Analysis Of Screening Data Research Articles

Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells.

Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells, and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here, we report the implementation of CRISPR/Cas-9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma (LUAD) cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression preferentially in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation (IR), oxidative stress, and ATR inhibition, strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A-expressing tumors.

Cervical length distribution and other sonographic ancillary findings of singleton nulliparous patients at midgestation

Short cervix at midgestation, the presence of intraamniotic debris, and cervical funneling are risk factors for preterm birth; however, cervical length measurements and cutoffs are not well documented among pregnant patients of different gestational ages and self-reported races and ethnicities. This study aimed to describe the distribution of cervical length and frequency of funneling and debris at midgestation in nulliparous women by gestational age and race/ethnicity. This secondary analysis of screening data from a multicenter treatment trial of singleton nulliparous patients with short cervix was conducted at 14 geographically distributed, university-affiliated medical centers in the United States. Singleton nulliparous patients with no known risk factors for preterm birth were screened for trial participation and asked to undergo a transvaginal ultrasound to measure cervical length by a certified sonographer. The distribution of cervical length and the frequency of funneling and debris were assessed for each gestational age week (16-22 weeks) and stratified by self-reported race and ethnicity, which for this study were categorized as White, Black, Hispanic, and other. Patients enrolled in the randomized trial were excluded from this analysis. A total of 12,407 nulliparous patients were included in this analysis. The racial or ethnic distribution of the study participants was as follows: White, 41.6%; Black, 29.6%; Hispanic, 24.2%; and others, 4.6%. The 10th percentile cervical length for the entire cohort was 31.1 mm and, when stratified by race and ethnicity, 31.9 mm for White, 30.2 mm for Black, 31.4 mm for Hispanic, and 31.2 mm for patients of other race and ethnicity (P<.001). At each gestational age, the cervical length corresponding to the tenth percentile was shorter in Black patients. The 25 mm value commonly used to define a short cervix and thought to represent the 10th percentile ranged from 1.3% to 5.4% across gestational age weeks and 1.0% to 3.8% across race and ethnicity groups. Black patients had the highest rate of funneling (2.6%), whereas Hispanic and Black patients had higher rates of intraamniotic debris than White and other patients (P<.001). Black patients had shorter cervical length and higher rates of debris and funneling than White patients. The racial and ethnic disparities in sonographic midtrimester cervical findings may provide insight into the racial disparity in preterm birth rates in the United States.

The Impact of Seasonal Changes on Thyroxine and Thyroid-Stimulating Hormone in Newborns

Newborn screening for congenital hypothyroidism (CH) is performed by measuring the concentration of thyroxine (T4) and/or thyroid-stimulating hormone (TSH) in dried blood spots. Unfortunately, the levels of T4 and TSH vary due to multiple factors, and therefore the false-positive rate for the test is a challenge. We analyzed screening data from 2008 to 2017 to determine the effect of seasonal changes and manufacturer kit lot changes on T4 and TSH values and on numbers of infants referred. Over a 10-year period, we screened 2.4 million infants using commercially available fluoroimmunoassays to measure T4 and TSH concentrations in dried blood spots. During colder months, daily mean T4 and TSH values were higher and referral rates and false-positive rates were higher. However, there was no significant difference between the number of confirmed CH cases. Furthermore, in rare instances, we observed differences in T4 daily mean values during the 10-year period when manufacturer kit lot changes were made. Seasonal temperature variations influence measured T4 and TSH values and consequently lower the positive predictive value for CH testing in colder months. Newborn screening (NBS) programs should be aware that manufacturer kit lot changes may also influence T4 values.

Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance.

Blood collection for newborn genetic disease screening is preferably performed within 24–48 h after birth. We used population-level newborn screening (NBS) data to study early postnatal metabolic changes and whether timing of blood collection could impact screening performance. Newborns were grouped based on their reported age at blood collection (AaBC) into early (12–23 h), standard (24–48 h), and late (49–168 h) collection groups. Metabolic marker levels were compared between the groups using effect size analysis, which controlled for group size differences and influence from the clinical variables of birth weight and gestational age. Metabolite level differences identified between groups were correlated to NBS data from false-positive cases for inborn metabolic disorders including carnitine transport defect (CTD), isovaleric acidemia (IVA), methylmalonic acidemia (MMA), and phenylketonuria (PKU). Our results showed that 56% of the metabolites had AaBC-related differences, which included metabolites with either decreasing or increasing levels after birth. Compared to the standard group, the early-collection group had elevated marker levels for PKU (phenylalanine, Cohen's d = 0.55), IVA (C5, Cohen's d = 0.24), MMA (C3, Cohen's d = 0.23), and CTD (C0, Cohen's d = 0.23). These findings correlated with higher false-positive rates for PKU (P < 0.05), IVA (P < 0.05), and MMA (P < 0.001), and lower false-positive rate for CTD (P < 0.001) in the early-collection group. Blood collection before 24 h could affect screening performance for some metabolic disorders. We have developed web-based tools integrating AaBC and other variables for interpretive analysis of screening data.

