Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes

Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.

Genotoxic colibactin mutational signature in colorectal cancer is associated with clinicopathological features, specific genomic alterations and better survival

Background and Aims

The microbiome has long been suspected of a role in colorectal cancer (CRC) tumorigenesis. The mutational signature SBS88 mechanistically links CRC development with the strain of Escherichia coli harboring the pks island that produces the genotoxin colibactin, but the genomic, pathological and survival characteristics associated with SBS88-positive tumors are unknown.

Methods

SBS88-positive CRCs were identified from targeted sequencing data from 5,292 CRCs from 17 studies and tested for their association with clinico-pathological features, oncogenic pathways, genomic characteristics and survival.

Results

In total, 7.5% (398/5,292) of the CRCs were SBS88-positive, of which 98.7% (392/398) were microsatellite stable/microsatellite instability low (MSS/MSI-L), compared with 80% (3916/4894) of SBS88 negative tumors (p=1.5x10-28). Analysis of MSS/MSI-L CRCs demonstrated that SBS88 positive CRCs were associated with the distal colon (OR=1.84, 95% CI=1.40-2.42, p=1x10-5) and rectum (OR=1.90, 95% CI=1.44-2.51, p=6x10-6) tumor sites compared with the proximal colon. The top seven recurrent somatic mutations associated with SBS88-positive CRCs demonstrated mutational contexts associated with colibactin-induced DNA damage, the strongest of which was the APC:c.835-8A>G mutation (OR=65.5, 95%CI=39.0-110.0, p=3x10-80). Large copy number alterations (CNAs) including CNA loss on 14q and gains on 13q, 16q and 20p were significantly enriched in SBS88-positive CRCs. SBS88-positive CRCs were associated with better CRC-specific survival (p=0.007; hazard ratio of 0.69, 95% CI=0.52-0.90) when stratified by age, sex, study, and by stage.

Conclusion

SBS88-positivity, a biomarker of colibactin-induced DNA damage, can identify a novel subtype of CRC characterized by recurrent somatic mutations, copy number alterations and better survival. These findings provide new insights for treatment and prevention strategies for this subtype of CRC.

Airway Resistance and Respiratory Distress in Laryngeal Cancer: A Computational Fluid Dynamics Study

BACKGROUND

Obstructive upper airway pathologies are a great clinical challenge for the airway surgeon. Protection against acute obstruction is critical, but avoidance of unnecessary tracheostomy must also be considered. Decision-making regarding airway, although supported by some objective findings, is largely guided by subjective experience and training. This investigation aims to study the relationship between clinical respiratory distress and objective measures of airway resistance in laryngeal cancer as determined by computational fluid dynamic (CFD) and morphometric analysis.

METHODS

Retrospective CT and clinical data were obtained for series of 20 cases, defined as newly diagnosed laryngeal cancer patients who required admission or urgent airway surgery, and 20 controls. Cases and controls were matched based on T-staging. Image segmentation and morphometric analysis were first performed. Computational models based on the lattice Boltzmann method were then created and used to quantify the continuous mass flow, rigid wall, and constant static pressure inlet boundary conditions.

RESULTS

The analysis demonstrated a significant relationship between airway resistance and acute obstruction (OR 1.018, 95% CI 1.001-1.045). Morphometric analysis similarly demonstrated a significant relationship when relating measurements based on the minimum cross-section, but not on length of stenosis. Morphometric measurements also showed significance in predicting CFD results, and their relationship demonstrated that airway pressures increase exponentially below 2.5 mm. Tumor subsite did not show a significant difference, although the glottic subgroup tended to have higher resistances.

CONCLUSION

Airway resistance analysis from CFD computation correlated with presence of acute distress requiring emergent management. Morphometric analysis showed a similar correlation, demonstrating a radiologic airway assessment technique on which future risk estimation could be performed.

LEVEL OF EVIDENCE

4 (case-control study) Laryngoscope, 133:2734-2741, 2023.

The Difference in Clinical Behavior of Gene Fusions Involving RET/PTC Fusions and THADA/IGF2BP3 Fusions in Thyroid Nodules

BACKGROUND

Molecular testing has been used as an adjunct to morphological evaluation in the workup of thyroid nodules. This study investigated the impact of two gene fusions, RET/PTC and THADA/IGF2BP3, that have been described as oncogenic events in thyroid neoplasms.

METHODS

We performed a retrospective, single-centered study at a McGill University teaching hospital in Montreal, Canada, from January 2016 to August 2021. We included patients who underwent surgery for thyroid nodules that pre-operatively underwent molecular testing showing either RET/PTC or THADA/IGF2BP3 gene fusion.

RESULTS

This study included 697 consecutive operated thyroid nodules assessed using molecular testing, of which five had the RET/PTC fusion and seven had the THADA/IGF2BP3 fusion. Of the five nodules in the RET/PTC group, 100% were malignant and presented as Bethesda V/VI. Eighty percent (4/5) were found to have lymph node metastasis. Twenty percent (1/5) had extrathyroidal extensions. Sixty percent (3/5) were a diffuse sclerosing variant of papillary thyroid carcinoma, and the rest were the classical variant. Of the seven THADA/IGF2BP3 nodules, all presented as Bethesda III/IV and 71.4% (5/7) were malignant based on the final pathology analysis, and 28.6% (2/7) were NIFTP. All the THADA/IGF2BP3 fusion malignancies were a follicular variant of papillary thyroid carcinoma. None had lymph node metastasis or displayed extrathyroidal extensions.

CONCLUSIONS

RET/PTC nodules presented as Bethesda V/VI and potentially had more aggressive features, whereas THADA/IGF2BP3 nodules presented as Bethesda III/IV and had more indolent behavior. This understanding may allow clinicians to develop more targeted treatment plans, such as the extent of surgery and adjuvant radioactive iodine treatment.

Does the likelihood of malignancy in thyroid nodules with RAS mutations increase in direct proportion with the allele frequency percentage?

BACKGROUND

Genomic testing has enhanced pre-surgical decision making for cytologically indeterminate thyroid nodules, but there remains uncertainty regarding RAS mutations. The addition of extra genetic alterations to previous driver mutation panels has been shown to improve predictive value. This study aims to evaluate the relationship between the mutant allele frequency (AF) and likelihood of malignancy in thyroid nodules with RAS mutations.

METHODS

A retrospective cohort review was performed evaluating patients with indeterminate cytology (Bethesda categories III, IV and V) and ThyroSeq® v3 testing demonstrating a RAS mutation, who underwent surgery. Univariate and multivariate regression analyses were used to evaluate relationships between AF, other genetic alterations, and malignancy.

RESULTS

Thirty-nine patients met criteria, 77% of the thyroid nodules (30/39) were found to be malignant. None demonstrated aggressive pathology. On univariate regression, there was no relationship between AF and likelihood of malignancy. There was, however, a significant correlation between AF and the rate of an additional genetic alteration. Multivariate analysis found a trend between RAS, a second genetic alteration and malignancy, but it did not reach statistical significance.

CONCLUSIONS

There was no direct relationship between the level of allelic frequency in thyroid nodules expressing RAS mutations and the likelihood of malignancy. There was a statistically significant relationship between increasing AF and the presence of a second genetic abnormality, suggesting a possible progression from initial driver mutation and then a second genetic alteration prior to malignant transformation.

Association between germline variants and somatic mutations in colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease with evidence of distinct tumor types that develop through different somatically altered pathways. To better understand the impact of the host genome on somatically mutated genes and pathways, we assessed associations of germline variations with somatic events via two complementary approaches. We first analyzed the association between individual germline genetic variants and the presence of non-silent somatic mutations in genes in 1375 CRC cases with genome-wide SNPs data and a tumor sequencing panel targeting 205 genes. In the second analysis, we tested if germline variants located within previously identified regions of somatic allelic imbalance were associated with overall CRC risk using summary statistics from a recent large scale GWAS (n≃125 k CRC cases and controls). The first analysis revealed that a variant (rs78963230) located within a CNA region associated with TLR3 was also associated with a non-silent mutation within gene FBXW7. In the secondary analysis, the variant rs2302274 located in CDX1/PDGFRB frequently gained/lost in colorectal tumors was associated with overall CRC risk (OR = 0.96, p = 7.50e-7). In summary, we demonstrate that an integrative analysis of somatic and germline variation can lead to new insights about CRC.

Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures

Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.

Genetic Regulation of DNA Methylation Yields Novel Discoveries in GWAS of Colorectal Cancer

BACKGROUND

Colorectal cancer has a strong epigenetic component that is accompanied by frequent DNA methylation (DNAm) alterations in addition to heritable genetic risk. It is of interest to understand the interrelationship of germline genetics, DNAm, and colorectal cancer risk.

METHODS

We performed a genome-wide methylation quantitative trait locus (meQTL) analysis in 1,355 people, assessing the pairwise associations between genetic variants and lymphocytes methylation data. In addition, we used penalized regression with cis-genetic variants ± 1 Mb of methylation to identify genome-wide heritable DNAm. We evaluated the association of genetically predicted methylation with colorectal cancer risk based on genome-wide association studies (GWAS) of over 125,000 cases and controls using the multivariate sMiST as well as univariately via examination of marginal association with colorectal cancer risk.

RESULTS

Of the 142 known colorectal cancer GWAS loci, 47 were identified as meQTLs. We identified four novel colorectal cancer-associated loci (NID2, ATXN10, KLHDC10, and CEP41) that reside over 1 Mb outside of known colorectal cancer loci and 10 secondary signals within 1 Mb of known loci.

CONCLUSIONS

Leveraging information of DNAm regulation into genetic association of colorectal cancer risk reveals novel pathways in colorectal cancer tumorigenesis. Our summary statistics-based framework sMiST provides a powerful approach by combining information from the effect through methylation and residual direct effects of the meQTLs on disease risk. Further validation and functional follow-up of these novel pathways are needed.

IMPACT

Using genotype, DNAm, and GWAS, we identified four new colorectal cancer risk loci. We studied the landscape of genetic regulation of DNAm via single-SNP and multi-SNP meQTL analyses.

Molecular and Pathology Features of Colorectal Tumors and Patient Outcomes Are Associated with Fusobacterium nucleatum and Its Subspecies animalis

BACKGROUND

Fusobacterium nucleatum (F. nucleatum) activates oncogenic signaling pathways and induces inflammation to promote colorectal carcinogenesis.

METHODS

We characterized F. nucleatum and its subspecies in colorectal tumors and examined associations with tumor characteristics and colorectal cancer-specific survival. We conducted deep sequencing of nusA, nusG, and bacterial 16s rRNA genes in tumors from 1,994 patients with colorectal cancer and assessed associations between F. nucleatum presence and clinical characteristics, colorectal cancer-specific mortality, and somatic mutations.

RESULTS

F. nucleatum, which was present in 10.3% of tumors, was detected in a higher proportion of right-sided and advanced-stage tumors, particularly subspecies animalis. Presence of F. nucleatum was associated with higher colorectal cancer-specific mortality (HR, 1.97; P = 0.0004). This association was restricted to nonhypermutated, microsatellite-stable tumors (HR, 2.13; P = 0.0002) and those who received chemotherapy [HR, 1.92; confidence interval (CI), 1.07-3.45; P = 0.029). Only F. nucleatum subspecies animalis, the main subspecies detected (65.8%), was associated with colorectal cancer-specific mortality (HR, 2.16; P = 0.0016), subspecies vincentii and nucleatum were not (HR, 1.07; P = 0.86). Additional adjustment for tumor stage suggests that the effect of F. nucleatum on mortality is partly driven by a stage shift. Presence of F. nucleatum was associated with microsatellite instable tumors, tumors with POLE exonuclease domain mutations, and ERBB3 mutations, and suggestively associated with TP53 mutations.

CONCLUSIONS

F. nucleatum, and particularly subspecies animalis, was associated with a higher colorectal cancer-specific mortality and specific somatic mutated genes.

IMPACT

Our findings identify the F. nucleatum subspecies animalis as negatively impacting colorectal cancer mortality, which may occur through a stage shift and its effect on chemoresistance.

Genetic architectures of proximal and distal colorectal cancer are partly distinct

OBJECTIVE

An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined.

DESIGN

To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling.

RESULTS

We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer.

CONCLUSION

Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.

A balance score between immune stimulatory and suppressive microenvironments identifies mediators of tumour immunity and predicts pan-cancer survival

BACKGROUND

The balance between immune-stimulatory and immune-suppressive mechanisms in the tumour microenvironment is associated with tumour rejection and can predict the efficacy of immune checkpoint-inhibition therapies.

