Family-based Whole Exome Sequencing of Autism Spectrum Disorder Reveals Novel De Novo Variants in Korean Population

Objectives

The objective of this family-based whole exome sequencing (WES) is to examine genetic variants of autism spectrum disorder (ASD) in Korean population.

Methods

The probands with ASD and their biological parents were recruited in this study. We ascertained diagnosis based on DSM-5™ criteria, using Autism Diagnostic Observation Schedule and Autism Diagnostic Interview–Revised. We selected probands with typical phenotypes of ASD both in social interaction/communication and repetitive behaviour/limited interest domains, with intellectual disability (IQ < 70), for attaining homogeneity of the phenotypes. First, we performed WES minimum 50× for 13 probands and high-coverage pooled sequencing for their parents. We performed additional WES for 38 trio families, at least 100× depth. De novo mutations were confirmed by Sanger sequencing. All the sequence reads were mapped onto the human reference genome (hg19 without Y chromosome). Bioinformatics analyses were performed by BWA-MEM, Picard, GATK, and snpEff for variant annotation. We selected de novo mutation candidates from probands, which are neither detected in two pooled samples nor both parents.

Results

Fifty-one subjects with ASD (5 females, 40∼175 months, mean IQ 42) and their families were included in this study. We discovered 109 de novo variants from 46 families. Twenty-nine variants are expected to be amino acid changing, potentially causing deleterious effects. We assume CELSR3, MYH1, ATXN1, IDUA, NFKB1, and C4A/C4B may have adverse effect on central nerve system.

Conclusions

We observed novel de novo variants which are assumed to contribute to development of ASD with typical phenotypes and low intelligence in WES study.

Disclosure of interest

This work has been supported by Healthcare Technology R&D project (No: A120029) by Ministry of Health and Welfare, Republic of Korea.

Designer drugs: Review and implications for emergency management

In the past 10 years, "designer drugs" such as synthetic cannabinoids and cathinones have emerged and come into widespread use, resulting in more overdose cases involving these new drugs in the United States. Emergency departments regularly treat a diverse array of drug intoxications, and providers must be cognizant of novel drugs of abuse and the associated clinical presentations in order to provide the most appropriate care. This review aims to describe the epidemiology, mechanism of action, clinical presentation, and treatment of intoxication for both the common and newest drugs of abuse.

Approach to the diagnosis of drug hypersensitivity reactions: similarities and differences between Europe and North America

Drug hypersensitivity reactions (DHRs) affect an unknown proportion of the general population, and are an important public health problem due to their potential to cause life-threatening anaphylaxis and rare severe cutaneous allergic reactions. DHR evaluations are frequently needed in both ambulatory and hospital settings and have a complex diagnosis that requires a detailed clinical history and other tests that may include in vitro tests and in vivo procedures such as skin tests and drug provocation tests. Although over the years both European and U.S. experts have published statements on general procedures for evaluating DHRs, a substantial discordance in their daily management exists. In this review, we highlight both the differences and the similarities between the European and U.S. perspectives. While a general consensus exists on the importance of skin tests for evaluating DHRs, concordance between Americans and Europeans exists solely regarding their use in immediate reactions and the fact that a confirmation of a presumptive diagnosis by drug provocation tests is often the only reliable way to establish a diagnosis. Finally, great heterogeneity exists in the application of in vitro tests, which require further study to be well validated.

Abstract P4-03-08: Mechanisms of CD8+ T cell immunosuppression in triple negative breast cancer

Triple negative breast cancer (TNBC), defined as tumors lacking expression of the estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), are especially difficult to treat effectively. While ER+ and HER2+ breast cancer subtypes can be treated with Tamoxifen and Herceptin, respectively, there are no targeted therapies for TNBC patients. Furthermore, while only 20-30% of TNBC patients respond to chemotherapy in the neoadjuvant setting, overall outcome remains poor for non-responding patients. However, mounting evidence suggests that immune-checkpoint inhibitor immunotherapies may be especially promising for TNBC patients. We and others have shown that the presence of CD8+ T cells, a crucial component of the cytotoxic arm of the adaptive immune response, is a sign of good clinical outcome in TNBC patients. However, good outcome only correlates with CD8 +T cell invasion of the tumor parenchyma. Some patients had an accumulation of CD8+ T cells in the surrounding tumor-associated stroma, but not the tumor epithelia, and these patients responded as poorly as patients with no CD8 T cells at all. Yet how cancer associated fibroblasts (CAFs), the dominant cell type of the tumor-associated stroma, affects CD8+ T cell invasion into the tumor epithelia is still poorly understood. To identify potential stroma-dependent mechanisms which potentiate or inhibit CD8+ T cells invasion into the tumor epithelia, we performed gene expression profiling of laser-capture microdissected tumor-associated stroma (and matched epithelia) from 38 TNBC cases. Here we identify several stromal and epithelial canonical pathways as well as biomarkers that are associated with and may explain the accumulation of CD8 T cells outside of the tumor epithelia.