Prevalence of HIV, viral hepatitis B/C and tuberculosis and treatment outcomes among people who use drugs: Results from the implementation of the first drop-in-center in Mozambique

BackgroundPeople who use drugs (PWUD) which includes both people who inject drugs (PWID) and non-injection drug users (NIDU) are marginalized, experience high levels of stigma and discrimination, and are likely to have challenges with accessing health services. Mozambique implemented the first drop-in center (DIC) for PWUD in Maputo City in 2018. This analysis aims to assess the prevalence of HIV, viral hepatitis B (HBV) and C (HCV) and tuberculosis (TB) among PWUD, and assess their linkage to care and associated correlates. MethodsWe conducted a cross-sectional retrospective analysis of routine screening data collected from the first visit at the drop-in center (DIC) during the period of May 2018 to November 2019 (18 months). Descriptive and multivariable logistic regression analysis were conducted to estimate adjusted odds ratios (aOR) and 95% confidence intervals (CI) of HIV, HBV, HCV and TB infections among PWID and NIDU. Cox proportional hazards models of determinants were used to estimate time from HIV diagnosis to linkage to care for PWUD. ResultsA total of 1,818 PWUD were screened at the DIC, of whom 92.6% were male. The median age was 27 years (range:14–63). Heroin was the most consumed drug (93.8%), and among people who used it, 15.5% injected it. Prevalence of HIV (43.9%), HCV (22.6%) and HBV (5.9%) was higher among PWID (p<0.001). Linkage to HIV care was observed in 40.5% of newly diagnosed PWID. Factors associated with shorter time to linkage to care included drug injection (aHR=1.6) and confirmed TB infection (aHR=2.9). ConclusionThis was the first analysis conducted on the implementation of the DIC in Mozambique and highlights the importance of targeted services for this high-risk population. Our analysis confirmed a high prevalence of HIV, HBV and HCV, and highlight the challenges with linkage to care among PWID. The expansion of DIC locations to other high-risk localities to enhance HIV testing, treatment services and linkage to care to reduce ongoing transmission of HIV, HBV, HCV and TB and improve health outcomes.

Lower dietary mineral intake is significantly associated with cervical cancer risk in a population-based cross-sectional study.

Population-based studies investigating the association between dietary mineral intake and risk of cervical intraepithelial neoplasia (CIN) or cervical cancer in Chinese women are few. We performed a cross-sectional analysis of screening data obtained from 2,304 women in 2014 within an ongoing cohort study comprising 40,000 women in China. Dietary intake was assessed using a semiquantitative food frequency questionnaire. Nutrition intake was calculated using a 26-item list of food sources drawn from a validated, comprehensive database. All participants were surveyed through in-person interviews, physical examinations, and laboratory tests. The Pearson chi-square test was used for categorical variables. Multivariable logistic regression models were used to evaluate the relationship between dietary mineral intake and CIN+ risk. The food frequency questionnaire exhibited acceptable reproducibility and reasonable validity in assessing nutrient intakes among these women. After adjusting for multiple potential confounders, low dietary calcium intake was associated with CIN2+ risk (first versus fourth quartile: odds ratio [OR]=1.52, 95% confidence interval [CI]: 1.01-2.32). Similar for magnesium (OR=1.80, 95% CI: 1.20-2.68), phosphorus (OR=1.69, 95% CI: 1.12-2.55), zinc (OR=1.55, 95% CI: 1.03-2.34), and potassium (OR=1.92, 95% CI: 1.28-2.88). Low dietary intakes of calcium and potassium were significantly associated with CIN1 risk. Increased CIN2+ risk correlated with rates of no oral contraceptives and lower levels of dietary Potassium. These results thus proposed that low dietary mineral intake was an independent risk factor, potential synergy may exist between low dietary mineral levels and oral contraceptives contribute to the development of higher-grade CIN and cervical cancer.