METHODS

We consider the observed differences between the transcriptional programmes associated with cancer types where the levels of immune infiltration predict a favourable prognosis versus those in which the immune infiltration predicts an unfavourable prognosis and defined a score named Mediators of Immune Response Against Cancer in soLid microEnvironments (MIRACLE). MIRACLE deconvolves T cell infiltration, from inhibitory mechanisms, such as TGFβ, EMT and PI3Kγ signatures.

RESULTS

Our score outperforms current state-of-the-art immune signatures as a predictive marker of survival in TCGA (n = 9305, HR: 0.043, p value: 6.7 × 10^-36). In a validation cohort (n = 7623), MIRACLE predicts better survival compared to other immune metrics (HR: 0.1985, p value: 2.73 × 10^-38). MIRACLE also predicts response to checkpoint-inhibitor therapies (n = 333). The tumour-intrinsic factors inversely associated with the reported score such as EGFR, PRKAR1A and MAP3K1 are frequently associated with immune-suppressive phenotypes.

CONCLUSIONS

The association of cancer outcome with the level of infiltrating immune cells is mediated by the balance of activatory and suppressive factors. MIRACLE accounts for this balance and predicts favourable cancer outcomes.

Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk

Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.

Cumulative Burden of Colorectal Cancer-Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer

BACKGROUND & AIMS

Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC.

METHODS

We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants.

RESULTS

Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28-4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80-3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10-5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61-5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70-3.00). Sensitivity analyses were consistent with these findings.

CONCLUSIONS

In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Abstract 1598: Deep targeted sequencing of colorectal cancer cases to study associations of molecular subtypes with clinical, genetic, and lifestyle risk factors

Colorectal cancer (CRC) is the 3rd most common cancer in men and women, excluding skin cancer, and the 2nd leading cause of cancer death in the United States. In this biologically heterogeneous disease, a comprehensive molecular characterization is valuable for understanding tumorigenesis and studying associations with clinical, lifestyle, environmental, and germline genetic factors.

The Colon Cancer Family Registry (CCFR) and Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) collected clinical, germline genetic, and epidemiologic data from over 125,000 CRC cases. In a subset of 2,500 CRC cases, we conducted targeted deep sequencing of tumor and matching normal DNA. The custom AmpliSeq sequencing panel includes 205 genes, which were prioritized from literature and analyses of existing CRC tumor whole exome sequencing data. Next-generation sequencing was conducted on Illumina Hi-Seq 2500, and mean sequence coverages of 748x and 287x were attained for tumors and normal DNA samples, respectively. So far, 1,705 cases have been analyzed. Strelka and MuTect were used to identify somatic single nucleotide variants, and VarsScan2, Verdict, and Strelka were used to call indels. Orthogonal technologies were used for validation and improving mutation calling algorithms. Approximately 18% of tumors were hypermutated, among which 70% exhibited microsatellite instability (MSI). Hypermutated tumors with MSI occurred more frequently in proximal colon compared to distal colon and rectum (OR, 10.10; 95% CI, 6.98-14.63; P&lt;0.0001). Hypermutated tumors carried non-silent mutations in DNA mismatch repair genes (MSH2, MSH6, MLH1, MLH3, and PMS2), POLE, and POLD1. In POLE, in microsatellite stable hypermutated tumors, non-silent mutations were frequent in the exonuclease domain. Approximately 96% of non-hypermutated and 99% of hypermutated tumors contained non-silent mutations in genes in the Wnt/beta-catenin, p53, receptor tyrosine kinases/RAS, transforming growth factor-beta, and phosphatidylinositide 3-kinases pathways. Most tumors carried non-silent mutations in genes in more than one of these signaling pathways. The APC gene was the most significantly mutated gene in non-hypermutated tumors followed by TP53, KRAS, and PIK3CA. In hypermutated tumors, RNF43 was the most significantly mutated gene followed by BMPR2, APC, and BRAF.

CRC-specific survival was significantly more favorable among individuals with hypermutated tumors, regardless of POLE mutation status (HR=0.36, 95% CI: 0.23-0.57). This survival benefit was attenuated in analyses of overall survival (HR=0.82, 95% CI: 0.65-1.02).

This large dataset is being used to study associations with clinical, lifestyle, and environmental factors. This study will provide valuable information to develop better strategies for the prevention, diagnosis, and treatment of CRC.

Citation Format: Syed H. Zaidi, Amanda I. Phipps, Tabitha A. Harrison, Robert S. Steinfelder, Quang Trinh, Barbara L. Banbury, Adilya Rafikova, Megan Van Tassel, Emma Reid, Stefanie Brezina, Marios Giannakis, Charles S. Fuchs, Li Hsu, Andrea Gsur, Shuji Ogino, Steven Gallinger, Polly A. Newcomb, Peter T. Campbell, Wei Sun, Thomas J. Hudson, Ulrike Peters. Deep targeted sequencing of colorectal cancer cases to study associations of molecular subtypes with clinical, genetic, and lifestyle risk factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1598.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer

Every author has erroneously been assigned to the affiliation "62". The affiliation 62 belongs to the author Graham Casey.

Activation of hedgehog signaling associates with early disease progression in chronic lymphocytic leukemia

Targeted sequencing of 103 leukemia-associated genes in leukemia cells from 841 treatment-naive patients with chronic lymphocytic leukemia (CLL) identified 89 (11%) patients as having CLL cells with mutations in genes encoding proteins that putatively are involved in hedgehog (Hh) signaling. Consistent with this finding, there was a significant association between the presence of these mutations and the expression of GLI1 (χ2 test, P < .0001), reflecting activation of the Hh pathway. However, we discovered that 38% of cases without identified mutations also were GLI1+ Patients with GLI1+ CLL cells had a shorter median treatment-free survival than patients with CLL cells lacking expression of GLI1 independent of IGHV mutation status. We found that GANT61, a small molecule that can inhibit GLI1, was highly cytotoxic for GLI1+ CLL cells relative to that of CLL cells without GLI1. Collectively, this study shows that a large proportion of patients have CLL cells with activated Hh signaling, which is associated with early disease progression and enhanced sensitivity to inhibition of GLI1.

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer

Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.

Novel Common Genetic Susceptibility Loci for Colorectal Cancer

BACKGROUND

Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.

METHODS

We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.

RESULTS

The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.

CONCLUSIONS

This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.

Morphological analysis of sigmoid sinus anatomy: clinical applications to neurotological surgery

OBJECTIVES

The primary objective of this study was to use high-resolution micro-CT images to create accurate three-dimensional (3D) models of several intratemporal structures, and to compare several surgically important dimensions within the temporal bone. The secondary objective was to create a statistical shape model (SSM) of a dominant and non-dominant sigmoid sinus (SS) to provide a template for automated segmentation algorithms.

METHODS

A free image processing software, 3D Slicer, was utilized to create three-dimensional reconstructions of the SS, jugular bulb (JB), facial nerve (FN), and external auditory canal (EAC) from micro-CT scans. The models were used to compare several clinically important dimensions between the dominant and non-dominant SS. Anatomic variability of the SS was also analyzed using SSMs generated using the Statismo software framework.

RESULTS

Three-dimensional models from 38 temporal bones were generated and analyzed. Right dominance was observed in 74% of the paired SSs. All distances were significantly shorter on the dominant side (p < 0.05), including: EAC - SS (dominant: 13.7 ± 3.4 mm; non-dominant: 15.3 ± 2.7 mm), FN - SS (dominant: 7.2 ± 1.8 mm; non-dominant: 8.1 ± 2.3 mm), 2nd genu FN - superior tip of JB (dominant: 8.7 ± 2.2 mm; non-dominant: 11.2 ± 2.6 mm), horizontal distance between the superior tip of JB - descending FN (dominant: 9.5 ± 2.3 mm; non-dominant: 13.2 ± 3.5 mm), and horizontal distance between the FN at the stylomastoid foramen - JB (dominant: 5.4 ± 2.2 mm; non-dominant: 7.7 ± 2.1). Analysis of the SSMs indicated that SS morphology is most variable at its junction with the transverse sinus, and least variable at the JB.

CONCLUSIONS

This is the first known study to investigate the anatomical variation and relationships of the SS using high resolution scans, 3D  models and statistical shape analysis. This analysis seeks to guide neurotological surgical approaches and provide a template for automated segmentation and surgical simulation.

Discovery of common and rare genetic risk variants for colorectal cancer

To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

To understand the genetic drivers of immune recognition and evasion in colorectal cancer, we analyzed 1,211 colorectal cancer primary tumor samples, including 179 classified as microsatellite instability-high (MSI-high). This set includes The Cancer Genome Atlas colorectal cancer cohort of 592 samples, completed and analyzed here. MSI-high, a hypermutated, immunogenic subtype of colorectal cancer, had a high rate of significantly mutated genes in important immune-modulating pathways and in the antigen presentation machinery, including biallelic losses of B2M and HLA genes due to copy-number alterations and copy-neutral loss of heterozygosity. WNT/β-catenin signaling genes were significantly mutated in all colorectal cancer subtypes, and activated WNT/β-catenin signaling was correlated with the absence of T-cell infiltration. This large-scale genomic analysis of colorectal cancer demonstrates that MSI-high cases frequently undergo an immunoediting process that provides them with genetic events allowing immune escape despite high mutational load and frequent lymphocytic infiltration and, furthermore, that colorectal cancer tumors have genetic and methylation events associated with activated WNT signaling and T-cell exclusion.Significance: This multi-omic analysis of 1,211 colorectal cancer primary tumors reveals that it should be possible to better monitor resistance in the 15% of cases that respond to immune blockade therapy and also to use WNT signaling inhibitors to reverse immune exclusion in the 85% of cases that currently do not. Cancer Discov; 8(6); 730-49. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 663.

Transcriptome-wide characterization of the endogenous miR-34A-p53 tumor suppressor network

microRNA-34A is a critical component of the p53 network and expression of miR- 34A is down-regulated by promoter hypermethylation or focal deletions in numerous human cancers. Although miR-34A deregulation may be an important driver in cancer, the endogenous role of this microRNA in cellular homeostasis is not well characterized. To address this knowledge gap, we aimed to determine the transcriptional landscape of the miR-34A-p53 axis in non-transformed cells. Using primary skin-derived fibroblast cell lines from patients who developed childhood cancers, and who harbor either germline TP53 mutations or are TP53 wild type, we sought to characterize the transcriptional response to miR-34A modulation. Through transcriptome-wide RNA-Sequencing, we show for the first time that in human non- transformed cells harboring TP53 mutations, miR-34A functions in a noncanonical manner to influence noncoding RNA networks, including RNA components of the minor (U12) spliceosome, as well as TP53-dependent and independent epigenetic pathways. miR- 34A-regulated transcripts include known cell cycle mediators and abrogation of miR-34A leads to a TP53-dependent increase in the fraction of cells in G2/M. Collectively, these results provide a framework for understanding the endogenous role of the miR-34A signaling axis and identify novel transcripts and pathways regulated by the essential miR-34A-p53 tumor suppressor network.

Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks

We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 cases, 118,538 controls) from ethnically-diverse populations. We identified five new asthma loci, uncovered two additional novel associations at two known asthma loci, established asthma associations at two loci implicated previously in comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. Enrichment of asthma risk loci in enhancer marks, especially in immune cells, suggests a major role of these loci in the regulation of immune-related mechanisms.

Abstract NG05: TP53-mediated human cancer susceptibility is defined by epigenetic dysregulation of microRNA-34A

Mutations in the TP53 tumor suppressor gene are the most common genetic aberrations across all human cancers. Germline TP53 mutations are also the hallmark genetic event in Li-Fraumeni syndrome (LFS), a highly penetrant human cancer susceptibility syndrome, conferring a predisposition to developing early-onset breast cancer, leukemias, bone and soft tissue sarcomas, brain tumors of various histologies, adrenocortical carcinomas, and a wide range of other malignancies. Although the link between mutant TP53 and human cancer is unequivocal, the mechanism by which this genetic aberration predisposes an individual to cancer remains to be elucidated.

To address this gap, we surveyed the epigenome and describe herein the largest systematic analysis of DNA methylation in patients harboring germline TP53 mutations and TP53 wild-type individuals. Specifically, we performed genome-wide methylation analyses of peripheral blood leukocyte DNA in germline TP53 mutation carriers (n=72) and TP53 wild-type individuals who developed histologically comparable cancers (n=111). Targeted bisulfite pyrosequencing was performed on peripheral blood DNA in a validation cohort (n=76), and candidate sites were further evaluated in primary tumors from LFS patients.

