Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses.

Genetic determinants of IgG antibody response to COVID-19 vaccination.

Human humoral immune responses to SARS-CoV-2 vaccines exhibit substantial inter-individual variability and have been linked to vaccine efficacy. To elucidate the underlying mechanism behind this variability, we conducted a genome-wide association study (GWAS) on the anti-spike IgG serostatus of UK Biobank participants who were previously uninfected by SARS-CoV-2 and had received either the first dose (n = 54,066) or the second dose (n = 46,232) of COVID-19 vaccines. Our analysis revealed significant genome-wide associations between the IgG antibody serostatus following the initial vaccine and human leukocyte antigen (HLA) class II alleles. Specifically, the HLA-DRB1∗13:02 allele (MAF = 4.0%, OR = 0.75, p = 2.34e-16) demonstrated the most statistically significant protective effect against IgG seronegativity. This protective effect was driven by an alteration from arginine (Arg) to glutamic acid (Glu) at position 71 on HLA-DRß1 (p = 1.88e-25), leading to a change in the electrostatic potential of pocket 4 of the peptide binding groove. Notably, the impact of HLA alleles on IgG responses was cell type specific, and we observed a shared genetic predisposition between IgG status and susceptibility/severity of COVID-19. These results were replicated within independent cohorts where IgG serostatus was assayed by two different antibody serology tests. Our findings provide insights into the biological mechanism underlying individual variation in responses to COVID-19 vaccines and highlight the need to consider the influence of constitutive genetics when designing vaccination strategies for optimizing protection and control of infectious disease across diverse populations.

The immunogenetics of viral antigen response is associated with subtype-specific glioma risk and survival.

Glioma is a highly fatal cancer with prognostically significant molecular subtypes and few known risk factors. Multiple studies have implicated infections in glioma susceptibility, but evidence remains inconsistent. Genetic variants in the human leukocyte antigen (HLA) region modulate host response to infection and have been linked to glioma risk. In this study, we leveraged genetic predictors of antibody response to 12 viral antigens to investigate the relationship with glioma risk and survival. Genetic reactivity scores (GRSs) for each antigen were derived from genome-wide-significant (p < 5 × 10-8) variants associated with immunoglobulin G antibody response in the UK Biobank cohort. We conducted parallel analyses of glioma risk and survival for each GRS and HLA alleles imputed at two-field resolution by using data from 3,418 glioma-affected individuals subtyped by somatic mutations and 8,156 controls. Genetic reactivity scores to Epstein-Barr virus (EBV) ZEBRA and EBNA antigens and Merkel cell polyomavirus (MCV) VP1 antigen were associated with glioma risk and survival (Bonferroni-corrected p < 0.01). GRSZEBRA and GRSMCV were associated in opposite directions with risk of IDH wild-type gliomas (ORZEBRA = 0.91, p = 0.0099/ORMCV = 1.11, p = 0.0054). GRSEBNA was associated with both increased risk for IDH mutated gliomas (OR = 1.09, p = 0.040) and improved survival (HR = 0.86, p = 0.010). HLA-DQA1∗03:01 was significantly associated with decreased risk of glioma overall (OR = 0.85, p = 3.96 × 10-4) after multiple testing adjustment. This systematic investigation of the role of genetic determinants of viral antigen reactivity in glioma risk and survival provides insight into complex immunogenomic mechanisms of glioma pathogenesis. These results may inform applications of antiviral-based therapies in glioma treatment.

Nivolumab and brentuximab vedotin with or without bendamustine for R/R Hodgkin lymphoma in children, adolescents, and young adults.