BaSDAS: a web-based pooled CRISPR-Cas9 knockout screening data analysis system.

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

Functional Dependency Analysis Identifies Potential Druggable Targets in Acute Myeloid Leukemia.

Simple SummaryNew drugs are needed for treating acute myeloid leukemia (AML). We analyzed data from genome-edited leukemia cells to identify druggable targets. These targets were necessary for AML cell survival and had favorable binding sites for drug development. Two lists of genes are provided for target validation, drug discovery, and drug development. The deKO list contains gene-targets with existing compounds in development. The disKO list contains gene-targets without existing compounds yet and represent novel targets for drug discovery.Refractory disease is a major challenge in treating patients with acute myeloid leukemia (AML). Whereas the armamentarium has expanded in the past few years for treating AML, long-term survival outcomes have yet to be proven. To further expand the arsenal for treating AML, we searched for druggable gene targets in AML by analyzing screening data from a lentiviral-based genome-wide pooled CRISPR-Cas9 library and gene knockout (KO) dependency scores in 15 AML cell lines (HEL, MV411, OCIAML2, THP1, NOMO1, EOL1, KASUMI1, NB4, OCIAML3, MOLM13, TF1, U937, F36P, AML193, P31FUJ). Ninety-four gene KOs met the criteria of (A) specifically essential to AML cell survival, (B) non-essential in non-AML cells, and (C) druggable according to three-dimensional (3D) modeling or ligand-based druggability scoring. Forty-four of 94 gene-KOs (47%) had an already-approved drug match and comprised a drug development list termed “deKO.” Fifty of 94 gene-KOs (53%) had no drug in development and comprised a drug discovery list termed “disKO.” STRING analysis and gene ontology categorization of the disKO targets preferentially cluster in the metabolic processes of UMP biosynthesis, IMP biosynthesis, dihydrofolate metabolism, pyrimidine nucleobase biosynthesis, vitellogenesis, and regulation of T cell differentiation and hematopoiesis. Results from this study serve as a testable compendium of AML drug targets that, after validation, may be translated into new therapeutics.

Screening characteristics of PSEN1 E280A mutation carriers and non‐carriers in the API Autosomal Dominant Alzheimer’s Disease Colombia Trial

AbstractBackgroundThe Colombia Alzheimer’s Prevention Initiative (API) Registry was a resource for enrollment into the API Colombia clinical trial. Potentially eligible candidates from the Colombia API Registry went through a prescreening and then in‐person screening process with the goal of enrolling them in the API ADAD Colombia Trial. Analysis of screening data might provide additional information to consider for other AD prevention trials. We present descriptive screening data from the API ADAD Colombia trial in Presenilin 1 (PSEN1) E280A mutation carriers vs non‐carriers.MethodConsent was obtained from 319 potentially eligible participants after prescreening. Screening data from 315, including 210 mutation carriers, were used to compare demographics, medical comorbidities, toxic and reproductive antecedents, selected clinical, functional, and anthropometric measurements, vital signs, and brain MRI and laboratory results in the mutation carrier and non‐carrier groups. Descriptive statistics comparing mutation carriers and non‐carriers were performed using generalized linear regression models using link function according to whether the outcome was categorical or numerical. Results were adjusted for age, sex, level of education, depression or body mass index (BMI) depending upon which measurements were compared.ResultResults of the above characteristics at screening for carriers and non‐carriers will be presented. Briefly, compared to mutation non‐carriers in screening, carriers were younger (mean 40 vs 48 years), had similar educational attainment (mean 8.3 vs 7.5 years), and showed generally lower cognitive performance, especially in memory (e.g., mean (sd) CERAD world list scores were 20.30 (3.82) vs 19.46 (3.68), respectively). There were no differences in other demographic characteristics, medical comorbidities, toxic and reproductive antecedents, anthropometric measurements, vital signs, MRI findings or laboratory results. Mutation non‐carriers compared to carriers showed a non‐significant trend towards more vascular risks according to medical comorbidities (hypertension, dyslipidemia), borderline higher level of triglycerides and cholesterol, microvascular changes in the brain and higher BMI. The higher prevalence of vascular risk factors among non‐carriers may be explained by an 8‐year age difference between non‐carriers vs carriers.ConclusionThe API ADAD Colombia Trial screening data provide insights into demographics as well as clinical, cognitive and non‐cognitive characteristics, and medical comorbidities of a (PSEN1) E280A population.