The differential methylation analysis demonstrates that in 183 patients, distinct DNA methylation signatures are associated with deleterious TP53 mutations. TP53 mutation-associated DNA methylation marks occur in genomic regions harboring known p53 binding sites and within genes encoding p53 pathway proteins. Moreover, loss-of-function TP53 mutations are significantly associated with differential methylation at the locus encoding miR-34A-a key component of the p53 regulatory network (adjusted p-value=3.1X10-15)-and validated in an independent patient cohort (n=76, 1.9X10-8). Targeted sequencing demonstrates that miR-34A is inactivated by hypermethylation across many different histologic types of primary tumors from LFS patients, such as brain tumors, osteosarcomas, rhabdomyosarcomas, and adrenocortical carcinomas. miR-34A promoter hypermethylation in tumors is also associated with decreased overall survival in a cohort of 29 patients with choroid plexus carcinomas, a characteristic LFS tumor (p&lt;0.05). The relationship between miR-34A hypermethylation and TP53 mutation was further validated in sporadic cancers, using the publicly available TCGA dataset. This demonstrates the robustness of this correlation and the applicability of these findings to other cancer contexts.

This study refines the role of epigenetics in a cancer predisposition syndrome and is the first to implicate a microRNA, miR-34A, in human cancer susceptibility and provides a repository of genomic regions of deregulated methylation in the context of dysfunctional TP53. These findings suggest that deregulated DNA methylation at defined genomic loci may be an important hallmark of TP53-mediated cancer susceptibility. The most striking finding from this study is the relative miR-34A promoter hypomethylation at two adjacent CpG sites in peripheral blood from TP53 mutation carriers, confirmed in two independent cohorts and shown to cosegregate with TP53 mutations in LFS families. This result is remarkable since miR-34A is a central microRNA in the p53 network and the first microRNA identified as a direct proapoptotic target of the p53 pathway.

The detection of miR-34A promoter hypomethylation in TP53 mutant cells that have not undergone malignant transformation supports a putative model whereby wild-type p53 may influence methylation patterns at this locus. In particular, in nontransformed cells that do not harbor mutations in TP53, wild-type p53 may be recruited to the miR-34A locus and sustain hypermethylation. We have performed a series of in vitro studies on primary patient-derived lymphoblastoid cell lines to corroborate this model. Conversely, in the setting of loss-of-function or deleterious mutations in TP53, mutant p53 may not able to maintain hypermethylation of the miR-34A promoter, leading to upregulation of miR-34A. Owing to the known redundant cellular roles of p53 and miR-34A, upregulation of miR-34A may be beneficial to cells harboring mutant p53 by supplementing the necessary basal tumor suppressive function that is lost when p53 is mutated. This mechanism may serve to guard against mutant p53, even when the wild-type allele remains. Accordingly, this may explain why miR-34A promoter hypermethylation is characteristic of TP53-mutant tumors that lack wild-type p53 because this microRNA serves a critical role in cell maintenance, and its loss may cooperate with other genetic and/or epigenetic events to drive malignancy. It is therefore not surprising that, akin to p53, somatic miR-34A deregulation is pervasive in human cancer and miR-34A inactivation by focal deletion or promoter hypermethylation has been reported in the literature to occur in a multitude of human malignancies. The precise mechanisms of how the miR-34A promoter undergoes somatic epimutation in tissues remains to be elucidated, and likely various pathways may converge to yield this outcome in different tissues.

Given the high frequency of TP53 mutations in human malignancies, the relationship between mutant p53 and miR-34A has strong implications for the targeting of miR-34A in cancer. Encouragingly, studies have demonstrated in vivo the utility of miR-34A-based therapies in cancer, including intratumor or systemic delivery of lipid-formulated synthetic miR-34A.

To further probe these intriguing findings, we conducted mechanistic studies aimed at functionally interrogating the the miR-34A-p53 axis. We utilized in vitro-based assays to modulate miR-34A levels in primary patient-derived fibroblast cell lines, and subsequently performed by RNA-sequencing of the transcriptional responses. Our results uncover a number of novel cellular roles for miR-34A in cell maintenance. Significantly, the transcriptional response to miR-34A inhibition revealed that this microRNA may be a crucial switch that can lead to numerous changes to noncoding RNA networks as well as known p53 pathways. Markedly increased expression of key components of the U12 (minor) spliceosome occurs when miR-34A expression is diminished, thereby identifying a novel putative role of miR-34A in modulating transcription of the U12 spliceosomal machinery. The majority of TP53 mutation-associated transcripts are involved in chromatin remodeling and nucleosome assembly, and are enriched for histone cluster 1 genes. These linker histones are crucial for maintaining higher-order chromatin structure and for regulating gene expression, demonstrating the interplay between genetic and epigenetic states. Lastly, miR-34A is associated with transcriptional regulation of a host of lincRNAs, including LINC-PINT, a p53-induced lincRNA. These results are the first to identify miR-34A as an important node in the transcriptional regulation of numerous noncoding RNAs and point to further study of these pathways.

Taken together, these findings provide strong support for the impact of TP53 mutations on epigenetic dysregulation in human cancer susceptibility and demonstrate that miR-34A may be important in the pathogenesis of TP53-mediated cancer susceptibility. Moreover, miR-34A may be a putative novel therapeutic target and a marker for clinical prognostication. These studies also demonstrate that miR-34A is a central node in numerous p53-dependent and independent networks and provide further insight into the role of this critical tumor-suppressive microRNA. Further work aimed at refining our understanding of miR-34A-mediated pathways may yield additional molecular insight into the role of this microRNA in malignant transformation.

Citation Format: Nardin Samuel, Gavin Wilson, Genevieve Deblois, Badr Id Said, Nicholas W. Fischer, Mathieu Lemire, Youliang Lou, Weili Li, Roumiana Alexandrova, Ana Novokmet, James Tran, Kim E. Nichols, Jonathan L. Finlay, Sanaa Choufani, Marc Remke, Vijay Ramaswamy, Florence M.G. Cavalli, Christine Elser, Lynn Meister, Michael D. Taylor, Uri Tabori, Meredith Irwin, Rosanna Weksberg, Jonathan D. Wasserman, Jean Gariepy, Mathieu Lupien, Daniele Merico, Andrew Paterson, Jordan R. Hansford, Maria Isabel W. Achatz, Thomas J. Hudson, David Malkin. TP53-mediated human cancer susceptibility is defined by epigenetic dysregulation of microRNA-34A [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr NG05. doi:10.1158/1538-7445.AM2017-NG05

Abstract 1300: Genetic predictors of gene expression associated with risk of colorectal cancer

To date, genome-wide association studies (GWAS) have reported common variants in over 50 loci

with weak to moderate effects on CRC risk. These genetic factors in aggregate explain only a small

fraction of familial risk of CRC. To aid in the discovery of novel CRC loci, we integrated large

transcriptome data, including those generated in the Genotype-Tissue Expression (GTEx) Project in

genetic association analyses of CRC. The computational method, PrediXcan, was used to predict

transcript levels in relevant tissues and perform gene-level association tests with CRC. Prediction

models were developed using whole blood transcriptomes (n=922) from the depression genes and

networks (DGN), as well as colon transcriptomes (transverse n=169 and sigmoid n=124) from

GTEx datasets, along with high-density genotyping data from the same subjects. Genetically

determined expression levels were tested for association with CRC in 12,186 cases and 14,718

controls from GECCO-CCFR and suggestive associations (false discovery rate = 0.2) were evaluated

in 7,481 cases and 17,796 controls from the Asia Colorectal Cancer Consortium (ACCC) and 22,974

cases and 14,392 controls from the Colorectal Transdisciplinary (CORECT) study. We attempted to

replicate novel associations for eight genes and found statistically significant associations with

CXCR1 (OR=1.21 (1.10-1.33), p-value=7.8x10-5) and CXCR2 (OR=1.24 (1.11-1.38), p-value=9.9x10-

5). We also recovered previous associations at six known GWAS loci, thereby providing additional

support for putative target genes. CXCR1 and CXCR2 are therapeutic targets for the anticancer agent

Reparixin, which is currently being investigated in a stage II clinical trial for triple negative breast

cancer. As such, these findings provide preliminary support for new molecular targets that could

potentially repurpose a putative cancer therapeutic. These findings highlight the utility integrating

transcriptome data for novel discovery and biological insight of risk loci.

Citation Format: Stephanie A. Bien, Xingyi Guo, Yu-Ru Su, Tabitha A. Harrison, Conghui Qu, Yingchang Lu, Jiron Long, Sai Chen, Andrew T. Chan, David V. Conti, Hyun M. Kang, Michael Hoffmeister, Thomas J. Hudson, Mark A. Jenkins, Loic Le Marchand, Polly A. Newcomb, Martha L. Slattery, Emily White, Goncalo R. Abeçasis, Stephen B. Gruber, Deborah A. Nickerson, Stephanie L. Schmit, Graham Casey, Li Hsu, Wei Zheng, Ulrike Peters, GECCO-CCFR-AAAC-CORECT. Genetic predictors of gene expression associated with risk of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1300. doi:10.1158/1538-7445.AM2017-1300

Disease variants alter transcription factor levels and methylation of their binding sites

Most disease-associated genetic variants are noncoding, making it challenging to design experiments to understand their functional consequences. Identification of expression quantitative trait loci (eQTLs) has been a powerful approach to infer the downstream effects of disease-associated variants, but most of these variants remain unexplained. The analysis of DNA methylation, a key component of the epigenome, offers highly complementary data on the regulatory potential of genomic regions. Here we show that disease-associated variants have widespread effects on DNA methylation in trans that likely reflect differential occupancy of trans binding sites by cis-regulated transcription factors. Using multiple omics data sets from 3,841 Dutch individuals, we identified 1,907 established trait-associated SNPs that affect the methylation levels of 10,141 different CpG sites in trans (false discovery rate (FDR) < 0.05). These included SNPs that affect both the expression of a nearby transcription factor (such as NFKB1, CTCF and NKX2-3) and methylation of its respective binding site across the genome. Trans methylation QTLs effectively expose the downstream effects of disease-associated variants.

4th Pediatric Allergy and Asthma Meeting (PAAM)

WORKSHOP 4: Challenging clinical scenarios (CS01–CS06)

CS01 Bullous lesions in two children: solitary mastocytoma

S. Tolga Yavuz, Ozan Koc, Ali Gungor, Faysal Gok

CS02 Multi-System Allergy (MSA) of cystic fibrosis: our institutional experience

Jessica Hawley, Christopher O’Brien, Matthew Thomas, Malcolm Brodlie, Louise Michaelis

CS03 Cold urticaria in pediatric age: an invisible cause for severe reactions

Inês Mota, Ângela Gaspar, Susana Piedade, Graça Sampaio, José Geraldo Dias, Miguel Paiva, Mário Morais-Almeida

CS04 Angioedema with C1 inhibitor deficiency in a girl: a challenge diagnosis

Cristina Madureira, Tânia Lopes, Susana Lopes, Filipa Almeida, Alexandra Sequeira, Fernanda Carvalho, José Oliveira

CS05 A child with unusual multiple organ allergy disease: what is the primer?

Fabienne Gay-Crosier

CS06 A case of uncontrolled asthma in a 6-year-old patient

Ioana-Valentina Nenciu, Andreia Florina Nita, Alexandru Ulmeanu, Dumitru Oraseanu, Carmen Zapucioiu

ORAL ABSTRACT SESSION 1: Food allergy (OP01–OP06)

OP01 Food protein-induced enterocolitis syndrome: oral food challenge outcomes for tolerance evaluation in a Pediatric Hospital

Adrianna Machinena, Olga Domínguez Sánchez, Montserrat Alvaro Lozano, Rosa Jimenez Feijoo, Jaime Lozano Blasco, Mònica Piquer Gibert, Mª Teresa Giner Muñoz, Marcia Dias da Costa, Ana Maria Plaza Martín

OP02 Characteristics of infants with food protein-induced enterocolitis syndrome and allergic proctocolitis

Ebru Arik Yilmaz, Özlem Cavkaytar, Betul Buyuktiryaki, Ozge Soyer, Cansin Sackesen

OP03 The clinical and immunological outcomes after consumption of baked egg by 1–5 year old egg allergic children: results of a randomised controlled trial

MerrynNetting, Adaweyah El-Merhibi, Michael Gold, PatrickQuinn, IrmeliPenttila, Maria Makrides

OP04 Oral immunotherapy for treatment of egg allergy using low allergenic, hydrolysed egg

Stavroula Giavi, Antonella Muraro, Roger Lauener, Annick Mercenier, Eugen Bersuch, Isabella M. Montagner, Maria Passioti, Nicolò Celegato, Selina Summermatter, Sophie Nutten, Tristan Bourdeau, Yvonne M. Vissers, Nikolaos G. Papadopoulos

OP05 Chemical modification of a peanut extract results in an increased safety profile while maintaining efficacy

Hanneke van der Kleij, Hans Warmenhoven, Ronald van Ree, Raymond Pieters, Dirk Jan Opstelten, Hans van Schijndel, Joost Smit

OP06 Administration of the yellow fever vaccine in egg allergic children

Roisin Fitzsimons, Victoria Timms, George Du Toit

ORAL ABSTRACT SESSION 2: Asthma (OP07–OP12)

OP07 Previous exacerbation is the most important risk factor for future exacerbations in school-age children with asthma

S. Tolga Yavuz, Guven Kaya, Mustafa Gulec, Mehmet Saldir, Osman Sener, Faysal Gok

OP08 Comparative study of degree of severity and laboratory changes between asthmatic children using different acupuncture modalities

Nagwa Hassan, Hala Shaaban, Hazem El-Hariri, Ahmed Kamel Inas E. Mahfouz

OP09 The concentration of exhaled carbon monoxide in asthmatic children with different controlled stadium

Papp Gabor, Biro Gabor, Kovacs Csaba

OP10 Effect of vitamin D3 supplementation during pregnancy on risk of persistent wheeze in the offspring: a randomised clinical trial

Bo Chawes, Klaus Bønnelykke, Jakob Stokholm, Lene Heickendorff, Susanne Brix, Morten Rasmussen, Hans Bisgaard

OP11 Lung function development in childhood

Henrik Wegener Hallas, Bo Chawes, Lambang Arianto, Hans Bisgaard

OP12 Is the effect of maternal and paternal asthma different in female and male children before puberty?