Children, adolescents, and young adults (CAYA) with relapsed/refractory (R/R) classic Hodgkin lymphoma (cHL) without complete metabolic response (CMR) before autologous hematopoietic cell transplantation (auto-HCT) have poor survival outcomes. CheckMate 744, a phase 2 study for CAYA (aged 5-30 years) with R/R cHL, evaluated a risk-stratified, response-adapted approach with nivolumab plus brentuximab vedotin (BV) followed by BV plus bendamustine for patients with suboptimal response. Risk stratification was primarily based on time to relapse, prior treatment, and presence of B symptoms. We present the primary analysis of the standard-risk cohort. Data from the low-risk cohort are reported separately. Patients received 4 induction cycles with nivolumab plus BV; those without CMR (Deauville score >3, Lugano 2014) received BV plus bendamustine intensification. Patients with CMR after induction or intensification proceeded to consolidation (high-dose chemotherapy/auto-HCT per protocol). Primary end point was CMR any time before consolidation. Forty-four patients were treated. Median age was 16 years. At a minimum follow-up of 15.6 months, 43 patients received 4 induction cycles (1 discontinued), 11 of whom received intensification; 32 proceeded to consolidation. CMR rate was 59% after induction with nivolumab plus BV and 94% any time before consolidation (nivolumab plus BV ± BV plus bendamustine). One-year progression-free survival rate was 91%. During induction, 18% of patients experienced grade 3/4 treatment-related adverse events. This risk-stratified, response-adapted salvage strategy had high CMR rates with limited toxicities in CAYA with R/R cHL. Most patients did not require additional chemotherapy (bendamustine intensification). Additional follow-up is needed to confirm durability of disease control. This trial was registered at www.clinicaltrials.gov as #NCT02927769.

VerSoX B07-B: a high-throughput XPS and ambient pressure NEXAFS beamline at Diamond Light Source.

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45-2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.

Accurate Identification of Mucinous Pancreatic Cystic Lesions Using Small-Volume Analytes.

INTRODUCTION: The accurate identification of mucinous pancreatic cystic lesions (PCLs) is paramount for cancer risk stratification. Cyst fluid carcinoembryonic antigen (CEA), the only routinely used test, requires high volumes and has low sensitivity. We aimed to compare the performance of two investigational small-volume biomarkers, glucose and the protease gastricsin, to CEA for PCL classification. METHODS: We obtained cyst fluid samples from 81 patients with pathologically confirmed PCLs from four institutions between 2003 and 2016. Gastricsin activity was measured using an internally quenched fluorescent substrate. Glucose levels were measured with a standard glucometer. CEA levels were obtained from the medical record. Models using Classification and Regression Trees were created to predict mucinous status. Model performance was evaluated using nested cross-validation. RESULTS: Gastricsin activity, CEA, and glucose levels from patients with mucinous (n = 50) and nonmucinous (n = 31) PCLs were analyzed. Area under the curve (AUC) was similar for individual classifiers (gastricsin volume normalized [GVN] 0.88; gastricsin protein concentration normalized [GPN] 0.95; glucose 0.83; CEA 0.84). The combination of two classifiers did not significantly improve AUC, with CEA + GVN (0.88) performing similarly to CEA + GPN (0.95), GVN + glucose (0.87), GPN + glucose (0.95), and CEA + glucose (0.84). The three-analyte combination performed similarly to single and dual classifiers (GPN + glucose + CEA AUC 0.95; GVN + glucose + CEA AUC 0.87). After multiple comparison corrections, there were no significant differences between the individual, dual, and triple classifiers. CONCLUSIONS: Gastricsin and glucose performed similarly to CEA and required <5% of the volume required for CEA; these classifiers may be useful in patients with limited cyst fluid. Future multicenter prospective studies are needed to validate and compare these novel small-volume biomarkers.

Pediatric brain tumors: Origins, epidemiology, and classification - The 2022 Brain Tumor Epidemiology Consortium meeting report.

The Brain Tumor Epidemiology Consortium (BTEC) is an international organization that fosters collaboration among scientists focused on understanding the epidemiology of brain tumors with interests ranging from the etiology of brain tumor development and outcomes to the control of morbidity and mortality. The 2022 annual BTEC meeting with the theme "Pediatric Brain Tumors: Origins, Epidemiology, and Classification" was held in Lyon, France on June 20 - 22, 2022. Scientists from North America and Europe presented recent research and progress in the field. The meeting content is summarized in this report.

Pre-surgery immune profiles of adult glioma patients.

