

The disrupted‐in‐schizophrenia 1 (DISC1) protein has been implicated in a range of biological mechanisms underlying chronic mental disorders such as schizophrenia. Schizophrenia is associated with abnormal striatal dopamine signalling, and all antipsychotic drugs block striatal dopamine 2/3 receptors (D_{2/3}Rs). Importantly, the DISC1 protein directly interacts and forms a protein complex with the dopamine D_{2} receptor (D_{2}R) that inhibits agonist‐induced D_{2}R internalisation. Moreover, animal studies have found large striatal increases in the proportion of D_{2}R receptors in a high affinity state (D_{2}^{high}R in DISC1 rodent models. Here, we investigated the relationship between the three most common polymorphisms altering the amino‐acid sequence of the DISC1 protein (Ser704Cys (rs821616), Leu607Phe (rs6675281) and Arg264Gln (rs3738401)) and striatal D_{2/3}R availability in 41 healthy human volunteers, using [{11}^C] ‐(+)‐PHNO positron emission tomography. We found no association between DISC1 polymorphisms and D_{2/3}R availability in the striatum and D_{2}R availability in the caudate and putamen. Therefore, despite a direct interaction between DISC1 and the D_{2}R, none of its main functional polymorphisms impact striatal D_{2/3}R binding potential, suggesting DISC1 variants act through other mechanisms.

Major depressive disorder and the anxiety disorders are highly prevalent, disabling and moderately heritable. Depression and anxiety are also highly comorbid and have a strong genetic correlation (rg ≈ 1). Cognitive behavioural therapy is a leading evidence-based treatment but has variable outcomes. Currently, there are no strong predictors of outcome. Therapygenetics research aims to identify genetic predictors of prognosis following therapy. We performed genome-wide association meta-analyses of symptoms following cognitive behavioural therapy in adults with anxiety disorders (n = 972), adults with major depressive disorder (n = 832) and children with anxiety disorders (n = 920; meta-analysis n = 2724). We estimated the variance in therapy outcomes that could be explained by common genetic variants (h2SNP) and polygenic scoring was used to examine genetic associations between therapy outcomes and psychopathology, personality and learning. No single nucleotide polymorphisms were strongly associated with treatment outcomes. No significant estimate of h2SNP could be obtained, suggesting the heritability of therapy outcome is smaller than our analysis was powered to detect. Polygenic scoring failed to detect genetic overlap between therapy outcome and psychopathology, personality or learning. This study is the largest therapygenetics study to date. Results are consistent with previous, similarly powered genome-wide association studies of complex traits.

Individuals with intact cognition and neuropathology consistent with Alzheimer’s disease (AD) are referred to as asymptomatic AD (AsymAD). These individuals are highly likely to develop AD, yet transcriptomic changes in the brain which might reveal mechanisms for their AD vulnerability are currently unknown. Entorhinal cortex, frontal cortex, temporal cortex and cerebellum tissue from 27 control, 33 AsymAD and 52 AD human brains were microarray expression profiled. Differential expression analysis identified a significant increase of transcriptomic activity in the frontal cortex of AsymAD subjects, suggesting fundamental changes in AD may initially begin within the frontal cortex region prior to AD diagnosis. Co-expression analysis identified an overactivation of the brain “glutamate-glutamine cycle”, and disturbances in the brain energy pathways in both AsymAD and AD subjects, while connectivity of key hub genes in this network indicates a shift from an already increased cell proliferation in AsymAD subjects to stress response and removal of amyloidogenic proteins in AD subjects. This study provides new insight into the earliest biological changes occurring in the brain prior to the manifestation of clinical AD symptoms and provides new potential therapeutic targets for early disease intervention.

Cell culture models are valuable tools to study biological mechanisms underlying health and disease in a controlled environment. Although their genotype influences their phenotype, subtle genetic variations in cell lines are rarely characterised and taken into account for in vitro studies. To investigate how the genetic makeup of a cell line might affect the cellular response to inflammation, we characterised the single nucleotide variants (SNPs) relevant to inflammation-related genes in an established hippocampal progenitor cell line (HPC0A07/03C) that is frequently used as an in vitro model for hippocampal neurogenesis (HN). SNPs were identified using a genotyping array, and genes associated with chronic inflammatory and neuroinflammatory response gene ontology terms were retrieved using the AmiGO application. SNPs associated with these genes were then extracted from the genotyping dataset, for which a literature search was conducted, yielding relevant research articles for a total of 17 SNPs. Of these variants, 10 were found to potentially affect hippocampal neurogenesis whereby a majority (n=7) is likely to reduce neurogenesis under inflammatory conditions. Taken together, the existing literature seems to suggest that all stages of hippocampal neurogenesis could be negatively affected due to the genetic makeup in HPC0A07/03C cells under inflammation. Additional experiments will be needed to validate these specific findings in a laboratory setting. However, this computational approach already confirms that in vitro studies in general should control for cell lines subtle genetic variations which could mask or exacerbate findings., Highlights • Cell lines are valuable tools to study mechanisms of health and disease. • Subtle genotypic variations of cell lines are rarely taken into account. • Genotyping array was performed on a human hippocampal progenitor cell line. • HPC0A07/03C cell line contains SNPs that may reduce neurogenesis under inflammation. • In vitro studies should control for cell lines genetic variations.