Maike Pincus, Thomas Keil, Andreas Reich, Ulrich Wahn, Susanne Lau, Linus Grabenhenrich

ORAL ABSTRACT SESSION 3: Epidemiology—genetics (OP13–OP18)

OP13 Lifestyle is associated with incidence and category of allergen sensitisation: the ALADDIN birth cohort

Sara Fagerstedt, Helena Marell Hesla, Emelie Johansson, Helen Rosenlund, Axel Mie, Annika Scheynius, Johan Alm

OP15 Maternal filaggrin mutations increase the risk of atopic dermatitis in children: an effect independent of mutation inheritance

Jorge Esparza-Gordillo, Anja Matanovic, Ingo Marenholz, Anja Bauerfeind, Klaus Rohde, Katja Nemat, Min-Ae Lee-Kirsch, Magnus Nordenskjöld, Marten C. G. Winge, Thomas Keil, Renate Krüger, Susanne Lau, Kirsten Beyer, Birgit Kalb, Bodo Niggemann, Norbert Hübner, Heather J. Cordell, Maria Bradley, Young-Ae Lee

OP16 Allergic multimorbidity of asthma, rhinitis and eczema in the first 2 decades of the German MAS birth cohort

Thomas Keil, Hannah Gough, Linus Grabenhenrich, Dirk Schramm, Andreas Reich, John Beschorner, Antje Schuster, Carl-Peter Bauer, Johannes Forster, Fred Zepp, Young-Ae Lee, Renate Bergmann, Karl Bergmann, Ulrich Wahn, Susanne Lau

OP17 Childhood anaphylaxis: a growing concern

Filipe Benito Garcia, Inês Mota, Susana Piedade, Ângela Gaspar, Natacha Santos, Helena Pité, Mário Morais-Almeida

OP18 Indoor exposure to molds and dampness in infancy and its association to persistent atopic dermatitis in school age. Results from the Greek ISAAC II study

Athina Papadopoulou, Despina Mermiri, Elpida Xatziagorou, Ioannis Tsanakas, Stavroula Lampidi, Kostas Priftis

ORAL ABSTRACT SESSION 4: Pediatric rhinitis—immunotherapy (OP19–OP24)

OP19 Associations between residential greenness and childhood allergic rhinitis and aeroallergen sensitisation in seven birth cohorts

Elaine Fuertes, Iana Markevych, Gayan Bowatte, Olena Gruzieva, Ulrike Gehring, Allan Becker, Dietrich Berdel, Michael Brauer, Chris Carlsten, Barbara Hoffmann, Anita Kozyrskyj, Caroline Lodge, Göran Pershagen, Alet Wijga, Heinrich Joachim

OP20 Full symptom control in pediatric patients with allergic rhinitis and asthma: results of a 2-year sublingual allergen immunotherapy study

Zorica Zivkovic, Ivana Djuric-Filipovic, Jasmina Jocić-Stevanovic, Snežana Zivanovic

OP21 Nasal epithelium of different ages of atopic subjects present increased levels of oxidative stress and increased cell cytotoxicity upon rhinovirus infection

Styliani Taka, Dimitra Kokkinou, Aliki Papakonstantinou, Panagiota Stefanopoulou, Anastasia Georgountzou, Paraskevi Maggina, Sofia Stamataki, Vassiliki Papaevanggelou, Evangelos Andreakos, Nikolaos G. Papadopoulos

OP22 Cluster subcutaneous immunotherapy schedule: tolerability profile in children

Monica Piquer Gibert, Montserrat Alvaro Lozano, Jaime Lozano Blasco, Olga Domínguez Sánchez, Rosa Jiménez Feijoo, Marcia Dias da Costa, Mª Teresa Giner Muñoz, Adriana Machinena Spera, Ana Maria Plaza Martín

OP23 Rhinitis as a risk factor for asthma severity in 11-year old children: population-based cohort study

Matea Deliu, Danielle Belgrave, Angela Simpson, Adnan Custovic

OP24 The Global Lung Function Initiative equations in airway obstruction evaluation of asthmatic children

João Gaspar Marques, Pedro Carreiro-Martins, Joana Belo, Sara Serranho, Isabel Peralta, Nuno Neuparth, Paula Leiria-Pinto

POSTER DISCUSSION SESSION 1: Food allergy (PD01–PD05)

PD01 Allergen-specific humoral and cellular responses in children who fail egg oral immunotherapy due to allergic reactions

Marta Vazquez-Ortiz, Mariona Pascal, Ana Maria Plaza, Manel Juan

PD02 FoxP3 epigenetic features in children with cow milk allergy

Lorella Paparo, Rita Nocerino, Rosita Aitoro, Ilaria Langella, Antonio Amoroso, Alessia Amoroso, Carmen Di Scala, Roberto Berni Canani

PD04 Combined milk and egg allergy in early childhood: let them eat cake?

Santanu Maity, Giuseppina Rotiroti, Minal Gandhi

PD05 Introduction of complementary foods in relation to allergy and gut microbiota in farm and non-farm children

Karin Jonsson, Annika Ljung, Bill Hesselmar, Ingegerd Adlerbert, Hilde Brekke, Susanne Johansen, Agnes Wold, Ann-Sofie Sandberg

POSTER DISCUSSION SESSION 2: Asthma and wheeze (PD06–PD16)

PD06 The association between asthma and exhaled nitric oxide is influenced by genetics and sensitisation

Björn Nordlund, Cecilia Lundholm, Villhelmina Ullemar, Marianne van Hage, Anne Örtqvist, Catarina Almqvist

PD09 Prevalence patterns of infant wheeze across Europe

Anna Selby, Kate Grimshaw, Thomas Keil, Linus Grabenhenrich, Michael Clausen, Ruta Dubakiene, Alessandro Fiocchi, Marek Kowalski, Nikos Papadopoulos, Marta Reche, Sigurveig Sigurdardottir, Aline Sprikkleman, Paraskevi Xepapadaki, Clare Mills, Kirsten Beyer, Graham Roberts

PD10 Epidemiologic changes in recurrent wheezing infants

Herberto Jose Chong Neto, Gustavo Falbo Wandalsen, Ana Carolina Dela Bianca, Carolina Aranda, Nelson Augusto Rosário, Dirceu Solé, Javier Mallol, Luis García Marcos

PD13 A single nucleotide polymorphism in the GLCCI1 gene is associated with response to asthma treatment in children

IvanaBanic, Matija Rijavec, Davor Plavec, Peter Korosec, Mirjana Turkalj

PD14 Pollen induced asthma: Could small molecules in pollen exacerbate the protein-mediated allergic response?

Alen Bozicevic, Maria De Mieri, Matthias Hamburger

PD15 A qualitative study to understand how we can empower teenagers to better self-manage their asthma

Simone Holley, Ruth Morris, Frances Mitchell, Rebecca Knibb, Susan Latter, Christina Liossi, Graham Roberts

PD16 Polymorphism of endothelial nitric oxide synthase (eNOS) gene among Egyptian children with bronchial asthma

Mostafa M. M. Hassan

POSTER DISCUSSION SESSION 3: Mechanisms—Epidemiology (PD17–PD21)

PD17 Pregnancy outcomes in relation to development of allergy in a Swedish birth cohort

Malin Barman, Anna Sandin, Agnes Wold, Ann-Sofie Sandberg

PD18 Evolution of the IgE response to house dust mite molecules in childhood

Daniela Posa, Serena Perna, Carl-Peter Bauer, Ute Hoffmann, Johannes Forster, Fred Zepp, Antje Schuster, Ulrich Wahn, Thomas Keil, Susanne Lau, Kuan-Wei Chen, Yvonne Resch, Susanne Vrtala, Rudolf Valenta, Paolo Maria Matricardi

PD19 Antibody recognition of nsLTP-molecules as antigens but not as allergens in the German-MAS birth cohort

Olympia Tsilochristou, Alexander Rohrbach, Antonio Cappella, Stephanie Hofmaier, Laura Hatzler, Carl-Peter Bauer, Ute Hoffmann, Johannes Forster, Fred Zepp, Antje Schuster, RaffaeleD’Amelio, Ulrich Wahn, Thomas Keil, Susanne Lau, Paolo Maria Matricardi

PD20 Early life colonization with Lactobacilli and Staphylococcus aureus oppositely associates with the maturation and activation of FOXP3+ CD4 T-cells

Sophia Björkander, Maria A. Johansson, Gintare Lasaviciute, Eva Sverremark-Ekström

PD21 Genome-wide meta-analysis identifies 7 susceptibility loci involved in the atopic march

Ingo Marenholz, Jorge Esparza-Gordillo, Franz Rüschendorf, Anja Bauerfeind, David P. Strachan, Ben D. Spycher, Hansjörg Baurecht, Patricia Margaritte-Jeannin, Annika Sääf, Marjan Kerkhof, Markus Ege, Svetlana Baltic, Melanie C Matheson, Jin Li, Sven Michel, Wei Q. Ang, Wendy McArdle, Andreas Arnold, Georg Homuth, Florence Demenais, Emmanuelle Bouzigon, Cilla Söderhäll, Göran Pershagen, Johan C. de Jongste, Dirkje S Postma, Charlotte Braun-Fahrländer, Elisabeth Horak, Ludmila M. Ogorodova, Valery P. Puzyrev, Elena Yu Bragina, Thomas J Hudson, Charles Morin, David L Duffy, Guy B Marks, Colin F Robertson, Grant W Montgomery, Bill Musk, Philip J Thompson, Nicholas G. Martin, Alan James, Patrick Sleiman, Elina Toskala, Elke Rodriguez, Regina Fölster-Holst, Andre Franke, Wolfgang Lieb, Christian Gieger, Andrea Heinzmann, Ernst Rietschel, Thomas Keil, Sven Cichon, Markus M Nöthen, Craig E Pennell, Peter D Sly, Carsten O Schmidt, Anja Matanovic, Valentin Schneider, Matthias Heinig, Norbert Hübner, Patrick G. Holt, Susanne Lau, Michael Kabesch, Stefan Weidinger, Hakon Hakonarson, Manuel AR Ferreira, Catherine Laprise, Maxim B. Freidin, Jon Genuneit, Gerard H Koppelman, Erik Melén, Marie-Hélène Dizier, A. John Henderson, Young Ae Lee

POSTER DISCUSSION SESSION 4: Food allergy—Anaphylaxis (PD22–PD26)

PD22 Atopy patch test in food protein induced enterocolitis caused by solid food

Purificacion González-Delgado, Esther Caparrós, Fernando Clemente, Begoña Cueva, Victoria M. Moreno, Jose Luis Carretero, Javier Fernández

PD23 Watermelon allergy: a novel presentation

Kate Swan, George Du Toit

PD24 A pilot study evaluating the usefulness of a guideline template for managing milk allergy in primary care

Mudiyur Gopi, Tim Smith, Edara Ramesh, Arun Sadasivam

PD26 Efficacy and safety of cow’s milk oral immunotherapy protocol

Inês Mota, Filipe Benito Garcia, Susana Piedade, Angela Gaspar, Graça Sampaio, Cristina Arêde, Luís Miguel Borrego, Graça Pires, Cristina Santa-Marta, Mário Morais-Almeida