Citation Format: Gruosso T, Gigoux M, Bertos N, Zuo D, Manem V, Monette A, Lapointe R, Haibe-Kains B, Park M. Mechanisms of CD8+ T cell immunosuppression in triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-03-08.

Abstract P1-06-11: A targetable EGFR-driven tumor-initiating program in breast cancer

Background: Inter- and intra-tumour heterogeneity underlies variability in therapeutic response. Although targeting of the epidermal growth factor receptor (EGFR) in breast cancer has failed to demonstrate clinical efficacy at the population level, complete and durable responses have been reported at low frequencies. The molecular determinants of these responses are unknown, but are of importance in the era of precision medicine.

Results: We performed a patient-derived xenograft (PDX) clinical trial with gefitinib in a breast cancer PDX cohort. Consistent with clinical trial data, gefitinib exhibited limited efficacy across most models. One PDX, however, demonstrated a complete and durable (&gt;6 months) clinical response, and was subject to deep molecular profiling to identify determinants of response. Exome sequencing revealed no single nucleotide variants or copy number alterations in EGFR pathway members. EGFR was differentially expressed between the two major cellular subpopulations identified by single-cell RNAseq and this cellular heterogeneity in EGFR expression was validated immunohistochemically. Fluorescence-activated cell sorting of the EGFRhi subpopulation revealed cells with enhanced stem-like properties, including ALDH activity, sphere-forming capacity in vitro, ability to form tumours in vivo and seeding lung micrometastases from orthotopically transplanted tumours. Tumourspheres derived from EGFRhi cells developed into mixed EGFRhi and EGFRlo subpopulations, as did macrometastases, supporting that EGFRhi subpopulation can self-renew and re-populate. Analysis of expressed SNVs in the single-cell RNAseq data, filtered by variants identified from exome sequencing, showed no clonal segregation, supporting a non-clonal origin of the functionally distinct EGFRhi and EGFRlo subpopulations. This EGFR-driven tumour initiating cell program was observed in independent PDX models, some which showed growth inhibition in response to gefitinib.

Conclusions: Using bulk and single-cell genomic profiling, we identified and functionally validated an EGFR-driven tumour-initiating program in a subset of aggressive breast tumours, which may be predictive of gefitinib sensitivity. This contradicts traditional beliefs that good therapeutic targets are homogenously expressed, in that we show that a target displaying intra-tumour heterogeneity can be effective so long that it is expressed in the tumour-initiating population.

Citation Format: Savage P, Saleh SMI, Wang Y-C, Revil T, Badescu D, Liu L, Iacucci E, Zuo D, Bertos N, Munoz-Ramos V, Asselah J, Meterissian S, Omeroglu A, Hébert S, Kleinman C, Park M, Ragoussis J. A targetable EGFR-driven tumor-initiating program in breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-11.

Abstract P3-10-07: Impact of enrollment in clinical trials on survival of metastatic breast cancer patients