Esophageal squamous cell carcinoma (ESCC) has a high incidence in sub-Saharan Africa and a poor prognosis, but little is known about the genetic contribution to ESCC susceptibility in this region. We carried out a GWAS in the South African Black (SAB) population with 1,686 ESCC cases and 3,217 controls as part of the Evolving Risk Factors for Cancer in African populations (ERICA-SA) study after ethical approval and informed consent. ESCC case samples from ERICA-SA and controls from the H3A AWI-Gen study were genotyped on the 2.3 million H3 Africa SNP Illumina array and additional SNPs imputed using the Wellcome Sanger Institute imputation service. Measures for correction of population structure included Eigen decomposition for Principal Component (PC) analysis. The final imputed dataset of 14.4M SNPs for 1,686 OSCC cases and 3,217 population controls was used in linear-mixed model analysis to test for association using GEMMA. A meta-analysis of SNP sets common to both our study and a GWAS of 2,013 Chinese ESCC cases and 2,701 controls was done using METAL. The GWAS of the SAB population identified a total of 62 SNPs with suggestive association with ESCC (P < 5x10-6), from 29 independent potential risk loci. A strong signal at genome-wide significance is located upstream of the FAM120A gene on chromosome 9 (rs1237966, p=4.58x10-8) and is supported by multiple SNPs at this locus. FAM120A encodes an RNA binding protein which is a critical component of oxidative stress-induced signalling. A strong association was also observed on chromosome 2, led by rs142741123 (p=5.49x10-8) in a region spanning the MYO1B and STAT4 genes with SNPs that are absent in non-African populations, suggesting that this is an African-specific risk locus for ESCC. There was limited support for the association of ESCC risk loci reported in other populations in our study. We did a meta-analysis of the SAB GWAS with a published GWAS of Chinese ESSC cases and controls with 4.85 million SNPs shared between the two studies. A total of 12 SNPs were associated with ESCC at genome-wide significance. These included 3 loci: chromosome 9, led by rs12379660 (p-valuemeta = 9.36x10-10), chromosome 10 led by rs7099485 (p-valuemeta = 1.48x10-8) and chromosome 22 led by rs1033667 (p-valuemeta = 1.47x10-9). The chromosome 9 locus at FAM120A is the novel locus identified in our African ESCC GWAS, the chromosome 10 locus at PLCE1 shows association only in the Chinese GWAS, and the chromosome 22 locus at CHEK2 was previously identified in the Chinese ESCC GWAS, and is supported further by the African ESCC GWAS. This study is, to our knowledge, the first cancer GWAS conducted in solely in a resident African population, and has detected two novel risk loci for ESCC at or near genome-wide significance, one of which is likely specific to African populations. It also demonstrates the power of trans-ethnic meta-analysis to identify common or distinct risk loci in populations of diverse ancestry. Citation Format: Wenlong C. Chen, Jean-Tristan Brandenburg, Ananyo Choudhury, Mahtaab Hayat, Dhriti Sengupta, Chantal Babb de Villiers, Lucien Ferndale, Cassandra Soo, Sang H. Lee, Charles Curtis, Robert Newton, Tim Waterboer, Frederic Sitas, Michele Ramsay, Christian C. Abnet, Colleen Aldous, Mohamed I. Parker, Elvira Singh, Deborah Bradshaw, Cathryn M. Lewis, Christopher G. Mathew. Genome-wide association study of African esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 31.