POSTER DISCUSSION SESSION 5: Prevention and treatment—Allergy (PD27–PD36)

PD27 Allergy-protection by the lactic acid bacterium Lactococcus lactis G121: mode-of-action as revealed in a murine model of experimental allergy

Stephanie Brand, Karina Stein, Holger Heine, Marion Kauth

PD29 The relationship between quality of life and morning salivary cortisol after acute bronchiolitis in infancy

Leif Bjarte Rolfsjord, Egil Bakkeheim, Johan Alm, Håvard Ove Skjerven, Kai-Håkon Carlsen, Jon Olav Hunderi, Teresa Løvold Berents, Petter Mowinckel, Karin C. Lødrup Carlsen

PD30 Randomised trial of the efficacy of MP29-02* compared with fluticasone propionate nasal spray in children aged ≥6 years to <12 years with allergic rhinitis

Ulrich Wahn, Ullrich Munzel, William Berger

PD31 10 mg of oral bilastine in 2 to 11 years old children has similar exposure to the adult therapeutic dose (20 mg)

Ulrich Wahn, Román Valiente, Valvanera Vozmediano, John C. Lukas, Mónica Rodríguez

PD33 Daily symptoms, nocturnal symptoms, activity limitations and reliever therapies during the three steps of IOEASMA programme: a comparison

Sebastiano Guarnaccia, Luigi Vitale, Ada Pluda, Emanuele D’Agata, Denise Colombo, Stefano Felici, Valeria Gretter, Susanna Facchetti, Gaia Pecorelli, Cristina Quecchia

PD34 Sensitisation to an inert aeroallergen in weaning rats and longstanding disease, in a sensitisation-tolerant and easily tolerisable rodent strain

George Guibas, Evangelia Spandou, Spyridon Megremis, Peter West, Nikolaos Papadopoulos

PD35 Bacterial and fungi exposure in school and allergic sensitisation in children

João Cavaleiro Rufo, Joana Madureira, Inês Paciência, Lívia Aguiar, Patrícia Padrão, Mariana Pinto, Luís Delgado, Pedro Moreira, João Paulo Teixeira, Eduardo Oliveira Fernandes, André Moreira

PD36 Comparative study of allergy rhinitis between two populations: children vs. adults

Adriana Izquierdo Dominguez, Antonio Valero, Joaquim Mullol, Alfonso Del Cuvillo, Javier Montoro, Ignacio Jauregui, Joan Bartra, Ignacio Davila, Marta Ferrer, Joaquin Sastre

POSTER VIEWING SESSION 1: Inflammation—Genetics—Immunology—Dermatology (PP01–PP09)

PP01 Immune profile in late pregnancy: immunological markers in atopic asthmaticwomen as risk factors for atopy in the progeny

Catarina Martins, Jorge Lima, Maria José Leandro, Glória Nunes, Jorge Cunha Branco, Hélder Trindade, Luis Miguel Borrego

PP02 The impact of neonatal sepsis on development of allergic diseases

Secil Conkar, Mehtap Kilic, Canan Aygun, Recep Sancak

PP03 Clinical overview of selective IgE deficiency in childhood

Athina Papadopoulou, Eleni Tagalaki, Lambros Banos, Anna Vlachou, Fotini Giannoula, Despina Mermiri

PP04 Inverse relationship between serum 25(ΟΗ) vitamin D3 and total IgE in children and adolescence

Athina Papadopoulou, Stavroula Lampidi, Marina Pavlakou, Maria Kryoni, Kostas Makris

PP05

PP06

PP07 Asthma control questionnaire and specific IgE in children

Snezhina Lazova, Guergana Petrova, Dimitrinka Miteva, Penka Perenovska

PP08 Features of chronic urticaria of adolescents

Aliya Klyucharova, Olesya Skorohodkina

PP09 Cutaneous mastocytosis in children: a clinical analysis of 8 cases in Greece

Dimitra Koumaki, Alkisti Manousaki, Maria Agrapidi, Lida Iatridou, Omima Eruk, Konstantinos Myridakis, Emmanouil Manousakis, Vasiliki Koumaki

POSTER VIEWING SESSION 2: Food allergy—Anaphylaxis (PP10–PP47)

PP10 Prognostic factors in egg allergy

Maria Dimou, Maria Ingemansson, Gunilla Hedlin

PP11 Evaluation of the efficacy of an amino acid-based formula in infants who are intolerant to extensively hydrolysed protein formula

Nitida Pastor, Delphine de Boissieu, Jon Vanderhoof, Nancy Moore, Kaitlin Maditz

PP12 Anaphylaxis and epinephrine auto-injector use: a survey of pediatric trainees

Adeli Mehdi, Shaza Elhassan, Carolin Beck, Ahmed Al-Hammadi

PP13 Anaphylaxis in children: acute management in the Emergency Department

Ioana Maris, Ronan O’Sullivan, Jonathan Hourihane,

PP14 Understanding Cumbrian schools preparedness in managing children at risk of anaphylaxis in order to provide training and support which will create healthy and safe environments for children with allergies

George Raptis, Louise Michaelis

PP15 A new valid and reliable parent and child questionnaire to measure the impact of food protein enterocolitis syndrome on children: the FPIES Quality of Life Questionnaire (FPIESQL), Parent and Child Short Form

Audrey DunnGalvin, Matthew Greenhawt, Carina Venter, Jonathan Hourihane

PP16 An in-depth case study investigation of the experiences of teenagers and young adults in growing up and living with food allergy with emphasis on coping, management and risk, support, and social and self-identity

Evelyn O’Regan, Duncan Cronin, Jonathan Hourihane, Anna O’Reilly, Audrey DunnGalvin

PP17 Cow’s milk protein allergy in Constantine. A retrospective study of 62 cases between 1996 and 2013

Foued Abdelaziz, Dounia Khelifi-Touhami, Nihad Selim, Tahar Khelifi-Touhami

PP18

PP19 Cow’s milk and egg oral immunotherapy in children older than 5 years

Pablo Merida, Ana Mª Plaza, Juan Heber Castellanos, Adrianna Machinena, Montserrat Alvaro Lozano, Jaime Lozano, Olga Dominguez, Monica Piquer, Rosa Jimenez, Mª Teresa Giner

PP20 Professionals’ awareness of management of Cow’s Milk Protein Allergy (CMPA) in North Wales Hospitals

Konstantinos Kakleas, Manohar Joishy, Wendmu Maskele, Huw R. Jenkins

PP21

PP22 Anaphylaxis: the great unknown for teachers. Presentation of a protocol for schools

Mercedes Escarrer, Agustín Madroñero, Maria Teresa Guerra, Juan Carlos Julia, Juan Carlos Cerda, Javier Contreras, Eulalia Tauler, Maria Jesus Vidorreta, Ana Rojo, Silvia Del Valle

PP23 Challenges facing children with food allergies and their parents in out of school activity sectors

Niamh Flynn

PP24 A review of food challenges at a Regional Irish Centre

Gary Foley, Carol Harmon, John Fitzsimons

PP25 The use of epinephrine in infants with anaphylaxis

Krasimira Baynova, Ávila Maria Del Robledo, Labella Marina

PP26

PP27

PP28 Mother’s psychological state predicts the expression of symptoms in food allergic children

Aaron Cortes, Alicia Sciaraffia, Angela Castillo

PP29 The correlation between sIgE towards tree nuts and birch pollen in a Danish Pediatric Allergy Clinic

Nanna Juel-Berg, Kirsten Skamstrup Hansen, Lars Kærgaard Poulsen

PP30 Food allergy in children: evaluation of parents’ use of online social media

Andreia Florina Nita, Ioana Valentina Nenciu, Adina Lazar, Dumitru Oraseanu

PP31 The impact of food allergy on quality of life: FAQLQ questionnaire

Rita Aguiar, Anabela Lopes, Maria J. Paes, Amélia S. Santos, M. A. Pereira-Barbosa

PP32 An unexpected cause of anaphylaxis: potato

Hatice Eke Gungor, Salih Uytun, Umit Murat Sahiner, Yasemin Altuner Torun

PP33 Is it clinical phenotype of allergic diseases determined by sensitisation to food?

Mirjana Zivanovic, Marina Atanasković-Marković

PP34

PP35 Prescribing adrenaline auto-injectors in children in 2014: the data from regional pediatricians

Tina Vesel, Mihaela Nahtigal, Andreja Obermayer-Temlin, Eva Šoster Križnik, Mirjana Maslar, Ruben Bizjak, Marjeta Tomšič-Matic, Sonja Posega-Devetak, Maja Skerbinjek-Kavalar, Mateja Predalič, Tadej Avčin

PP36 Who should have an adrenaline autoinjector? Adherence to the European and French guidelines among 121 allergists from the Allergy Vigilance Network

Guillaume Pouessel, Etienne Beaudouin, Anne M. Moneret-Vautrin, Antoine Deschildre, Allergy Vigilance Network

PP37 Anaphylaxis by Anacardium Occidentale

Marta Viñas, Bartolomé Borja, Nora Hernández, Mª José Castillo, Adriana Izquierdo, Marcel Ibero

PP38 Anaphylaxis with honey in a child

S. Tolga Yavuz, Ali Gungor, Betul Buyuktiryaki, Ozan Koc, Can Naci Kocabas, Faysal Gok

PP39 Evaluation of courses adopted to children on prevention, recognition and management of anaphylaxis

Tina Vesel, Mihaela Nahtigal

PP40 Symptomatic dust mites and shrimp allergy: three pediatric case reports

Filipa Almeida, Susana Lopes, Cristina Madureira, Tânia Lopes, Fernanda Carvalho

PP41 Poor identification rates of nuts by high risk individuals: a call for improved education and support for families

Camille Heming, Emily Garrett, Adam Blackstock, Santanu Maity, Rahul Chodhari

PP42 DAFALL: database of food allergies in the Czech Republic

Simona Belohlavkova, Eliska Kopelentova, Petr Visek, Ivana Setinova, Ivana Svarcova

PP43 Serological cross-reactivity between grass and wheat is not only caused by profilins and CCDs

Sigrid Sjölander, Nora Nilsson, Malin Berthold, Helena Ekoff, Gunilla Hedlin, Magnus Borres, Caroline Nilsson

PP44 Oil body associated proteins in children with nuts allergy. Allergens to consider in IgE-mediated nuts allergy

Loreto González Domínguez, Cristina Muñoz Archidona, Ana Moreira Jorge, Sergio Quevedo Teruel, Teresa Bracamonte Bermejo, Miriam Castillo Fernández, Fernando Pineda de la Losa, Luis Ángel Echeverría Zudaire

PP45

PP46 Protective effect of helicobacter pylori infection against food allergy in children

Olga Vrani, Antigone Mavroudi, Maria Fotoulaki, Maria Emporiadou, Kleomenis Spiroglou, Ioannis Xinias

PP47 Anaphylaxis pathway: A road tryp-tase to success?

Helyeh A. Sadreddini, Mia Warnes, Donna Traves

POSTER VIEWING SESSION 3: Miscellaneous (PP48–PP58)

PP48 Surveillance study on safety of SLIT in pediatric population

Ivana Djuric-Filipovic, Zorica Zivkovic, Snežana Zivanovic, Gordana Kostić, Đorđe Filipovic

PP49 Efficacy and safety of mixed mite subcutaneous immunotherapy among allergic rhinitis patients in the Northeastern Thailand

Sawapon Sittisomwong, Siripong Sittisomwong

PP50 Effect of inhaled beclomethasone or placebo on brain stem activity in a patient chronically treated with steroids: preliminary report

Zygmunt Podolec, Marcin Hartel, Daria Panek, Magdalena Podolec-Rubiś, Tomasz Banasik

PP51 Sensitisation to aeroallergens in patients with allergic rhinitis, asthma and atopic dermatitis in Shiraz, Southwestern Iran

Elham Abbasi, Mozhgan Moghtaderi

PP52 Referring a child for allergy test: how appropriate are we?

Phani Sanneerappa, Alina Deliu, Moosa Kutty, Nagabathula Ramesh

PP53 EBV lymphoproliferative disease and cardiac lymphoma in a STK4 deficient patient

Roya Sherkat, Mohammad Reza Sabri, Bahar Dehghan, Hamid Bigdelian, Nahid Raeesi, Mino Afshar, Hamid Rahimi, Christoph Klein

PP54 A case study: the effect of massive honeybees attack on various body parameters atopic girl including allergy

Mohemid Al-Jebouri

PP55 The role of TLR9, NLRP3 and proIL-1β in activation of antiviral innate immunity

Oxana A. Svitich, Daria O. Zubacheva, Dmitrii A. Potemkin, Ludmila V. Gankovskaya, Vitalii V. Zverev

PP56 Overnight pulse oximetry, as a screening tool to diagnose obstructive sleep apnoea. How effective is it?