Background: The number of patients worldwide with metastatic breast cancer (MBC) who participate in therapeutic clinical trials has remained so far low. One of the reasons is a lack of opportunity, whereas another is fear of health care providers and patients of poor outcome of the use of new drugs. We therefore investigated whether survival in patients with MBC who participated in first-line therapeutic clinical trials is worse than that in patients who received only standard care and never enrolled in a clinical trial. We hypothesized that first-line therapeutic clinical trials do not negatively affect survival outcome. Methods: We reviewed the records of 5501 patients with MBC treated at The University of Texas MD Anderson Cancer Center from January 2000 to December 2010. We extracted a first cohort of 285 patients enrolled in a therapeutic clinical trial for the first time for first-line systemic MBC treatment. The second cohort, referred to as the eligible control population, consisted of 367 patients without comorbidities who did not participate in a clinical trial at any stage of their disease; these patients lived in Harris County, in which MD Anderson is located, and thus could be potentially eligible for MD Anderson's financial assistance program. To limit confounding factors, we excluded male patients and patients with known brain metastasis from both cohorts. Results: The median follow-up duration in our cohort was 7.16 years (95% confidence interval [CI], 6.53-7.64 years). We observed discrepancies in race (minorities were less represented in the clinical trial arm), estrogen receptor (ER) status (more ER-positive than ER-negative patients participated in clinical trials), and metastatic disease site (fewer patients with bone metastasis participated in clinical trials) between the two groups. Overall, we observed no significant differences in progression-free survival (PFS) or overall survival (OS) duration between the treatment arms. Specifically, in the clinical trial cohort, the median PFS duration was 7.00 months (95% CI, 5.72-8.71 months), and the median OS duration was 28.48 months (95% CI, 22.70-34.60 months). In the control cohort, the median PFS duration was 10.02 months (95% CI, 7.13-11.99 months), and the median OS duration was 28.71 months (95% CI, 24.41-31.31 months) (P = .089 and .335, respectively). Conclusion: In MBC patients, enrolling in first-line therapeutic clinical trials does not result in worse survival than does never enrolling in a clinical trial. This study should reassure health care providers in demonstrating that enrollment in a clinical trial does not negatively affect survival in MBC patients.

Citation Format: Le Du F, FUJII T, Park M, Liu D, Hsu L, Gonzalez-Angulo A-M, Ueno NT. Impact of enrollment in clinical trials on survival of metastatic breast cancer patients [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-10-07.

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Measurements of the [Formula: see text] production cross section in lepton+jets final states in pp collisions at 8 [Formula: see text] and ratio of 8 to 7 [Formula: see text] cross sections

A measurement of the top quark pair production ([Formula: see text]) cross section in proton-proton collisions at the centre-of-mass energy of 8[Formula: see text] is presented using data collected with the CMS detector at the LHC, corresponding to an integrated luminosity of 19.6[Formula: see text]. This analysis is performed in the [Formula: see text] decay channels with one isolated, high transverse momentum electron or muon and at least four jets, at least one of which is required to be identified as originating from hadronization of a b quark. The calibration of the jet energy scale and the efficiency of b jet identification are determined from data. The measured [Formula: see text] cross section is [Formula: see text]. This measurement is compared with an analysis of 7[Formula: see text] data, corresponding to an integrated luminosity of 5.0[Formula: see text], to determine the ratio of 8[Formula: see text] to 7[Formula: see text] cross sections, which is found to be [Formula: see text]. The measurements are in agreement with QCD predictions up to next-to-next-to-leading order.

Multiplexed efficient on-chip sample preparation and sensitive amplification-free detection of Ebola virus

An automated microfluidic sample preparation multiplexer (SPM) has been developed and evaluated for Ebola virus detection. Metered air bubbles controlled by microvalves are used to improve bead-solution mixing thereby enhancing the hybridization of the target Ebola virus RNA with capture probes bound to the beads. The method uses thermally stable 4-formyl benzamide functionalized (4FB) magnetic beads rather than streptavidin coated beads with a high density of capture probes to improve the target capture efficiency. Exploiting an on-chip concentration protocol in the SPM and the single molecule detection capability of the antiresonant reflecting optical waveguide (ARROW) biosensor chip, a detection limit of 0.021pfu/mL for clinical samples is achieved without target amplification. This RNA target capture efficiency is two orders of magnitude higher than previous results using streptavidin beads and the limit of detection (LOD) improves 10×. The wide dynamic range of this technique covers the whole clinically applicable concentration range. In addition, the current sample preparation time is ~1h which is eight times faster than previous work. This multiplexed, miniaturized sample preparation microdevice establishes a key technology that intended to develop next generation point-of-care (POC) detection system.

Chemical manipulation of edge-contact and encapsulated graphene by dissociated hydrogen adsorption

We investigate the hydrogenation in the h-BN/graphene/h-BN heterostructure and report the successful intercalation and modification of electrical properties.

Neutral plane control by using polymer/graphene flake composites for flexible displays

PMMA/graphene composites with varying graphene content can control the modulus and thus the neutral plane of flexible displays while enhancing barrier properties.

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Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].