Reasons for study exclusion by sex in lanabecestat studies AMARANTH and DAYBREAK‐ALZ

AbstractBackgroundSex‐based differences in pathophysiology and clinical presentation of Alzheimer’s Disease (AD) have been reported. These differences could impact trial eligibility. This analysis of screening data assesses the most common reasons for exclusion within sex.MethodPhase 2/3 AMARANTH (NCT02245737) enrolled early AD (MCI due to AD, mild AD dementia) with MMSE 20‐30 and RBANS DMI ≤85. Phase 3 DAYBREAK‐ALZ (NCT02783573) enrolled mild AD with MMSE 20‐26. For MCI, NIA‐AA criteria were met, with CDR of 0.5 and memory box score ≥0.5. For mild AD, NIA‐AA criteria were met, with CDR of 0.5 or 1 and memory box score ≥0.5. Both studies enrolled participants 55‐85 years‐of‐age with proof of amyloid (PET scan or cerebrospinal fluid). Excluded participants meeting prespecified criteria were permitted ≤2 rescreens. Reasons for exclusion and patients randomized are presented by sex. The top three reasons for exclusion are compared by female and male subsets. In AMARANTH, participants could fail &gt;1 criterion. For DAYBREAK‐ALZ, MMSE exclusion is further divided into MMSE score subsets (&lt;20 or &gt;26, when available). Statistical comparisons are made using Pearson’s Chi‐Square and not adjusted for multiplicity.ResultFor both studies, proportions of females represented in reasons for exclusion and randomization are similar (AMARANTH: 52% vs. 53%; DAYBREAK‐ALZ: 57% vs. 59%). In AMARANTH, MMSE score not within range was more commonly reported and lack of presence of amyloid was less commonly reported in the female subset than the male subset (17.8% vs 13.5% (p&lt;0.001) and 22.4% vs 24.5% (p&lt;0.05) of reasons, respectively). In DAYBREAK‐ALZ, proportions of reasons for exclusion in sex subsets were similar. However, MMSE score &lt;20 was more common and MMSE score &gt;26 less common as a reason for exclusion in the female subset compared to the male subset (females vs. males: score &lt;20: 24.6% vs 18.3%, score &gt;26: 12.8% vs 19.7%; p&lt;0.001 for each).ConclusionThese results suggest females presenting for screening may have more advanced disease. Possible reasons include late referral of females due to advanced verbal memory skills delaying recognition of disease, social circumstances, faster disease progression of females identified from clinical trial site databases, or differences in educational attainment.

Analysis of quantitative high throughput screening data using a robust method for nonlinear mixed effects models

Quantitative high throughput screening (qHTS) assays are used to assess toxicity for many chemicals in a short period by collectively analyzing them at several concentrations. Data are routinely analyzed using nonlinear regression models; however, we propose a new method to analyze qHTS data using a nonlinear mixed effects model. qHTS data are generated by repeating the same experiment several times for each chemical; therefor, they can be viewed as if they are repeated measures data and hence analyzed using a nonlinear mixed effects model which accounts for both intra- and inter-individual variabilities. Furthermore, we apply a one-step approach incorporating robust estimation methods to estimate fixed effect parameters and the variance-covariance structure since outliers or influential observations are not uncommon in qHTS data. The toxicity of chemicals from a qHTS assay is classified based on the significance of a parameter related to the efficacy of the chemicals using the proposed method. We evaluate the performance of the proposed method in terms of power and false discovery rate using simulation studies comparing with one existing method. The proposed method is illustrated using a dataset obtained from the National Toxicology Program.

Abstract PO-242: Viral hepatitis among foreign-born communities in the Washington- Baltimore metropolitan area: 5-year prevalence data and implications for linkage to care follow-up