Background Psychosis is a condition influenced by an interaction of environmental and genetic factors. Gene expression studies can capture these interactions; however, studies are usually performed in patients who are in remission. This study uses blood of first episode psychosis patients, in order to characterise deregulated pathways associated with psychosis symptom dimensions. Methods Peripheral blood from 149 healthy controls and 131 first episode psychosis patients was profiled using Illumina HT-12 microarrays. A case/control differential expression analysis was performed, followed by correlation of gene expression with positive and negative syndrome scale (PANSS) scores. Enrichment analyses were performed on the associated gene lists. We test for pathway differences between first episode psychosis patients who qualify for a Schizophrenia diagnosis against those who do not. Results A total of 978 genes were differentially expressed and enriched for pathways associated to immune function and the mitochondria. Using PANSS scores we found that positive symptom severity was correlated with immune function, while negative symptoms correlated with mitochondrial pathways. Conclusions Our results identified gene expression changes correlated with symptom severity and showed that key pathways are modulated by positive and negative symptom dimensions.

In this study, we aimed to test if the schizophrenia (SCZ) polygenic risk score (PRS) was associated with clinical symptoms in (a) the first episode of psychosis pre-treatment (FEP), (b) at nine weeks after initiation of risperidone treatment (FEP-9W) and (c) with the response to risperidone. We performed a detailed clinical assessment of 60 FEP patients who were antipsychotic-naive and, again, after nine weeks of standardized treatment with risperidone. After blood collection and DNA isolation, the samples were genotyped using the Illumina PsychArrayChip and then imputed. To calculate PRS, we used the latest available GWAS summary statistics from the Psychiatric Genomics Consortium wave-2 SCZ group as a training set. We used Poisson regression to test association between PRS and clinical measurements correcting for the four principal components (genotyping). We considered a p-value

Genome-wide significant variants associated with combined risk for major psychiatric disorders on chromosome 10q24 affect the expression of the cytosolic 5’-nucleotidase II (NT5C2, cN-II) in population controls, implicating it as a psychiatric susceptibility gene. Risk alleles are associated with reduced expression of this gene in the developing and adult brain, but the resulting neurobiological risk mechanisms remain elusive. In this study, we provide further evidence for the association ofNT5C2with psychiatric disorders, and use a functional genetics approach to gain a deeper understanding of the function of this risk gene in the nervous system.NT5C2expression was significantly reduced in thepost-mortembrain of schizophrenia and bipolar disorder patients, and its protein predominately expressed in neurons within the adult brain. Using human neural progenitor cells (hNPCs), we found thatNT5C2expression peaked at the neural progenitor state, where the encoded protein was ubiquitously distributed through the cell.NT5C2knockdown in hNPCs elicited transcriptomic changes associated with protein translation, that were accompanied by regulation of adenosine monophosphate-activated protein kinase (AMPK) signalling and ribosomal protein S6 (rpS6) activity. To identify the effect of reduced neuronalNT5C2expression at a systems level, we knockdown its homologue,CG32549, inDrosophila melanogasterCNS. This elicited impaired climbing behaviour in the model organism. Collectively, our data implicateNT5C2expression in risk for psychiatric disorders and inDrosophila melanogastermotility, and further suggest that risk is mediated via regulation of AMPK signalling and protein translation during early neurodevelopment.

Acne vulgaris is a highly heritable common, chronic inflammatory disease of the skin for which five genetic risk loci have so far been identified. Here, we perform a genome-wide association study of 3823 cases and 16,144 controls followed by meta-analysis with summary statistics from a previous study, with a total sample size of 26,722. We identify 20 independent association signals at 15 risk loci, 12 of which have not been previously implicated in the disease. Likely causal variants disrupt the coding region of WNT10A and a P63 transcription factor binding site in SEMA4B. Risk alleles at the 1q25 locus are associated with increased expression of LAMC2, in which biallelic loss-of-function mutations cause the blistering skin disease epidermolysis bullosa. These findings indicate that variation affecting the structure and maintenance of the skin, in particular the pilosebaceous unit, is a critical aspect of the genetic predisposition to severe acne. Acne vulgaris is a chronic inflammation of the skin, the genetic basis of which is incompletely understood. Here, Petridis et al. perform GWAS and meta-analysis for acne in 26,722 individuals and identify 12 novel risk loci that implicate structure and maintenance of the skin in severe acne risk.

We used a case-control genome-wide association (GWA) design with cases consisting of 1238 individuals from the top 0.0003 (∼170 mean IQ) of the population distribution of intelligence and 8172 unselected population-based controls. The single-nucleotide polymorphism heritability for the extreme IQ trait was 0.33 (0.02), which is the highest so far for a cognitive phenotype, and significant genome-wide genetic correlations of 0.78 were observed with educational attainment and 0.86 with population IQ. Three variants in locus ADAM12 achieved genome-wide significance, although they did not replicate with published GWA analyses of normal-range IQ or educational attainment. A genome-wide polygenic score constructed from the GWA results accounted for 1.6% of the variance of intelligence in the normal range in an unselected sample of 3414 individuals, which is comparable to the variance explained by GWA studies of intelligence with substantially larger sample sizes. The gene family plexins, members of which are mutated in several monogenic neurodevelopmental disorders, was significantly enriched for associations with high IQ. This study shows the utility of extreme trait selection for genetic study of intelligence and suggests that extremely high intelligence is continuous genetically with normal-range intelligence in the population. usc Refereed/Peer-reviewed