INTRODUCTION: Although immunosuppression is a known characteristic of glioma, no previous large studies have reported peripheral blood immune cell profiles prior to patient surgery and chemoradiation. This report describes blood immune cell characteristics and associated variables prior to surgery among typical glioma patients seen at a large University practice. METHODS: We analyzed pre-surgery blood samples from 139 glioma patients diagnosed with a new or recurrent grade II/III glioma (LrGG, n = 64) or new glioblastoma (GBM, n = 75) and 454 control participants without glioma. Relative cell fractions of CD4, CD8, B-cells, Natural Killer cells, monocytes, and neutrophils, were estimated via a validated deconvolution algorithm from blood DNA methylation measures from Illumina EPIC arrays. RESULTS: Dexamethasone use at time of blood draw varied by glioma type being highest among patients with IDH wild-type (wt) GBM (75%) and lowest for those with oligodendroglioma (14%). Compared to controls, glioma patients showed statistically significant lower cell fractions for all immune cell subsets except for neutrophils which were higher (all p-values < 0.001), in part because of the higher prevalence of dexamethasone use at time of blood draw for IDHwt GBM. Patients who were taking dexamethasone were more likely to have a low CD4 count (< 200, < 500), increased neutrophils, low absolute lymphocyte counts, higher total cell count and higher NLR. CONCLUSION: We show that pre-surgery blood immune profiles vary by glioma subtype, age, and more critically, by use of dexamethasone. Our results highlight the importance of considering dexamethasone exposures in all studies of immune profiles and of obtaining immune measures prior to use of dexamethasone, if possible.

Socioeconomic status and childhood central nervous system tumors in California.

PURPOSE: Childhood central nervous system (CNS) tumors are the leading cause of cancer mortality in children. Previous studies have suggested that some childhood cancers, including primary CNS tumors, may be associated with higher socioeconomic status (SES). METHODS: We linked data from the California Cancer Registry to California birth records for children (age 0-19 years) diagnosed with primary CNS tumors during 1988-2011 and analyzed multiple measures of parental SES around the birth of their children and subsequent risk for childhood CNS tumors. Our SES measures included birth record-derived parental education and insurance utilization. For a subset of subjects born between 1997 and 2007, we geocoded addresses and examined census-derived median household income and educational level. RESULTS: We analyzed data for 3,022 children with primary CNS tumors and 10,791 matched controls. We found consistent evidence across multiple measures that lower estimates of SES are associated with a reduced risk of CNS tumors. In tumor subgroup analyses, this relationship was most consistent in astrocytomas and ependymomas, with varying findings for embryonal tumors. CONCLUSION: Higher parental SES appears to be a risk factor for childhood CNS tumors in California. Further research is needed to determine specific exposures that may explain this increased risk.

Epidemiology of Brain and Other CNS Tumors.

PURPOSE OF REVIEW: Brain and other central nervous system (CNS) tumors, while rare, cause significant morbidity and mortality across all ages. This article summarizes the current state of the knowledge on the epidemiology of brain and other CNS tumors. RECENT FINDINGS: For childhood and adolescent brain and other CNS tumors, high birth weight, non-chromosomal structural birth defects and higher socioeconomic position were shown to be risk factors. For adults, increased leukocyte telomere length, proportion of European ancestry, higher socioeconomic position, and HLA haplotypes increase risk of malignant brain tumors, while immune factors decrease risk. Although no risk factor accounting for a large proportion of brain and other CNS tumors has been discovered, the use of high throughput "omics" approaches and improved detection/measurement of environmental exposures will help us refine our current understanding of these factors and discover novel risk factors for this disease.

Application of goal-directed therapy for the use of concentrated antithrombin for heparin resistance during cardiac surgery.