Abstract Background: Viral hepatitis is a major public health problem around the world and in the United States, with significant morbidity and mortality. This research aimed to provide updated prevalence estimates and linkage-to-care rates for hepatitis B virus (HBV) and hepatitis C virus (HCV) infections among foreign-born immigrants in the Washington-Baltimore metropolitan area. Methods: This retrospective cohort study analyzed screening data obtained from over 275 community-based outreach events held from 2015 to 2019. Through strategic collaborations and culturally-appropriate programs, the Hepatitis B Initiative of Washington DC was able to provide no-cost HBV and HCV testing, vaccination, and treatment linkage-to-care services to 9,489 and 9,427 individuals, respectively. We examined the prevalence of positive HBV (HBsAg+) and HCV (HCVAb+) infections and linkage-to-care with associated sociodemographic characteristics. Results: Overall, prevalence amongst foreign-born clients screened over the 5-year period was 4.3% for HBV and 1.1% for HCV. The highest HBV prevalence was among participants born in Malaysia (8.5%), Cambodia (7.7%), and Vietnam (6.9%), whereas HCV prevalence was highest among participants born in Mongolia (5.0%), Cameroon (3.2%), and Burma (1.5%). Among the 378 HBV- and 102 HCV-infected individuals who were referred to care, linkage- to-care rates were 87.0% (2016-2019) and 47.1% (2017-2019) respectively. Among those linked to care, an overwhelming proportion reported not having health insurance (74.8%) and/or a usual source of care (75.3%); the majority were also female (52.8%), over 30 years of age (96.6%), and born in Asia (78.0%). Conclusions: Foreign-born individuals from Asia and Africa had the highest prevalence of viral hepatitis. These results underscore the need to disaggregate screening data by country of birth to inform prevention and linkage-to-care programs and their impact. Additionally, optimal HBV and HCV screening and linkage-to-care can be achieved among harder-to-reach at-risk populations through partnerships with community organizations, health centers, and public health departments. Citation Format: Daisy Le, Annie Coriolan, Jane Pan, Carla Jean Berg, Y. Alicia Hong, Angeline Nguyen, Hai Chi Le, Lorien Cindy Abroms, Hee-Soon Juon, Y. Tony Yang. Viral hepatitis among foreign-born communities in the Washington- Baltimore metropolitan area: 5-year prevalence data and implications for linkage to care follow-up [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-242.

El uso de las mascarillas en la protección de las infecciones respiratorias: una revisión de revisiones

IntroductionThe global health emergency caused by the current COVID-19 pandemic is resulting in a huge challenge at all levels. The use of masks may reduce the spread of the infection by minimising the excretion of Flügge droplets. The objective of this study was to compile the evidence available on the use of masks in relation to respiratory infections. MethodologyAn umbrella review (review of systematic reviews) was conducted. Two reviewers independently carried out the screening process, data extraction and data analysis. Discrepancies were resolved with a third reviewer, and the assessment of the risk of bias of the studies was carried out using the AMSTAR 2 tool. The Rayyan QCRI program was used for the screening process. ResultsA total of eight systematic reviews were included. The studies analysed the use of masks in the general population, in long-term care facilities, in hospitals and at mass gatherings, and compared the effectiveness thereof in preventing infection. The results of this review revealed that the use of masks is associated with a protective effect against respiratory infections in healthcare facilities, in long-term care facilities and at mass gatherings. ConclusionsIn light of the results, it seems reasonable to recommend the use of masks to the general population, but this use should be accompanied by a training programme to improve compliance, as not using them properly may increase the risk of infection.

Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens

BackgroundPooled library CRISPR/Cas9 knockout screening across hundreds of cell lines has identified genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the number of essential genes detected from these monogenic knockout screens is low compared to the number of constitutively expressed genes in a cell.ResultsThrough a systematic analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we observe that half of all constitutively expressed genes are never detected in any CRISPR screen and that these never-essentials are highly enriched for paralogs. We investigated functional buffering among approximately 400 candidate paralog pairs using CRISPR/enCas12a dual-gene knockout screening in three cell lines. We observe 24 synthetic lethal paralog pairs that have escaped detection by monogenic knockout screens at stringent thresholds. Nineteen of 24 (79%) synthetic lethal interactions are present in at least two out of three cell lines and 14 of 24 (58%) are present in all three cell lines tested, including alternate subunits of stable protein complexes as well as functionally redundant enzymes.ConclusionsTogether, these observations strongly suggest that functionally redundant paralogs represent a targetable set of genetic dependencies that are systematically under-represented among cell-essential genes in monogenic CRISPR-based loss of function screens.

Using blood donors and solid organ transplant donors and recipients to estimate the seroprevalence of cytomegalovirus and Epstein-Barr virus in Canada: A cross-sectional study.

Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections are common, causing significant morbidity in pregnancy (congenital CMV) and transplant recipients (CMV, EBV). Canadian prevalence data are needed to model disease burden and develop strategies for future vaccines. We estimated prevalence using screening data from blood donors and solid organ transplant (SOT) donors and recipients. We retrospectively analyzed CMV and EBV serology from Alberta SOT donors (n = 3,016) and recipients (n = 4,614) (1984-2013) and Canadian Blood Services blood donors (n = 1,253,350) (2005-2014), studying associations with age, sex, organ, year, and geographic region. CMV seroprevalence rises gradually with age. By age 70, CMV seropositivity ranged from 67% (blood donors) to 73% (SOT recipients). Significant proportions of women of child-bearing age were CMV-seronegative (organ donors, 44%; SOT recipients, 43%; blood donors, 61%). Blood donor CMV seroprevalence decreased from 48% in Western Canada to 30% in Eastern Canada. Women were more likely to be CMV-seropositive (ORs = 1.58, 1.45, and 1.11 for organ donors, SOT recipients, and blood donors, respectively) and EBV-seropositive (ORs = 1.87 and 1.46 for organ donors and SOT recipients, respectively). EBV prevalence rises rapidly, and by age 17-29 years, 81% of SOT recipients and 90% of organ donors were seropositive. Canada has relatively low and perhaps decreasing age-specific EBV and CMV prevalence, making Canadians vulnerable to primary infection-associated morbidity and suggesting benefit from future vaccines. Collection and analysis of routine serology screening data are useful for observing trends.

Analysis of the HIV antibody screening results among the preoperative examination patients in Beijing Tongren Hospital from 2008 to 2018

Objective: To understand the HIV antibody screening results among the preoperative examination patients in Beijing Tongren Hospital from 2008 to 2018. Methods: A retrospective analysis of the HIV antibody screening data of thepreoperative examination patients from 2008 to 2018 in Beijing Tongren Hospital was performed with software SPSS19.0. Trend chi-square was used to analyze the positive rate, age, marital status, household registration and so on. Results: Among the 750 013 clinical patients, 428 (0.057%) cases were screened anti-HIV positive and 370(0.049%) cases were confirmed anti-HIV positive when detected with western blotting.Most of the HIV-infectedindividuals were non-Beijing nationality, accounting for 60.27%.Among the 370 HIV-infected patients, there were 334 males (90.27%) and 36 females (9.73%). The age was distributed mainly between 20-40 years old (62.43%), secondly between 40-60 years old (28.65%).361 (97.57%)HIV-infected cases were transmitted by the sex and the MSM men increased from 2008 to 2018 (trend χ²=7.307, P=0.007). There were 22 cases (5.95%) with HBsAg positive, 11 cases (2.97%) with anti-HCV positive. Among the 159 HIV-positive patients (42.97%) companied with syphilis specific antibody positive, there were 64 cases (17.30%) with TRUST tests positive. Additionally, 178 (48.11%) HIV-infected patientsfirst visited doctors because of ocular disease in the hospital; secondly, 71 (19.19%) HIV-infected patientsfirst visited the dermatology. Conclusions: The number of HIV-infected patientsmarkedly increased from 2008 to 2018. The sexual transmission is still the main pathway for HIV infection, particularly homosexual transmission. Moreover, the results indicate that it is necessary to detect HIV antibody for the ocular disease patients.

S1330 High Discovery Rate of Previously Undiagnosed Patients With Eosinophilic Gastritis and Duodenitis Using a Systematic Endoscopic Biopsy Protocol: Screening Data Analysis From ENIGMA, a Randomized Controlled Trial