Phani Sanneerappa, Elaine OB Doyle, Paul Gallagher, Nagabathula Ramesh

PP57 The presentation and management of acute urticaria and allergic reactions in children in a multi-ethnic, inner city Emergency Department (ED)

Sherine Dewlett, Kin Man, Minal Gandhi, James Pocock, Anna Gerrardhughes

PP58 Food allergens responsible for delayed-type sensitisation in atopy patch test in children diagnosed with autism spectrum disorder

Jolanta Wasilewska, Maciej Kaczmarski, Dariusz Lebensztejn

POSTER VIEWING SESSION 4: Asthma—Rhinitis (PP59–PP87)

PP59 Systematic review of incense as a trigger factor for asthma

Chandramani Thuraisingham, Davendralingam Sinniah

PP60 Increased risks of mood and anxiety disorders in children with asthma

Yue Chen, Xiaomei Mei

PP61

PP62 Asthma Control Test (ACT) and Pediatric Asthma Quality of Life Questionnaire (PAQLQ) association in children

Sebnem Ozdogan, Pinar Karadeniz, Durdugul Ayyildiz-Emecen, Ummuhan Oncul

PP63 Seasonal and gender variations in vitamin D levels in children with asthma and its association with pulmonary function tests

Sebnem Ozdogan, Gizem Sari, Sabanur Cavdar

PP64 Defining treatment response in childhood asthma: rationale and design of the Pharmacogenomics in the Childhood Asthma (PiCA) consortium

Niloufar Farzan, Susanne J. Vijverberg, Colin J. Palmer, Kelan G. Tantisira, Anke-Hilseon Maitland-van der Zee behalf of the PiCA consortium

PP65 Prevalence of asthma and allergic disease in patients with inflammatory disease compared to celiac disease

Fatma Yavuzyilmaz, Sebnem Ozdogan, Nafiye Urganci, Merve Usta

PP66 A severe case with cystic fibrosis (CF) asthma

Mehmet Hoxha, Maksim Basho

PP67 Severe asthma exacerbation complicated with pneumothorax in a child with uncontrolled asthma due to poor treatment compliance

Ioana Valentina Nenciu, Andreia Florina Nita, Adina Lazar, Alexandru Ulmeanu, Carmen Zapucioiu, Dumitru Oraseanu

PP68 Evaluation of the Pediatric Quality of Life inventory (PedsQL) asthma module among low income asthmatic children and adolescents in Sao Paolo, Brazil

Gustavo F. Wandalsen, Fernanda Monteiro, Dirceu Solé

PP69 Early initiation of specific immunotherapy in asthma patients leads to higher benefits

Blerta Lame, Eris Mesonjesi, Arjeta Sherri

PP70 Treatment resistant asthma and rhinosinusitis with recurrent pulmonary infections. Is it primary ciliary dyskinesia?

Alkerta Ibranji, Laert Gjati, Gjustina Loloci, Ardii Bardhi

PP71 The comparison of sensitisation to animal allergens in children- and adult- onset patients with asthma

Behnam Moghtaderi, Shirin Farjadian, Dorna Eghtedari

PP72 Characterisation of children less than five years with wheezing episodes in Cali, Colombia

Manuela Olaya, Laura Del Mar Vasquez, Luis Fernando Ramirez, Carlos Daniel Serrano

PP73 Evaluation of the patients with recurrent croup

Belgin Usta Guc, Suna Asilsoy, Fulya Ozer

PP74 Obesity in adolescence compromising the asthma control

Guergana Petrova, Sylvia Shopova, Vera Papochieva, Snezhina Lazova, Dimitrinka Miteva, Penka Perenovska

PP75 Sleep behavior in children with persistent allergic rhinitis

Gustavo F. Wandalsen, Jessica Loekmanwidjaja, Márcia Mallozi, Dirceu Solé

PP76 Randomised trial of the safety of MP29-02* compared with fluticasone propionate nasal spray in children aged ≥4 years to <12 years with allergic rhinitis

William Berger, Ulrich Wahn, Paul Ratner, Daniel Soteres

PP77 Safety and tolerability evaluation of bilastine 10 mg in children from 2 to 11 years of age with allergic rhinoconjunctivitis or urticaria

Zoltán Novák, Anahí Yáñez, Kiss Ildikó, Piotr Kuna, Miguel Tortajada, Román Valiente, the Bilastine Pediatric Safety Study Group

PP78 Sensitisation to Alternaria alternata: Is it a risk factor for severe rhinitis?

Susana Lopes, Filipa Almeida, Tânia Lopes, Cristina Madureira, José Oliveira, Fernanda Carvalho

PP79 Validation of the Patient Benefit Index (PBI) for the assessment of patient-related outcomes in allergic rhinitis in children

Julia Feuerhahn, Christine Blome, Meike Hadler, Efstrathios Karagiannis, Anna Langenbruch, Matthias Augustin

PP80 Efficacy of sublingual tablet of house dust mite allergen extracts in adolescents with house dust mite-associated allergic rhinitis

Michel Roux, Shinji Kakudo, Efstrathios Karagiannis, Robert K. Zeldin

PP81 Lung function improvement in a child treated with omalizumab for bronchial asthma

Anna Sokolova, Tiago Milheiro Silva

PP82 How to treat a child suffering from asthma, allergic rhinitis, allergy to peanuts and diabetes at the same time?

Snezana S. Zivanovic, Vesna Cvetkovic, Ivana Nikolic, Sonja J. Zivanovic

PP83 Nitric oxide in exhaled air in the relationship of the degree of sensitisation to aeroallergens

Snezana S. Zivanovic, Ljiljana Saranac, Ivana Nikolic, Sonja J. Zivanovic, Zorica Zivkovic

PP84 Clinical basis of diagnostic errors in pediatric asthma

Zoia Nesterenko

PP85

PP86 Childhood asthma control in Serbia and organised Asthma Educational Intervention (AEI)

Snezana Radic, Branislava Milenkovic, Spomenka Smiljanic, Milka Micic-Stanijevic, Olivera Calovic

PP87 Experience from a group of adolescents with severe allergic asthma treated with Omalizumab

Anne Marie Bro Hofbauer, Lone Agertoft

THEMATIC POSTER SESSION 1: Prevention and Treatment—Epidemiology (TP01–TP18)

TP01 A cost effective primary school asthma education program: pilot study from inner London schools

Lucy Everson, Jessica Kearney, Jonny Coppel, Simon Braithwaite, Rahul Chodhari

TP02 The prevalence of allergic diseases among 14–15 years old adolescents in two Danish birth cohorts 14 years apart

Elisabeth S. Christiansen, Henrik Fomsgaard Kjaer, Esben Eller, Charlotte G. Mørtz, Susanne Halken

TP03 Does pattern of sensitisation to phleum pratense change with age? Is it different in children with allergic rhinitis or asthma?

Cristina Román India, Ana Moreira Jorge, Loreto González Domínguez, Cristina Muñoz Archidona, Sergio Quevedo Teruel, Teresa Bracamonte Bermejo, Juana Jiménez Jiménez, Luis Echeverría Zudaire

TP04 Practicalities of prevention of peanut allergy: modelling a national response to LEAP

Cathal O’Connor, Jonathan Hourihane

TP05 Comparison of the influence of sunflower seed oil and skin care lotion on the skin barrier function of newborns: a randomised controlled trial

Varvara Kanti, Lena Lünnemann, Günther Malise, Laine Ludriksone, Andrea Stroux, Wolfgang Henrich, Michael Abu-Dakn, Ulrike Blume-Peytavi, Natalie Garcia Bartels

TP06 The effect of daily skin care on skin barrier properties in infants with dry skin and risk for atopic dermatitis

Varvara Kanti, Lena Lünnemann, Laine Ludriksone, Marianne Schario, Andrea Stroux, Ulrike Blume-Peytavi, Natalie Garcia Bartels

TP07 Change in sum total aeroallergen skin prick test wheal diameters at 6 months predicts which children will respond to subcutaneous immunotherapy by three years

Thorsten Stanley, Nicolien Brandenbarg

TP08 Are mobile apps regarding adrenaline auto-injectors accessed by adolescents for support and education in the community?

Alia Boardman, Gary McGreevy, Emily Rodger, Katherine Knight, Victoria Timms, Trisha Taylor, Gemma Scanlan, Roisin Fitzsimons

TP09

TP10 Prevention of early atopic dermatitis among low-atopy-risk infants by immunoactive prebiotics is not sustained after the first year of life

Grüber Christoph, Ulrich Wahn, Margriet van Stuivenberg, Fabio Mosca, Guido Moro, Gaetano Chirico, Christian P. Braegger, Joseph Riedler, Yalcin Yavuz, Günther Boehm

TP11

TP12

TP13 Treatment with Omalizumab in a 16-year-old Caucasian girl with refractory solar urticaria

Stefania Arasi, Giuseppe Crisafulli, Lucia Caminiti, Federica Porcaro, Giovanni Battista Pajno

TP14 Ultra-pure soft water ameliorates skin conditions of adult and child patients with atopic dermatitis

Akane Tanaka, Yaei Togawa, Kumiko Oida, Naotomo Kambe, Peter Arkwright, Yosuke Amagai, Naoki Shimojo, Yasunori Sato, Hiroyuki Mochizuki, Hyosun Jang, Saori Ishizaka, Hiroshi Matsuda

TP15 Potential adjuvant effect of immunomodulator to improve specific immunotherapy in asthmatic child

Wisnu Barlianto, Ery Olivianto, H. M. S. Chandra Kusuma

TP16 How can Component Resolved Diagnosis (CRD) influence in Specific Immunotherapy (SIT) prescription, in a Spanish children population

Ana Moreira Jorge, Cristina Román India, Loreto González Domínguez, Cristina Muñoz Archidona, Juana Jiménez Jiménez, Teresa Bracamonte Bermejo, Sergio Quevedo Teruel, Luis Echeverría Zudaire

TP17 Mitochondrial dysfunction in food allergy: effects of L. rhamnosus GG in a mice model of peanut allergy

Rosita Aitoro, Mariapia Mollica, Roberto Berni Canani, Giovanna Trinchese, Elena Alfano, Antonio Amoroso, Lorella Paparo, Francesco Amato, Claudio Pirozzi, Antonio Calignano, Rosaria Meli

TP18 Prediction of atopic diseases in childhood: elevated blood eosinophils in infancy in a high risk birth cohort

Siri Rossberg, Kerstin Gerhold, Kurt Zimmermann, Mohammad Zaino, Thomas Geske, Eckard Hamelmann, Susanne Lau

THEMATIC POSTER SESSION 2: Food allergy—Anaphylaxis (TP19–TP38)

TP19

TP20

TP21 Double-blind provocation tests in non-IgE mediated cow’s milk allergy and the occurrence of placebo reactions

Sarah Bogovic, Jochem van den Berg, Chantal Janssen

TP22 Gradual introduction of baked egg (BE) in egg allergic patients under 2 years old

Angela Claver

TP23 Randomised controlled trial of SOTI with raw hen’s egg in children with persistent egg allergy I: safety and efficacy of daily vs. weekly protocols of induction

Mª Flor Martin-Muñoz, C. Martorell, M. T. Belver, E. Alonso Lebrero, L. Zapatero, V. Fuentes, M. Piqué, A. Plaza, C. Muñoz, A. Martorell, Cristina Blasco, B. Villa, C. Gómez, S. Nevot, J. M. García, L. Echeverria

TP24 Randomised controlled trial of SOTI with raw hen’s egg in children with persistent egg allergy II: a randomised controlled trial to study a safer, more effective and easy to perform maintenance (daily vs. every two days) pattern of egg SOTI

Mª Flor Martin-Muñoz, C. Martorell, M. T. Belver, E. Alonso Lebrero, L. Zapatero, V. Fuentes, M. Piqué, A. Plaza, C. Muñoz, A. Martorell, Cristina Blasco, B. Villa, C. Gómez, S. Nevot, J. M. García, L. Echeverria

TP25 Determining the safety of baked egg home reintroduction for children with mild egg allergy

Brenda DeWitt, Judith Holloway, Donald Hodge

TP26 Demographics, investigations and patterns of sensitisation in children with oral allergy syndrome in a London Teaching Hospital

Sian Ludman, Merhdad Jafari-Mamaghani, Rosemary Ebling, Adam T. Fox, Gideon Lack, George Du Toit

TP27 Airborne peanut challenge in children: allergic reactions are rare

Sofia Lovén Björkman, Caroline Nilsson, Natalia Ballardini

TP28 The nutty question on Pediatric Wards: to be or “nut” to be?