Many antipsychotics promote weight gain, which can lead to non-compliance and relapse of psychosis. By developing models that accurately identify individuals at greater risk of weight gain, clinicians can make informed treatment decisions and target intervention measures. We examined clinical, genetic and expression data for 284 individuals with psychosis derived from a previously published randomised controlled trial (IMPACT). These data were used to develop regression and classification models predicting change in Body Mass Index (BMI) over one year. Clinical predictors included demographics, anthropometrics, cardiac and blood measures, diet and exercise, physical and mental health, medication and BMI outcome measures. We included genetic polygenic risk scores (PRS) for schizophrenia, bipolar disorder, BMI, waist-hip-ratio, insulin resistance and height, as well as gene co-expression modules generated by Weighted Gene Co-expression Network Analysis (WGCNA). The best performing predictive models for BMI and BMI gain after one year used clinical data only, which suggests expression and genetic data do not improve prediction in this cohort.

An increased risk of developing Alzheimer's disease (AD) has previously been found to be associated with variants at the MS4A6A locus. We sought to identify which genes and transcripts in this region have altered expression in AD and mild cognitive impairment (MCI) and are influenced by the AD risk variant(s), as a first step to understanding the molecular basis of AD susceptibility at this locus. Common variants located within highly expressed MS4A6A transcripts were significantly associated with AD and MS4A6A expression levels in blood from MCI and AD subjects (p < 0.05, rs610932, rs7232, rs583791). More copies of the protective (minor) allele were associated with lower MS4A6A expression of each transcript (e.g., p = 0.019; rs610932-total MS4A6A). Furthermore, in heterozygous AD subjects, relative expression of the protective allele of V4-MS4A6A transcripts was lower (p < 0.008). Irrespective of genotype, MS4A6A transcripts were increased in blood from people with AD (p < 0.003), whereas lower expression of full length V1-MS4A6A (p = 0.002) and higher expression of V4-MS4A6A (p = 1.8 × 10−4) were observed in MCI, relative to elderly controls. The association between genotype and expression was less consistent in brain, although BA9 did have a similar genotype association with V4-MS4A6A transcripts as in blood. MS4A6A transcripts were widely expressed in tissues and cells, with the exception of V4-MS4A6A, which was not expressed in neuronal cells. Together these results suggest that high levels of MS4A6A in emerging AD pathology are detrimental. Persons with MCI may lower MS4A6A expression to minimize detrimental disease associated MS4A6A activity. However, those with the susceptibility allele appear unable to decrease expression sufficiently, which may explain their increased risk for developing AD. Inhibiting MS4A6A may therefore promote a more neuroprotective phenotype, although further work is needed to establish whether this is the case.

Supplemental Digital Content is available in the text., Objectives Clozapine is an atypical antipsychotic primarily prescribed for treatment-resistant schizophrenia. We tested the specific effect of clozapine versus other drug treatments on whole-blood gene expression in a sample of patients with psychosis from the UK. Methods A total of 186 baseline whole-blood samples from individuals receiving treatment for established psychosis were analysed for gene expression on Illumina HumanHT-12.v4 BeadChips. After standard quality-control procedures, 152 samples remained, including 55 from individuals receiving clozapine. In a within-case study design, weighted gene correlation network analysis was used to identify modules of coexpressed genes. The influence of mood stabilizers, lithium carbonate/lithium citrate and sodium valproate was studied to identify their possible roles as confounders. Results Individuals receiving clozapine as their only antipsychotic (clozapine monotherapy) had a nominal association with one gene-expression module, whereas no significant change in gene expression was found for other drugs. Conclusion Overall, this study does not provide evidence that clozapine treatment induces medium to large different gene-expression patterns in human whole blood versus other antipsychotic treatments. This does not rule out the possibility of smaller effects as observed for other common antipsychotic treatments.