INTRODUCTION: Eosinophilic gastrointestinal (GI) disorders (EGIDs) such as eosinophilic gastritis (EG) and duodenitis (EoD) are chronic inflammatory conditions characterized by aberrant accumulation and activation of localized tissue eosinophils and mast cells. Patients (pts) with EG/EoD present with non-specific, often debilitating GI symptoms including abdominal pain and cramping, early satiety, nausea and diarrhea. Non-specific symptoms, the absence of consensus diagnostic histopathologic guidelines, and the perception of rarity contribute to a delay in diagnosis of pts with EG/EoD. While the prevalence of EG/EoD is currently estimated to be ∼50,000 in the US, this may be an underestimate. We aimed to evaluate the prevalence of EG/EoD among symptomatic patients not previously diagnosed. METHODS: We reviewed screening data from ENIGMA, a multi-center, randomized, double-blind, placebo-controlled phase 2 trial assessing the safety and efficacy of AK002, an anti-Siglec-8 monoclonal antibody, in pts with EG/EoD. Adult pts were screened with a validated, daily 8-symptom EG/EoD questionnaire to capture moderate-severely symptomatic pts. Those who met symptom inclusion criteria underwent upper endoscopy (EGD) with gastric and duodenal biopsies as per protocol (12 total: 4 biopsies each from the gastric antrum, gastric corpus, and duodenum). Symptomatic pts meeting histologic definition of EG (≥30 eos/hpf in ≥5 hpfs) and/or EoD (≥30 eos/hpf in ≥3hpfs) were eligible for randomization. RESULTS: 113 pts entered screening for ENIGMA. 51 had no prior history of EG/EoD, 26 (51%) of whom met symptom criteria and underwent screening endoscopy. Of these 26 symptomatic pts, 15 (58%) met histologic criteria for EG/EoD, 13 of whom were randomized in the study. These 13 pts, previously given functional GI diagnoses, were clinically similar in constellation and magnitude of symptoms compared to the 52 randomized pts with previously established EG/EoD. CONCLUSION: There is growing evidence that EG/EoD is underdiagnosed, and that the true US prevalence may be higher than 50,000. Among moderate-severely symptomatic pts without known history of EG/EoD who entered screening for ENIGMA, 58% met histologic criteria for EG/EoD. EGD with multiple systematic gastric and duodenal biopsies of pts with chronic non-specific GI symptoms, including those with functional GI conditions, may demonstrate a higher prevalence of EG/EoD than is currently estimated.Figure 1.: Discovery Rate of Newly Diagnosed EG/EoD Patients in ENIGMA Screening 1) Consortium of Eosinophilic Gastrointestinal disease Researchers (CEGIR) sites; n = 62 entered screening 2) Primarily general gastrointestinal practices and professional GI research centers; n = 51 entered screening.Figure 2.: Similar Symptom Burden in Established and Newly Diagnosed EG/EoD Patients.Table 1.: Characteristics of Established and Newly Diagnosed EG/EoD Patients

Abstract 830: New bioinformatics workflow of genome-wide CRISPR-Cas9 knockout screens

Abstract Introduction: Genome-wide CRISPR-Cas9 based loss-of-function screens can be used to find essential genes for proliferation and survival of cancer cells. While recent studies have focused on establishing reference sets of essential and non-essential genes, correcting copy number effect and characterizing off-target effect, it lacks in-depth studies of the effects of gene abundance and sgRNAs that targeting multi-genomic loci. To fill this gap timely, we here present a bioinformatics workflow to reduce false positives in CRISPR-Cas9 screens. Description: Gastric adenocarcinoma cell line AGS was infected with CRISPR knockout library (TKOv3) at a multiplicity of infection of 0.3~0.4. We used the cells right after puromycin selection as the baseline sample, and the cells cultured for 14 days or 20 days as the negative selection samples. The sgRNA inserts were amplified by PCR and the corresponding libraries were sequenced on NextSeq 500 with a single-end 75 bp run, followed by analysis by MAGeCK. The read counts of sgRNAs were normalized by non-essential genes to reduce false positives. The RNA-seq data and copy number data were obtained by CCLE portal. To characterize sgRNAs targeting multiple-genomic loci, Bowtie was used to align sgRNA to the reference human genome (GRCh38) with no mismatch, and only the alignments followed by NGG PAM site were remained for downstream analysis. Summary: Integration of RNA-seq data with CRISPR negative screen results showed that the selection signal was noisy for the lowly expressed genes. The fraction of selected essential genes (overall FDR&amp;lt;0.05, absolute value of beta score &amp;gt;1) was as low as 0.11% among the genes with the bottom 10% expression level, while 27% among the genes with the top 10% expression level. After filtering out the lowly expressed genes (&amp;lt;0.06 RPKM), the selected essential genes had an FDR much closer to 0. Out of the 40 essential genes selected without filtering out lowly expressed genes, none of them was reported oncogenes in literature. To study the influences of multiple alignments of sgRNAs, we only considered the ones with perfect alignments (i.e., no mismatch) so that we can prevent it from being confounding with off-target effects caused by mismatch tolerance. Log fold changes in read counts were calculated for each sgRNA between a later time point (day 14 or 20) vs. baseline (day 0). The median log fold change significantly decreased as a function of the number of perfect alignments (p = 0.0001, Jonckheere trend test). This supports the hypothesis that a sgRNA aligned to several DNA targets will introduce multiple double stranded cuts, and thus will result in biased essentiality scores. Conclusions: Filtering out lowly-expressed genes prior to CRISPR screen data analysis can reduce false positives. In addition, multiple-target sgRNAs can lead to false positives but the effect needs further analysis in a case by case manner. Citation Format: Yue Zhao, Xue Wu, Yuru Wang, Kin Fai Au, Lijun Cheng, Lang Li. New bioinformatics workflow of genome-wide CRISPR-Cas9 knockout screens [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 830.