The maintenance of anticoagulation in adult patients undergoing cardiopulmonary bypass is dependent upon a number of factors, including heparin concentration and adequate antithrombin activity. Inadequate anticoagulation increases the risk of thrombosis and jeopardizes both vascular and extracorporeal circuit integrity. The purpose of this study was to evaluate a goal-directed approach for the use of antithrombin in patients who were resistant to heparin. Following institutional review board approval, data were obtained from quality improvement records. A goal-directed protocol for antithrombin was established based upon heparin dosing (400 IU kg-1 body weight) and achieving an activated clotting time of ⩾500 seconds prior to cardiopulmonary bypass. Two groups of patients were identified as those receiving antithrombin and those not receiving antithrombin. Outcome measures included activated clotting time values and transfusion rates. Consecutive patients (n = 140) were included in the study with 10 (7.1%) in the antithrombin group. The average antithrombin dose was 1,029.0 ± 164.5 IU and all patients had restoration to the activated clotting time levels. Patients in the antithrombin group were on preoperative heparin therapy (80.0% vs. 24.6%, p = 0.001). Prior to cardiopulmonary bypass the activated clotting time values were lower in the antithrombin group (417.7 ± 56.1 seconds vs. 581.1 ± 169.8 seconds, p = 0.003). Antithrombin patients had a lower heparin sensitivity index (0.55 ± 0.17 vs. 1.05 ± 0.44 seconds heparin-1 IU kg-1, p = 0.001), received more total heparin (961.3 ± 158.5 IU kg-1 vs. 677.5 ± 199.0 IU kg-1, p = 0.001), more cardiopulmonary bypass heparin (22,500 ± 10,300 IU vs. 12,100 ± 13,200 IU, p = 0.016), and more protamine (5.4 ± 1.2 vs. 4.1 ± 1.1 mg kg-1, p = 0.003). The intraoperative transfusion rate was higher in the antithrombin group (70.0% vs. 35.4%, p = 0.035), but no differences were seen postoperatively. Utilization of a goal-directed algorithm for the administration of antithrombin for the treatment of heparin resistance is effective in patients undergoing cardiac surgery.

Maternal Infection in Pregnancy and Childhood Leukemia: A Systematic Review and Meta-analysis.

OBJECTIVE: To summarize the published evidence regarding the association between maternal infection during pregnancy and childhood leukemia. STUDY DESIGN: In this systematic review and meta-analysis (PROSPERO number, CRD42018087289), we searched PubMed and Embase to identify relevant studies. We included human studies that reported associations of at least one measure of maternal infection during pregnancy with acute lymphoblastic leukemia (ALL) or all childhood leukemias in the offspring. One reviewer extracted the data first using a standardized form, and the second reviewer independently checked the data for accuracy. Two reviewers used the Newcastle-Ottawa Scale to assess the quality of included studies. We conducted random effects meta-analyses to pool the ORs of specific type of infection on ALL and childhood leukemia. RESULTS: This review included 20 studies (ALL, n = 15; childhood leukemia, n = 14) reported in 32 articles. Most (>65%) included studies reported a positive association between infection variables and ALL or childhood leukemia. Among specific types of infection, we found that influenza during pregnancy was associated with higher risk of ALL (pooled OR, 3.64; 95% CI, 1.34-9.90) and childhood leukemia (pooled OR, 1.77; 95% CI, 1.01-3.11). Varicella (pooled OR, 10.19; 95% CI, 1.98-52.39) and rubella (pooled OR, 2.79; 95% CI, 1.16-6.71) infections were also associated with higher childhood leukemia risk. CONCLUSIONS: Our findings suggest that maternal infection during pregnancy may be associated with a higher risk of childhood leukemia.

ClustR: A Space-Time Cluster Analysis R Package for Individual-level Data.

BACKGROUND: Until recently, large individual-level longitudinal data were unavailable to investigate clusters of disease, driving a need for suitable statistical tools. We introduce a robust, efficient, intuitive R package, ClustR, for space-time cluster analysis of individual-level data. METHODS: We developed ClustR and evaluated the tool using a simulated dataset mirroring the population of California with constructed clusters. We assessed Cluster's performance under various conditions and compared it with another space-time clustering algorithm: SaTScan. RESULTS: ClustR mostly exhibited high sensitivity for urban clusters and low sensitivity for rural clusters. Specificity was generally high. Compared with SaTScan, ClustR ran faster and demonstrated similar sensitivity, but had lower specificity. Select cluster types were detected better by ClustR than SaTScan and vice versa. CONCLUSION: ClustR is a user-friendly, publicly available tool designed to perform efficient cluster analysis on individual-level data, filling a gap among current tools. ClustR and SaTScan exhibited different strengths and may be useful in conjunction.

Spatial-Temporal Cluster Analysis of Childhood Cancer in California.