Objectives: Exposure-based cognitive behavioural therapy (eCBT) is an effective treatment for anxiety disorders. Response varies between individuals. Gene expression integrates genetic and environmental influences. We analysed the effect of gene expression and genetic markers separately and together on treatment response.\ud \ud Methods: Adult participants (n ≤ 181) diagnosed with panic disorder or a specific phobia underwent eCBT as part of standard care. Percentage decrease in the Clinical Global Impression severity rating was assessed across treatment, and between baseline and a 6-month follow-up. Associations with treatment response were assessed using expression data from 3,233 probes, and expression profiles clustered in a data- and literature-driven manner. A total of 3,343,497 genetic variants were used to predict treatment response alone and combined in polygenic risk scores. Genotype and expression data were combined in expression quantitative trait loci (eQTL) analyses.\ud \ud Results: Expression levels were not associated with either treatment phenotype in any analysis. A total of 1,492 eQTLs were identified with q

BackgroundRecent studies point to overlap between neuropsychiatric disorders in symptomatology and genetic aetiology.AimsTo systematically investigate genomics overlap between childhood and adult attention-deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD) and major depressive disorder (MDD).MethodAnalysis of whole-genome blood gene expression and genetic risk scores of 318 individuals. Participants included individuals affected with adult ADHD (n = 93), childhood ADHD (n = 17), MDD (n = 63), ASD (n = 51), childhood dual diagnosis of ADHD–ASD (n = 16) and healthy controls (n = 78).ResultsWeighted gene co-expression analysis results reveal disorder-specific signatures for childhood ADHD and MDD, and also highlight two immune-related gene co-expression modules correlating inversely with MDD and adult ADHD disease status. We find no significant relationship between polygenic risk scores and gene expression signatures.ConclusionsOur results reveal disorder overlap and specificity at the genetic and gene expression level. They suggest new pathways contributing to distinct pathophysiology in psychiatric disorders and shed light on potential shared genomic risk factors.

Objectives. To evaluate whether genetic and environmental factors associated with RA in European and Asian ancestry populations are also associated with RA in African ancestry individuals. Methods. A case–control study was undertaken in 197 RA cases and 868 controls of African ancestry (Black African, Black Caribbean or Black British ethnicity) from South London. Smoking and alcohol consumption data at RA diagnosis was captured. Genotyping was undertaken (Multi-Ethnic Genotyping Array) and human leukocyte antigen (HLA) alleles imputed. The following European/Asian RA susceptibility factors were tested: 99 genome-wide loci combined into a genetic risk score; HLA region [20 haplotypes; shared epitope (SE)]; smoking; and alcohol consumption. The SE was tested for its association with radiological erosions. Logistic regression models were used, including ancestry-informative principal components, to control for admixture. Results. European/Asian susceptibility loci were associated with RA in African ancestry individuals. The genetic risk score provided an odds ratio (OR) for RA of 1.53 (95% CI: 1.31, 1.79; P = 1.3 × 10 −7). HLA haplotype ORs in European and African ancestry individuals were highly correlated (r = 0.83, 95% CI: 0.56, 0.94; P = 1.1 × 10 −4). Ever-smoking increased (OR = 2.36, 95% CI: 1.46, 3.82; P = 4.6 × 10 −4) and drinking alcohol reduced (OR = 0.34, 95% CI: 0.20, 0.56; P = 2.7 × 10 −5) RA risk in African ancestry individuals. The SE was associated with erosions (OR = 2.61, 95% CI: 1.36, 5.01; P = 3.9 × 10 −3). Conclusion. Gene–environment RA risk factors identified in European/Asian ancestry populations are relevant in African ancestry individuals. As modern statistical methods facilitate analysing ancestrally diverse populations, future genetic studies should incorporate African ancestry individuals to ensure their implications for precision medicine are universally applicable.

We propose a novel optical design method for small F/number (F/#) compact camera module using wavefront coding. Decreasing the F/# decreases the focus depth of the optical system, which can result in manufacturing tolerances so tight that fabrication is impossible. To obtain reasonable tolerances for easy fabrication and alignment of compact camera module, we designed the final imaging system to have a target wavefront with an extended focus depth. Because additional optical elements, such as phase plates, are not available for compact camera modules, target wavefront should be the combination of the wavefront errors of all lenses in the optical system. Wavefront-coded compact camera modules have higher tolerances and an extended focus depth, so that the images obtained from them have high resolution over a broad defocus range. Images simulated by a wavefront-coded optical system can be restored to much higher resolution using deconvolution of images and a point spread function given by the coded target wavefront.

We introduce the design method of a hybrid lens composed a refractive lens and a diffractive optical element (DOE) considering the diffraction effect for a compact camera module. When imaging optical system is designed using the DOE, diffraction efficiency of the DOE and stray light due to the unintended diffraction light should be considered. Therefore, to analyze the effect of diffraction efficiency of the DOE on image characteristics, we evaluate the performances of two designed compact camera lenses, which have different construction wavelengths, using the modulation transfer function (MTF) considering diffraction efficiency. The stray light that is induced by the diffraction effect of the DOE is analyzed by calculating the focal position according to each diffraction order, and a method for the reduction of the stray light is proposed.