Bayesian modelling of high-throughput sequencing assays with malacoda.

NGS studies have uncovered an ever-growing catalog of human variation while leaving an enormous gap between observed variation and experimental characterization of variant function. High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged. In the massively parallel reporter assay (MPRA), short barcodes are counted by sequencing DNA libraries transfected into cells and the cell's output RNA in order to simultaneously measure the shifts in transcription induced by thousands of genetic variants. These counts present many statistical challenges, including overdispersion, depth dependence, and uncertain DNA concentrations. So far, the statistical methods used have been rudimentary, employing transformations on count level data and disregarding experimental and technical structure while failing to quantify uncertainty in the statistical model. We have developed an extensive framework for the analysis of NGS functionalization screens available as an R package called malacoda (available from github.com/andrewGhazi/malacoda). Our software implements a probabilistic, fully Bayesian model of screen data. The model uses the negative binomial distribution with gamma priors to model sequencing counts while accounting for effects from input library preparation and sequencing depth. The method leverages the high-throughput nature of the assay to estimate the priors empirically. External annotations such as ENCODE data or DeepSea predictions can also be incorporated to obtain more informative priors-a transformative capability for data integration. The package also includes quality control and utility functions, including automated barcode counting and visualization methods. To validate our method, we analyzed several datasets using malacoda and alternative MPRA analysis methods. These data include experiments from the literature, simulated assays, and primary MPRA data. We also used luciferase assays to experimentally validate several hits from our primary data, as well as variants for which the various methods disagree and variants detectable only with the aid of external annotations.

A Detailed Analysis of the Factors Influencing Neonatal TSH: Results From a 6-Year Congenital Hypothyroidism Screening Program.

Background: Neonatal thyrotropin (TSH) on dried blood spot (DBS), the most common screening strategy for primary congenital hypothyroidism (CH), is influenced by numerous factors that may hinder a true CH diagnosis. A second test can thus be performed to clarify the initial findings, although its application varies among screening programs.Objectives: The aim of this study was to evaluate the effect of maternal and neonatal factors on neonatal TSH levels and offer practical screening recommendations.Methods: We retrospectively analyzed screening data of 62,132 neonates born in Abruzzo, an Italian region considered mildly iodine deficient, between 2011 and 2016. We then performed a multiple linear regression to model the relationship between TSH (the dependent variable) and 13 independent variables extracted from blood collection cards.Results: Most neonates (53,551 of 62,132, 86%) had normal TSH and no clinical indications for a second screening. A minority (1,423, 2.3%) had elevated TSH in the initial DBS, which was confirmed in 97 cases (7%) on a second screen. The remaining neonates (6,594, 10.6%) had a normal initial TSH but underwent a second test in accordance with screening protocols, and were found to have delayed TSH elevation in 23 cases (0.4%). Those 120 newborns (97 + 23), considered highly suspicious for primary CH, were referred to a pediatrician for confirmatory testing and excluded from subsequent analysis of factors influencing TSH levels. Sex (β regression coefficient, β = 1.11 female to male, 95% CI 1.09, 1.12) and age at collection (β = 0.78 day 5 to days 2–3, 95% CI 0.74, 0.83) affected neonatal TSH, suggesting the utility of specific nomograms. In addition, prematurity (β = 0.85 term to preterm, 95% CI 0.80, 0.91), dopamine use (β = 0.71, 95% CI 0.62, 0.81), and birth weight (β = 1.40 normal vs. very low, 95% CI 1.05, 1.89) strongly influenced neonatal TSH.Conclusions: Neonatal TSH is influenced by several factors supporting the delineation of local sex- and age-adjusted TSH cutoffs, and the universal adoption of a second TSH test in neonates at risk of missed primary CH diagnosis.