Supriyo Basu, Jenny Hallet, Jyothi Srinivas

TP29

TP30

TP31 Allergy education in nursery schools

Hazel Stringer, Nicola Jay

TP32 Food allergy in the first year of life

Tânia Lopes, Cristina Madureira, Filipa Almeida, Susana Lopes, Paula Fonseca, Clara Vieira, Fernanda Carvalho

TP33 Prevalence and geographic distribution of oral allergy syndrome in Italian children: a multicenter study

Carla Mastrorilli, Carlo Caffarelli, Riccardo Asero, Salvatore Tripodi, Arianna Dondi, Gianpaolo Ricci, Carlotta Povesi Dascola, Elisabetta Calamelli, Francesca Cipriani, Andrea Di Rienzo Businco, Annamaria Bianchi, Paolo Candelotti, Tullio Frediani, Carmen Verga, Paolo Maria Matricardi

TP34 Are common standardised allergen extracts used in skin test enough in the diagnosis of nuts allergy?

Cristina Muñoz Archidona, Loreto González Domínguez, Ana Moreira Jorge, Sergio Quevedo Teruel, Teresa Bracamonte Bermejo, Miriam Castillo Fernández, Fernando Pineda de la Losa, Luis Ángel Echeverría Zudaire

TP35 Evaluation of IgE sensitisation in children with allergic proctocolitis and its relationship to atopic dermatitis

Despina Mermiri, Paraskevi Korovessi, Skevi Tiliakou, Evaggelia Tavoulari, Kalliopi-Maria Moraiti, Fotini Giannoula, Athina Papadopoulou

TP36 Food allergy in children: are we managing them appropriately in the Emergency Department?

Wan Jean Tee, Samir Deiratany, Raymond Seedhoo, Roisin McNamara, Ike Okafor

TP37 Importance of oil body associated allergenic proteins in nuts suspected allergy children

Loreto González Domínguez, Ana Moreira Jorge, Cristina Muñoz Archidona, Teresa Bracamonte Bermejo, Sergio Quevedo Teruel, Fernando Pineda de la Losa, Miriam Castillo Fernández, Luis Ángel Echeverría Zudaire

TP38 Practical application of basophil activation test in children with food allergy

Ekaterina Khaleva, Gennady Novic, Natalia Bychkova

THEMATIC POSTER SESSION 3: Asthma (TP39–TP57)

TP39 Effect of corticosteroid therapy upon serum magnesium level in chronic asthmatic children

Amany Abd Al-Aziz, Amany Fatouh, Ayat Motawie, Eman El Bostany, Amr Ibrahim

TP40 ADAM33 in Bulgarian children with asthma

Guergana Petrova, Dimitrinka Miteva, Snezhina Lazova, Penka Perenovska, Sylvia Andonova, Alexey Savov

TP41

TP42 The impact of vitamin D serum levels in asthma and allergic rhinitis

Maria Zoto, Marialena Kyriakakou, Paraskevi Xepapadaki, Nikolaos G. Papadopoulos

TP43 Life-threatening, first reported, paradoxical bronchospasm after nebulised Salbutamol in a 10 year old child

Paraskevi Korovessi, Mariza Vassilopoulou, Athina Balaska, Lambros Banos, Stavroula Kostaridou, Despina Mermiri

TP44

TP45 Asthma symptoms in children with treatment for allergic rhinoconjunctivitis

Jorien Wartna, Arthur M. Bohnen, Gijs Elshout, David H. J. Pols, Patrick J. E. Bindels

Erasmus MC, Rotterdam, The Netherlands

TP46 Atopy increased the risk of developing exercise-induced bronchoconstriction in young athletes

Sven F. Seys; Ellen Dilissen, Sarah Van der Eycken, An-Sofie Schelpe, Gudrun Marijsse, Thierry Troosters, Vincent Vanbelle, Sven Aertgeerts, Jan L. Ceuppens, Lieven J. Dupont, Koen Peers, Dominique M. Bullens

TP47 The effect of higher BMI on risk for asthma and treatment outcome in overweight and obese children

Ivana Banic, Sandra Bulat Lokas, Jelena Zivkovic, Boro Nogalo, Iva Mrkic Kobal, Davor Plavec, Mirjana Turkalj

TP48

TP49

TP50

TP51

TP52 The impact of a multidisciplinary project intended to change the culture of nebulisers towards pressurised metered dose inhalers

Georgeta Oliveira, Katharine Pike, Alda Melo, Tomás Amélia, José Carlos Cidrais Rodrigues, Cristina Serrano, José Manuel Lopes dos Santos, Carla Lopes

TP53

TP54

TP55

TP56 Increased asthma control in patients with severe persistent allergic asthma after 12 month of nightly temperature controlled laminar airflow (TLA)

Eckard Hamelmann, Uwe Schauer, Karl-Christian Bergmann

TP57

THEMATIC POSTER SESSION 4: Drug allergy—Dermatology (TP58–TP77)

TP58 Should we proceed directly to provocation challenges to diagnose drug allergy? Our experience says yes

Luis Moral, Teresa Toral, Nuria Marco, Beléns García Avilés, Mª Jesús Fuentes, Jesús Garde, Cristina Montahud, Javier Perona, Mª José Forniés

TP59 Anaphylaxis to 13-valent pneumococcal vaccine

Esozia Arroabarren, Marta Anda, Maria Luisa Sanz, Maria Teresa Lizaso, Candida Arregui

TP60 Intrapartum antibiotic exposure for treatment of group B streptococcus was not associated with the development of penicillin allergy in children

Sara May, Martha Hartz, Avni Joshi, Miguel A. Park

TP61 Evaluation of suspected drug hypersensitivity reactions in 169 children referred to the General Hospital

Sonja Posega Devetak, Tina Vesel, Anja Koren Jeverica, Tadej Avčin

TP62 Drug provocation testing: experience of a tertiary hospital

Leonor Castro, Carolina Gouveia, Ana Carvalho Marques, Antonio Jorge Cabral

TP63 Perioperative anaphylaxis: a growing concern in pediatric population

Luis Amaral, Fabrícia Carolino, Eunice Castro, Madalena Passos, Josefina R. Cernadas

TP64 Raising awareness of hypersensitivity to non-steroidal anti-inflammatory drugs in the pediatric age

Fabrícia Carolino, Luís Amaral, Eunice Dias de Castro, Josefina R. Cernadas

TP65 Perioperative anaphylaxis in young children: how to confirm the suspicion

Josefina R. Cernadas, Fabrícia Carolino, Luís Amaral, Fernando Pineda, Armanda Gomes

TP66 A case study of a child suspected to be penicillin allergic-digging deeper

Katherine Knight, Roisin Fitzsimons, Helen Brough

TP67 Prevalence, characteristics and risk factors of hypersensitivity reactions to antibiotics in patients with cystic fibrosis

Jobst Röhmel, Carsten Schwarz, Anne Mehl, Philippe Stock, Doris Staab

TP68 Antibiotic drug hypersensitivity in cystic fibrosis: A pilot study using cellular allergy tests for diagnostics

Jobst Röhmel, Carsten Schwarz, Christine Seib, Doris Staab, Philippe Stock

TP69 Oral antibiotics challenges in children

Anita Critchlow, Alyson Barber, Nicola Jay

TP70 Hypersensitivity reaction to vancomycin: a new successful desensitization protocol

Belen Delavalle, Teresa Garriga, Blanca Vilá, Cristina Blasco

TP71

TP72 Clinical phenotypes according to FLG gene loss of function mutations in children with atopic dermatitis

Francesca Cipriani, Annalisa Astolfi, Costanza Di Chiara, Elisabetta Calamelli, Iria Neri, Annalisa Patrizi, Gianpaolo Ricci

TP73

TP74 Urticaria in children: clinical and epidemiological features

Katerina Neskorodova, Asya Kudryavtseva

TP75

TP76 Acute urticaria at the Pediatrics Emergency Department: is it allergy?

Esozia Arroabarren, Jorge Alvarez, Marta Anda, Miriam Palacios, Marta Martinez-Merino, Ibone Vaquero

TP77

Genome-Wide DNA Methylation Analysis Reveals Epigenetic Dysregulation of MicroRNA-34A in TP53-Associated Cancer Susceptibility

PURPOSE

Although the link between mutant TP53 and human cancer is unequivocal, a significant knowledge gap exists in clinically actionable molecular targets in Li-Fraumeni syndrome (LFS), a highly penetrant cancer predisposition syndrome associated with germline mutations in TP53. This study surveyed the epigenome to identify functionally and clinically relevant novel genes implicated in LFS.

PATIENTS AND METHODS

We performed genome-wide methylation analyses of peripheral blood leukocyte DNA in germline TP53 mutation carriers (n = 72) and individuals with TP53 wild type in whom histologically comparable malignancies developed (n = 111). Targeted bisulfite pyrosequencing was performed on a validation cohort of 30 TP53 mutation carriers and 46 patients with TP53 wild type, and candidate sites were evaluated in primary tumors from patients with LFS across multiple histologic tumor types.

RESULTS

In 183 patients, distinct DNA methylation signatures were associated with deleterious TP53 mutations in peripheral blood leukocytes. TP53-associated DNA methylation marks occurred in genomic regions that harbored p53 binding sites and in genes encoding p53 pathway proteins. Moreover, loss-of-function TP53 mutations were significantly associated with differential methylation at the locus encoding microRNA miR-34A, a key component of the p53 regulatory network (adjusted P < .001), and validated in an independent patient cohort (n = 76, P < .001). Targeted bisulfite pyrosequencing demonstrated that miR-34A was inactivated by hypermethylation across many histologic types of primary tumors from patients with LFS. Moreover, miR-34A tumor hypermethylation was associated with decreased overall survival in a cohort of 29 patients with choroid plexus carcinomas, a characteristic LFS tumor (P < .05).

CONCLUSION

Epigenetic dysregulation of miR-34A may comprise an important path in TP53-associated cancer predisposition and represents a therapeutically actionable target with potential clinical relevance.

A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development. The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations (KRAS, followed by CDKN2A, then TP53 and SMAD4); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage, indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage. However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection, suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory. In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.

Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820 controls) to identify pleiotropic loci. Findings were replicated in independent association studies (55,789 cases, 330,490 controls). We identified a novel pleiotropic association at 1q22 involving breast and lung squamous cell carcinoma, with eQTL analysis showing an association with ADAM15/THBS3 gene expression in lung. We also identified a known breast cancer locus CASP8/ALS2CR12 associated with prostate cancer, a known cancer locus at CDKN2B-AS1 with different variants associated with lung adenocarcinoma and prostate cancer, and confirmed the associations of a breast BRCA2 locus with lung and serous ovarian cancer. This is the largest study to date examining pleiotropy across multiple cancer-associated loci, identifying common mechanisms of cancer development and progression. Cancer Res; 76(17); 5103-14. ©2016 AACR.

Common variants in the obesity-associated genes FTO and MC4R are not associated with risk of colorectal cancer

BACKGROUND

Obesity is a convincing risk factor for colorectal cancer. Genetic variants in or near FTO and MC4R are consistently associated with body mass index and other body size measures, but whether they are also associated with colorectal cancer risk is unclear.

METHODS

In the discovery stage, we tested associations of 677 FTO and 323 MC4R single nucleotide polymorphisms (SNPs) 100kb upstream and 300kb downstream from each respective locus with risk of colorectal cancer in data from the Colon Cancer Family Registry (CCFR: 1960 cases; 1777 controls). Next, all SNPs that were nominally statistically significant (p<0.05) in the discovery stage were included in replication analyses in data from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO: 9716 cases; 9844 controls).

RESULTS

In the discovery stage, 43 FTO variants and 18 MC4R variants were associated with colorectal cancer risk (p<0.05). No SNPs remained statistically significant in the replication analysis after accounting for multiple comparisons.

CONCLUSION

We found no evidence that individual variants in or near the obesity-related genes FTO and MC4R are associated with risk of colorectal cancer.

Abstract 5287: Heterogeneity of mutation calling and annotation: a survey of cancer next-generation sequencing initiatives by the Global Alliance for Genomics and Health (GA4GH)

Although genomic data sharing is widely endorsed, practical barriers exist. For example, annotation and calling of mutations vary significantly with the method used. This poses clear challenges in data harmonization and sharing. In this setting, GA4GH conducted a survey of Cancer Next Generation Sequencing (NGS) initiatives globally to chart the technical implementation of genomic programs.