© 2015 Optical Society of America. Adaptive optics scanning laser ophthalmoscopy (AO-SLO) has recently been used to achieve exquisite subcellular resolution imaging of the mouse retina. Wavefront sensing-based AO typically restricts the field of view to a few degrees of visual angle. As a consequence the relationship between AO-SLO data and larger scale retinal structures and cellular patterns can be difficult to assess. The retinal vasculature affords a largescale 3D map on which cells and structures can be located during in vivo imaging. Phase-variance OCT (pv-OCT) can efficiently image the vasculature with near-infrared light in a label-free manner, allowing 3D vascular reconstruction with high precision. We combined widefield pv-OCT and SLO imaging with AO-SLO reflection and fluorescence imaging to localize two types of fluorescent cells within the retinal layers: GFP-expressing microglia, the resident macrophages of the retina, and GFP-expressing cone photoreceptor cells. We describe in detail a reflective afocal AO-SLO retinal imaging system designed for high resolution retinal imaging in mice. The optical performance of this instrument is compared to other state-of-the-art AO-based mouse retinal imaging systems. The spatial and temporal resolution of the new AO instrumentation was characterized with angiography of retinal capillaries, including blood-flow velocity analysis. Depth-resolved AO-SLO fluorescent images of microglia and cone photoreceptors are visualized in parallel with 469 nm and 663 nm reflectance images of the microvasculature and other structures. Additional applications of the new instrumentation are discussed.