BACKGROUND: The observance of nonrandom space-time groupings of childhood cancer has been a concern of health professionals and the general public for decades. Many childhood cancers are suspected to have initiated in utero; therefore, we examined the spatial-temporal randomness of the birthplace of children who later developed cancer. METHODS: We performed a space-time cluster analysis using birth addresses of 5,896 cases and 23,369 population-based, age-, sex-, and race/ethnicity-matched controls in California from 1997 to 2007, evaluating 20 types of childhood cancer and three a priori designated subgroups of childhood acute lymphoblastic leukemia (ALL). We analyzed data using a newly designed semiparametric analysis program, ClustR, and a common algorithm, SaTScan. RESULTS: We observed evidence for nonrandom space-time clustering for ALL diagnosed at 2-6 years of age in the South San Francisco Bay Area (ClustR P = 0.04, SaTScan P = 0.07), and malignant gonadal germ cell tumors in a region of Los Angeles (ClustR P = 0.03, SaTScan P = 0.06). ClustR did not identify evidence of clustering for other childhood cancers, although SaTScan suggested some clustering for Hodgkin lymphoma (P = 0.09), astrocytoma (P = 0.06), and retinoblastoma (P = 0.06). CONCLUSIONS: Our study provides evidence that childhood ALL diagnosed at 2-6 years and malignant gonadal germ cell tumors sporadically occurs in nonrandom space-time clusters. Further research is warranted to identify epidemiologic features that may inform the underlying etiology.

Shape controlled assembly of carboxylic acids: formation of a binary monolayer by intercalation into molecular nanotunnels.

Binary self-assembled monolayers (SAMs) combining a Y-shaped aromatic carboxylic acid (1,3,5-benzenetribenzoic acid, H3BTB) and a cage-type alicyclic carboxylic acid (adamantane carboxylic acid, AdCA) were investigated by scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The SAMs, prepared by molecular adsorption from solution on Au substrates modified by underpotential deposition of Ag, exhibit a pronounced dependence of their structure on the assembly protocol. Exposing an H3BTB SAM to AdCA, the highly regular row structure of the native H3BTB layer persists and STM imaging does not show signs of AdCA adsorption. This is in striking contrast to the disordered arrangements of H3BTB and the presence of AdCA employing the inverted adsorption sequence or coadsorption of the two molecules. However, spectroscopic analysis of the H3BTB SAM exposed to AdCA reveals the presence also of the latter, suggesting that the AdCA molecules are hidden in the nanotunnels of the H3BTB monolayer. Direct evidence for the intercalation of AdCA is obtained by STM manipulation experiments which lay bare areas of AdCA molecules upon local removal of H3BTB. Surprisingly, these are densely packed and arranged into a highly ordered monolayer. Formation of such a compact AdCA layer is explained by expulsion of AdCA from the H3BTB nanotunnels of the surrounding intact mixed SAM, driven by release of stress in the nanotunnels built up when AdCA is intercalated.

In utero cytomegalovirus infection and development of childhood acute lymphoblastic leukemia.

It is widely suspected, yet controversial, that infection plays an etiologic role in the development of acute lymphoblastic leukemia (ALL), the most common childhood cancer and a disease with a confirmed prenatal origin in most cases. We investigated infections at diagnosis and then assessed the timing of infection at birth in children with ALL and age, gender, and ethnicity matched controls to identify potential causal initiating infections. Comprehensive untargeted virome and bacterial analyses of pretreatment bone marrow specimens (n = 127 ALL in comparison with 38 acute myeloid leukemia cases in a comparison group) revealed prevalent cytomegalovirus (CMV) infection at diagnosis in childhood ALL, demonstrating active viral transcription in leukemia blasts as well as intact virions in serum. Screening of newborn blood samples revealed a significantly higher prevalence of in utero CMV infection in ALL cases (n = 268) than healthy controls (n = 270) (odds ratio [OR], 3.71, confidence interval [CI], 1.56-7.92, P = .0016). Risk was more pronounced in Hispanics (OR=5.90, CI=1.89-25.96) than in non-Hispanic whites (OR=2.10 CI= 0.69-7.13). This is the first study to suggest that congenital CMV infection is a risk factor for childhood ALL and is more prominent in Hispanic children. Further investigation of CMV as an etiologic agent for ALL is warranted.

The Effect of Standardizing Autologous Prime Techniques in Patients Undergoing Cardiac Surgery with Cardiopulmonary Bypass.