Letters Author Response: Outer Retinal Bands We thank Richard F. Spaide 1 for his careful reading of our article, 2 and we welcome this opportunity to address some of his concerns. Given the complexity of the relevant concepts, we have chosen to present a summary of our findings followed by a list of Spaide’s relevant criticisms (in italic) along with our rebuttals. In the interest of brevity, we have chosen not to respond to criticisms that do not bear on the scientific impact of our article (e.g., the availability of raw, linear data in the Spectralis [Heidelberg Engineering, Heidelberg, Germany] software). In cross-sectional optical coherence tomography (OCT) images (B-scans) of the retina, several bands are seen in the outer retina. Our article sought to investigate one of these bands—‘‘band 2’’—which originates from a structure confined to photoreceptor cells. We aimed to quantitatively characterize this structure by resolving it within single cones and measuring its average thickness and its position with respect to the adjacent bands 1 and 3. We hypothesized that the outer retinal band 2 would be thinner than the inner segment ellipsoid (16– 20 lm) and that it would lie near the inner and outer segment (IS/OS) junction, approximately half way between the external limiting membrane (ELM) and cone outer segment tips (COST). We imaged four healthy eyes at two retinal locations (foveal and parafoveal) using adaptive optics (AO)-OCT, which permits three-dimensional resolution of cone photoreceptors. 3 From the resulting eight volumetric images, we segmented 9593 cones and measured the two parameters relevant to our hypotheses. We segmented each cone in three dimensions, using its lateral extent in en face projection and the locations of bands 1 and 3. Bands 1 and 3 were identified by identifying the A-lines comprising each cone and averaging them together to form the cone’s longitudinal reflectance profile (LRP). By quantifying cellular morphology on each of the 9593 cones, we found that band 2 has a thickness of 4.7 lm, corresponding to an object thickness of 3.5 lm or less, and that it lies approximately equidistant from the ELM and COST. These findings are consistent with the interpretation that band 2 arises from the junction between IS and OS, but inconsistent with the recent hypothesis 4 that the band arises from the IS ellipsoid. Spaide’s letter 1 raised seven significant criticisms of our methods and our interpretation of results. These are listed below, in order of perceived relative importance, along with our responses. Criticism 1: The mismatch between images of IS/OS and COST suggests that the cones were not segmented correctly. Our response: To measure cellular morphology, bands 1, 2, and 3 must be readily identifiable in the cone’s LRP. Spaide points out that the IS/OS and COST images in our figure 2 are not identical, and that these differences manifest in the transverse locations of peaks (his fig. 1) and mismatch between their en face projections (his fig. 2). Moreover, he points out that the ELM is not visible in our figure 5. He reasons that if we cannot identify structures in the images, we cannot provide accurate morphological measurements. First and most importantly, the AO-OCT B-scan to which he refers was a conceptual illustration, not data fit for further analysis. It is a single, unaveraged, unprocessed B-scan. It represents a transverse cut through the cones, but not necessarily through their centers, as they form a somewhat irregular mosaic that is not aligned to the imaging source’s scanned path across the retina. In short, each cone in the B- scan is represented by between one and five A-lines, significantly smaller than the 22 A-line volumetric image of each cone we used to compute an LRP. Worse, the image has lost four bits of dynamic range for publication. In the article, we described figure 5 as providing context for our results, and specifically not necessary for the scientific conclusions of the article, and that is because qualitative observations based on a single B-scan are of limited usefulness. Spaide does not describe precisely how he generated his figures 1 and 2. Given the diversity of methods for generating such images, we would prefer to deal with this question quantitatively. The Pearson correlation of the two original images in our figure 2 is 0.504 (see cross-correlation in attached Figure). Considering that this coefficient is computed over 19,370 pixels, the resulting P value is less than 10 -6 , which is consistent with the conclusion that the images originate from corresponding features. Due to bit-depth compression and smoothing, the publication images are even more highly correlated. Spaide is right that the images of IS/OS and COST are not identical, and this observation is confirmed by the fact that the Pearson correlation is less than 1.0. There are (at least) three possible reasons for the mismatch. First, it is known that the cone IS and OS diameter differ throughout most of the retina. There is now evidence that these differences affect the transverse waveguide modes supported by these respective segments, which can cause the IS/OS and COST reflections to differ, slightly in the fovea and dramatically in the periphery (Liu Z, Kocaoglu OP, Turner TL, Miller DT, manuscript submitted, 2015). 5 Second, because our main goal was characterization of band 2, focus of the system was optimized for that band, which may have contributed to differences in their appearance as well. Third, like all images, these have some random, uncorrelated noise. For any given cone, these factors may have caused differences in the lateral distribution of light at each layer, which explains the imperfect correspondence shown in his figure 2. The high statistical correspondence between the images (P < 10 - 6 ) suggests that although the noise and transverse modes may not be aligned, the bulk of the features in the images are. The low visibility of ELM in the B-scan is due, as Spaide recognized, to the linear scaling of the image, limited dynamic range of print images, and absence of any lateral integration of signal. After averaging a sufficient number of A- lines from each cone, the ELM was always identifiable in our experiment, in spite of its dark appearance in single B-scans. The ELM is comparably dark in Spaide’s own linearly scaled Spectralis B-scans, 4 even with the latter instrument’s greater optical blur, averaging, and postprocessing. Nevertheless, we are confident that his use of it as a morphological landmark was also justified. Criticism 2: Speckle and waveguiding made image analysis difficult. Our response: Spaide argues that averaging produces a smooth topography that ‘‘more accurately represents’’ the structure of interest. He is correct that averaging adjacent B- scans can reduce speckle contrast and increase signal, but this is true only if the extent of averaging is smaller than the structure of interest and larger than the speckle. This principle guided the design of our morphological analysis, in which we averaged all the A-lines originating from each cone (i.e., the structure of interest). We specifically avoided averaging Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc. www.iovs.org j ISSN: 1552-5783 Downloaded From: http://iovs.arvojournals.org/pdfaccess.ashx?url=/data/Journals/IOVS/933739/ on 02/10/2016

A novel image quality evaluation method, which is based on combination of the rigorous grating diffraction theory and the ray-optic method, is proposed. It is applied for design optimization and, tolerance analysis of optical imaging systems implementing diffractive optical elements (DOE). The evaluation method can predict the quality and resolution of the image on the image sensor plane through the optical imaging system. Especially, we can simulate the effect of diffraction efficiencies of DOE in the camera lenses module, which is very effective for predicting different color sense and MTF performance. Using this method, we can effectively determine the fabrication tolerances of diffractive and refractive optical elements such as the variations' in profile thickness, and the shoulder of the DOE, as well as conventional parameters such as decenter and tilt in optical-surface alignments. A DOE-based 2M-resolution camera lens module designed by the optimization process based on the proposed image quality evaluation method shows ${\sim}15%$ MTF improvement compared with a design without such an optimization.

TMSCN asymmetrically adds to a variety of ketones by catalysis with 1 /Ph 3 PO. This is a double activation where 1 acts as a Lewis acid and Ph 3 PO as a Lewis base. Various ketones were subjected to the enantioselective addition to give up to 85% ee.

Various aldehydes undergo enantioselective silylcyanation with (CH3)3SiCN trimethylsilylcyanation (TMSCN) employing chiral Mn(salen) and achiral POPh3 as the catalysts. This is the double activation where Mn(salen) plays the role of Lewis acid and POPh3 Lewis base. Numerous aldehydes are subject to the enantioselective addition of TMSCN at 0°C. Hydrolysis of the adduct gave cyanohydrin with up to 96% yield and 62% ee.