Autologous priming (AP) of the extracorporeal circuit has been used as a technique to reduce iatrogenic anemia in patients undergoing cardiac surgery with cardiopulmonary bypass (CPB). The purpose of this study was to review the results of standardizing AP techniques to reduce variation among clinicians and its effect on clinical outcomes. Standardized goal-directed protocols for AP were established by the cardiac team and applied to all adult cardiac surgical patients where CPB was used. Following Institutional Review Board approval, data were analyzed for two sequential groups of patients: Non-standardized AP (NST-AP) and standardized AP (ST-AP). Exclusion criteria included pre-CPB hemodynamic instability and preoperative hematocrit (Hct) values less than 30%. The primary end point was the transfusion of red blood cells (RBCs), whereas secondary end points included Hct change and other perioperative allogeneic blood product transfusions. Data are presented as mean and SD. Of the 192 patients evaluated, 82 were in the NST-AP group and 110 in the ST-AP group. There were no preoperative demographic differences across groups. Total AP volume was lower in the NST-AP group than in the ST-AP patients (486.8 ± 259.6 mL vs. 1,048.2 ± 218.7 mL, p < .001). Whereas pre-CPB Hct values were identical between the groups, the first on-CPB (25.7% ± 4.5% vs. 27.9% ± 4.2%, p < .001), high CPB (27.7% ± 3.5% vs. 29.1% ± 3.6%, p < .008), and first postoperative (32.5% ± 4.0% vs. 34.3% ± 3.9%, p < .003) were all significantly higher in ST-AP patients. Perioperative transfusion rate was higher in NST-AP patients (63.6%) vs. ST-AP (44.6%), p < .01. There was no difference in intraoperative RBC transfusion, but postoperatively, more patients in the NST-AP group received RBCs than those in the ST-AP group (51.2% vs. 28.2%, p < .01). The application of an ST-AP protocol was effective in reducing hemodilution, which was associated within higher Hcts and lower postoperative transfusion rates.

BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia.

Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latino white ALL cases and controls from two independent California childhood leukemia studies, and additional Genetic Epidemiology Research on Aging study controls. Ethnicity-stratified association analyses were performed using logistic regression, with meta-analysis including 3,133 cases (1,949 Latino, 1,184 non-Latino white) and 12,135 controls (8,584 Latino, 3,551 non-Latino white). SNP associations were identified at both BMI1 and PIP4K2A. After adjusting for the lead PIP4K2A SNP, genome-wide significant associations remained at BMI1, and vice-versa (pmeta < 10-10 ), supporting independent effects. Lead SNPs differed by ethnicity at both peaks. We sought functional variants in tight linkage disequilibrium with both the lead Latino SNP among Admixed Americans and lead non-Latino white SNP among Europeans. This pinpointed rs11591377 (pmeta = 2.1 x 10-10 ) upstream of BMI1, residing within a hematopoietic stem cell enhancer of BMI1, and which showed significant preferential binding of the risk allele to MYBL2 (p = 1.73 x 10-5 ) and p300 (p = 1.55 x 10-3 ) transcription factors using binomial tests on ChIP-Seq data from a SNP heterozygote. At PIP4K2A, we identified rs4748812 (pmeta = 1.3 x 10-15 ), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.

Herpesvirus Infection in Infants with Gastroschisis.

BACKGROUND: Gastroschisis is a congenital malformation that has been shown to be more common in younger mothers and appears to be increasing in prevalence in the United States and elsewhere. Epidemiologic data suggest a potential role of infection and recent studies report an association between maternal antibodies to human herpesviruses (HHV) and development of gastroschisis. METHODS: In this study, we examined newborn bloodspots from 50 children with gastroschisis and 50 healthy controls using a highly sensitive digital droplet polymerase chain reaction assay covering eight human herpesviruses [herpes simplex sirus 1/2, Epstein-Barr virus (HHV-4), cytomegalovirus (HHV-5), HHV-6A/B, HHV-7, and HHV-8], to examine the presence of herpesvirus DNA at birth, which would suggest in utero infection. RESULTS: One control tested positive for low-level cytomegalovirus infection. We found no evidence of an association between herpesvirus DNA in neonatal blood spots taken at birth and gastroschisis. CONCLUSIONS: Our results do not support direct involvement of herpesviruses in the etiology of gastroschisis. However, there are several limitations in our study, most notably the known induction of this congenital malformation early in pregnancy and our analysis of blood taken at birth. Therefore, we cannot conclude that herpesviruses play no role in the etiology of gastroschisis and further research is needed to better define this relationship.