Author(s): Jonnal, Ravi S; Kocaoglu, Omer P; Zawadzki, Robert J; Lee, Sang-Hyuck; Werner, John S; Miller, Donald T | Abstract: PurposeTo test the recently proposed hypothesis that the second outer retinal band, observed in clinical OCT images, originates from the inner segment ellipsoid, by measuring: (1) the thickness of this band within single cone photoreceptors, and (2) its respective distance from the putative external limiting membrane (band 1) and cone outer segment tips (band 3).MethodsAdaptive optics-optical coherence tomography images were acquired from four subjects without known retinal disease. Images were obtained at foveal (2°) and perifoveal (5°) locations. Cone photoreceptors (n = 9593) were identified and segmented in three dimensions using custom software. Features corresponding to bands 1, 2, and 3 were automatically identified. The thickness of band 2 was assessed in each cell by fitting the longitudinal reflectance profile of the band with a Gaussian function. Distances between bands 1 and 2, and between 2 and 3, respectively, were also measured in each cell. Two independent calibration techniques were employed to determine the depth scale (physical length per pixel) of the imaging system.ResultsWhen resolved within single cells, the thickness of band 2 is a factor of three to four times narrower than in corresponding clinical OCT images. The distribution of band 2 thickness across subjects and eccentricities had a modal value of 4.7 μm, with 48% of the cones falling between 4.1 and 5.2 μm. No significant differences were found between cells in the fovea and perifovea. The distance separating bands 1 and 2 was found to be larger than the distance between bands 2 and 3, across subjects and eccentricities, with a significantly larger difference at 5° than 2°.ConclusionsOn the basis of these findings, we suggest that ascription of the outer retinal band 2 to the inner segment ellipsoid is unjustified, because the ellipsoid is both too thick and proximally located to produce the band.

We present an aberration cancelling optical design for a reflective adaptive optics - optical coherence tomography (AO-OCT) retinal imaging system. The optical performance of this instrument is compared to our previous multimodal AO-OCT/AO-SLO retinal imaging system. The feasibility of new instrumentation for improved visualization of microscopic retinal structures is discussed. Examples of images acquired with this new AO-OCT instrument are presented.

We present a new design for a reflective afocal AO-OCT retinal imaging system. The optical performance of this instrument is compared to our previous multimodal AO-OCT/AO-SLO retinal imaging system. The feasibility of new instrumentation for improved visualization of microscopic retinal structures will be discussed. Examples of images acquired with this new AO-OCT instrument will be presented. © 2013 Copyright SPIE.

The Nyquist aperture is used to increase the storage density. To reduce the bit errors caused by the Nyquist aperture, we applied an image restoration method which restores the degraded image in the enhanced spatial frequency domain using its PSF as a restoration filter.

We propose an image-resolution upscaling method for compact imaging systems. The image resolution is calculated using the resolving power of the optics and the pixel size of a digital image sensor. The resolution limit of the compact imaging system comes from its size and the number of allowed lenses. To upscale the image resolution but maintain the small size, we apply wavefront coding and image restoration. Conventional image restoration could not enhance the image resolution of the sensor. Here, we use the upscaled image of a wavefront-coded optical system and apply an image-restoration algorithm using a more precisely calculated point-spread function (PSF) as the deconvolution filter. An example of a wavefront-coded optical system with a 5-megapixel image sensor is given. The final image had a resolution equivalent to that of a 10-megapixel image using only four plastic lenses. Moreover, image degradation caused by hand motion could also be reduced using the proposed method.

Image of mobile camera is easily blurred during the exposure time by hand motion. To reduce hand motion blur of image, optical image stabilization technologies are widely used. They need additional mechanism and fine alignment of optical components and make the size of system bulky. In the mobile devices, however, using minimum number of optical and mechanical component is important. In this paper, we propose noble image restoration algorithm using upscaled image and recalculated deconvolution filter from the point spread function of optical system not to use any additional mechanical or optical components. Upscaled and restored image represents higher image resolution than the reference image which is not upscaled.

Level of Evidence: V, Case Report

We propose a resolution enhancement method for mobile small f-number compact imaging systems based on wavefront coding and superresolution image processing. Wavefront coding increases the focus depth of an optical system and produces point spread functions (PSFs) with similar characteristics at different field and defocus positions. The designed target wavefront is realized as a combination of wavefront errors of each rotationally symmetric lens, without including an additional phase plate. Finally, using one deconvolution filter containing all the characteristics of the PSFs, we achieve high resolution, breaking the diffraction limit of small f-number and the resolution limit of the image sensor by super-resolution image processing.