A total of 59 of 108 invited initiatives responded (response rate = 55%) via a web-based survey. In total, 63% of programs share their data, and 10% are partially sharing or planning to share. Most initiatives were North American (33%) or European (28%) based. Of the 59 respondents, 51 responded to queries on technical aspects of their NGS program (Table 1). For diagnostic application, 67% employ a small panel (&lt;50 genes), 55% a medium panel (50-250 genes), 45% a large panel (251-1000 genes); only 22% indicated they (also) use whole exome sequencing (WES). Diagnostic programs tend to favor panels and deep sequencing, while research programs favor WES/WGS. Overall, mutation and copy number calls were stored centrally in a single project database (96% and 92% respectively), with lower rates for raw data (BAM files, 86%) and histological data (75%). Somatic mutations were identified primarily via GATK (57%), Samtools (49%), Varscan (47%), MuTect (40%); all but 7 initiatives used combinations of these tools. Mutational variants were annotated by Cosmic (73%), PolyPhen (66%), and dbSnp (64%). Germline samples were used as control in only 62% of initiatives.

In conclusion, the majority of initiatives use an ensemble of tools for calling and annotating mutational variants. Harmonization efforts on gene panel composition and the standardization of tools (eg, methods, application program interfaces (APIs)) are urgently needed to prevent continued generation of isolated data silos that hamper NGS-enabled advances in precision medicine. Primary purpose of test% Diagnostic (n = 9)% Research (n = 22)% Diagnostic & Research (n = 20)OrganizationCentralized testing22%64%30%Unique sample identifiers89%77%70%Certification ISO/CLIA/NE88%45%65%Initiative &gt; 1000 Patients33%36%35%SequencingSequencing depth 50-250x0%55%80%Sequencing depth &gt;250x100%45%20%Panel sequencing89%68%60%Whole Exome/Genome Sequencing22%77%65%SamplesFresh frozen (FF)11%23%15%Formalin Fixed Paraffin Embedded (FFPE)44%27%20%FFPE or FF44%50%65%Germline as control22%68%65%

Citation Format: Daniel J. Vis, Jeremy Lewin, Lillian Siu, Rachel Liao, Jean Claude Zenklusen, Fabien Calvo, Edit Szepessy, Ana Vivancos, Valtteri Wirta, Subha Madhavan, Keunchil Park, Daniel Tan, Janessa Laskin, Melissa Brammer, Emmanuel Dias-Neto, Anthony Tolcher, Thomas J. Hudson, Charles Sawyers, Mark Lawler, Emile E. Voest. Heterogeneity of mutation calling and annotation: a survey of cancer next-generation sequencing initiatives by the Global Alliance for Genomics and Health (GA4GH). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5287.

Abstract 5230: Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer

Whole-genome sequencing (WGS) has started a new era in human genetics in which data can be used to more fully understand the role of genetic variation in common complex diseases, including the role of less frequent and rare variants and structural variation. To explore the impact of these variants on colorectal cancer risk we conducted the first large scale WGS study for colorectal cancer (CRC) including 1,961 CRC cases and 981 controls. These WGS data as well as those from the Haplotype Reference Consortium were imputed in 13,104 CRC cases and 15,521 controls with genome-wide association study (GWAS) data that are part of the Colorectal Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Focusing on rare and less frequent variants, insertions and deletions we observed potentially novel variants: a less frequent variant (MAF = 0.026) on chromosome 5 located in NREP/STARD4-AS1 (p = value 4E-08); and a novel rare multi-allelic variant (MAF = 0.003) on chromosome 9 near KLF9 and TRPM3 (p-value 2E-09; the other allele of this multi-allelic variant had a MAF of 0.0003 and p-value of 0.55). Furthermore, we observed an independent locus close to the known region 8q24 that was located upstream of GSDMC (MAF = 0.16, p-value 5E-08). Within the known region 8q23/EIF3H we identified several low frequency variants with similar MAF (0.0181 to 0.0204) including a 6bp deletion with p-values between 4E-08 and 1E-09 that were independent of the common variant signal in this region. In addition, we identified statistically significant (p&lt;5E-08) deletions, insertions, and an essential splice site within known GWAS loci that present interesting candidates for functional studies. We will follow up these findings in independent samples from the Colorectal Cancer Transdisciplinary Study (CORECT) and CCFR, as well as additional samples currently genotyped in GECCO. In conclusion, next generation sequencing combined with imputation in large GWAS data sets has the potential to identify novel low frequency and rare genetic variants, aid fine-mapping of known CRC susceptibility loci and point to interesting functional candidates.

Citation Format: Jeroen Huyghe, Sai Chen, Hyun M. Kang, Tabitha A. Harrison, Sonja I. Berndt, Stephane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Gallinger J. Steven, Stephen B. Gruber, Andrea Gsur, Michael Hoffmeister, Thomas J. Hudson, Loic Le Marchand, Polly A. Newcomb, John D. Potter, Conghui Qu, Martha L. Slattery, Joshua D. Smith, Emily White, Li Hsu, Goncalo R. Abecasis, Deborah A. Nickerson, Ulrike Peters. Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5230.

Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).

Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases

Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 genes in 589,306 genomes led to the identification of 13 adults harboring mutations for 8 severe Mendelian conditions, with no reported clinical manifestation of the indicated disease. Our findings demonstrate the promise of broadening genetic studies to systematically search for well individuals who are buffering the effects of rare, highly penetrant, deleterious mutations. They also indicate that incomplete penetrance for Mendelian diseases is likely more common than previously believed. The identification of resilient individuals may provide a first step toward uncovering protective genetic variants that could help elucidate the mechanisms of Mendelian diseases and new therapeutic strategies.

CYP24A1 variant modifies the association between use of oestrogen plus progestogen therapy and colorectal cancer risk

BACKGROUND

Menopausal hormone therapy (MHT) use has been consistently associated with a decreased risk of colorectal cancer (CRC) in women. Our aim was to use a genome-wide gene-environment interaction analysis to identify genetic modifiers of CRC risk associated with use of MHT.

METHODS

We included 10 835 postmenopausal women (5419 cases and 5416 controls) from 10 studies. We evaluated use of any MHT, oestrogen-only (E-only) and combined oestrogen-progestogen (E+P) hormone preparations. To test for multiplicative interactions, we applied the empirical Bayes (EB) test as well as the Wald test in conventional case-control logistic regression as primary tests. The Cocktail test was used as secondary test.

RESULTS

The EB test identified a significant interaction between rs964293 at 20q13.2/CYP24A1 and E+P (interaction OR (95% CIs)=0.61 (0.52-0.72), P=4.8 × 10(-9)). The secondary analysis also identified this interaction (Cocktail test OR=0.64 (0.52-0.78), P=1.2 × 10(-5) (alpha threshold=3.1 × 10(-4)). The ORs for association between E+P and CRC risk by rs964293 genotype were as follows: C/C, 0.96 (0.61-1.50); A/C, 0.61 (0.39-0.95) and A/A, 0.40 (0.22-0.73), respectively.

CONCLUSIONS

Our results indicate that rs964293 modifies the association between E+P and CRC risk. The variant is located near CYP24A1, which encodes an enzyme involved in vitamin D metabolism. This novel finding offers additional insight into downstream pathways of CRC etiopathogenesis.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study

Epidemiological studies have reported inconsistent associations between telomere length (TL) and risk for various cancers. These inconsistencies are likely attributable, in part, to biases that arise due to post-diagnostic and post-treatment TL measurement. To avoid such biases, we used a Mendelian randomization approach and estimated associations between nine TL-associated SNPs and risk for five common cancer types (breast, lung, colorectal, ovarian and prostate cancer, including subtypes) using data on 51 725 cases and 62 035 controls. We then used an inverse-variance weighted average of the SNP-specific associations to estimate the association between a genetic score representing long TL and cancer risk. The long TL genetic score was significantly associated with increased risk of lung adenocarcinoma (P = 6.3 × 10(-15)), even after exclusion of a SNP residing in a known lung cancer susceptibility region (TERT-CLPTM1L) P = 6.6 × 10(-6)). Under Mendelian randomization assumptions, the association estimate [odds ratio (OR) = 2.78] is interpreted as the OR for lung adenocarcinoma corresponding to a 1000 bp increase in TL. The weighted TL SNP score was not associated with other cancer types or subtypes. Our finding that genetic determinants of long TL increase lung adenocarcinoma risk avoids issues with reverse causality and residual confounding that arise in observational studies of TL and disease risk. Under Mendelian randomization assumptions, our finding suggests that longer TL increases lung adenocarcinoma risk. However, caution regarding this causal interpretation is warranted in light of the potential issue of pleiotropy, and a more general interpretation is that SNPs influencing telomere biology are also implicated in lung adenocarcinoma risk.

The effect of 5-fluorouracil/leucovorin chemotherapy on CpG methylation, or the confounding role of leukocyte heterogeneity: An illustration

Blood-based epigenome-wide association studies that aim at comparing CpG methylation between colorectal cancer (CRC) patients and controls can lead to the discovery of diagnostic or prognostic biomarkers. Numerous confounders can lead to spurious associations. We aimed to see if 5-fluorouracil (5-FU)/leucovorin chemotherapy administered to cases prior to the collection of their blood has an effect on methylation. 304 patients who received treatment and 273 who did not were profiled on the HumanMethylation450 array. Association tests were adjusted for confounders, including proxies for leukocyte cell counts. There were substantial methylation differences between these two groups that vanished once the leukocyte heterogeneity was accounted for. We observed a significant decrease of T cells in the treatment group (CD4+: p=10(-6); CD8+: p=0.036) and significant increase of NK cells (p=0.05) and monocytes (p=0.0006). 5-FU/leucovorin has no effect on global and local blood-based methylation profiles, other than through differences in the leukocyte compositions that the treatment induced.

Abstract 1058: Novel insights into the genetic and epigenetic regulation of the MLH1 CpG island and shore in colorectal cancer

Gene silencing via CpG island hypermethylation contributes to colorectal cancer (CRC). We previously demonstrated that genetic variants (single nucleotide polymorphisms, or SNPs) in the MLH1 gene promoter region are associated with MLH1 CpG island hypermethylation, MLH1 protein loss, and DNA mismatch repair deficiency in tumors. Recently, CpG-rich “shore” regions were identified flanking many CpG islands which exhibiting distinct methylation profiles among different tissues and in normal versus tumor states. To explore the role of MLH1 CpG island shore methylation, we performed global methylation profiling (Illumina 450K microarrays) to investigate DNA methylation in peripheral blood cell (PBC) DNA of over 800 CRC cases and 800 controls (Savio et al., 2012). We found that MLH1 CpG island shore hypomethylation occurred in PBC DNA of both cases and controls. Intriguingly, individuals carrying variant alleles of the MLH1 promoter SNP rs1800734 incur significant hypomethylation at the MLH1 CpG island shore, located 1.5 kb upstream irrespective of disease status. Based on these observations we sought to determine whether these SNP-associated epigenetic changes were apparent in other tissues, including CRC and normal colonic tissue. To address this, we investigated MLH1 CpG island shore methylation in matched PBC, normal colon, and tumor DNA of 349 CRC cases using the real-time PCR-based technique, MethyLight. Methylation was significantly lower in PBC DNA of CRC cases with variant SNP genotypes (both heterozygous and homozygous variant carriers) and this association was also observed in normal colonic DNA. The association between genotype and epigenotype was lost in tumor DNA, as no differences in methylation were seen among different genotypes. Hypermethylation in tumor DNA compared to normal tissues (PBC and colon) was also observed. This hypermethylation and lack of association between SNP genotype and shore methylation in tumors may indicate an epigenetic switch occurring. Bisulfite sequencing of DNA from fresh frozen tumors and paired normal colonic mucosa have recapitulated these results, with hypomethylation incurred in variant SNP carriers. Hypermethylation in tumor compared to normal DNA was also observed. Bisulfite sequencing of four CRC cell lines has also revealed SNP-dependent hypermethylation at the MLH1 CpG island shore. Taken together, we have integrated methylation data from a microarray platform, sensitive real-time PCR, and bisulfite sequencing for a comprehensive and systematic analysis of DNA methylation at the CpG island shore of MLH1 in multiple tissues of CRC cases, controls, and cell lines. These results indicate that static genetic variants can modulate dynamic epigenetic regulation at the MLH1 gene region, and may play a role in colorectal tumorigenesis.

Citation Format: Andrea J. Savio, Mathieu Lemire, Miralem Mrkonjic, Steven Gallinger, Brent W. Zanke, Thomas J. Hudson, Bharati Bapat. Novel insights into the genetic and epigenetic regulation of the MLH1 CpG island and shore in colorectal cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1058. doi:10.1158/1538-7445.AM2015-1058

Abstract 2988: International cancer genome consortium (ICGC)

The International Cancer Genome Consortium (ICGC) was established to bring together researchers from around the globe to comprehensively analyze the genomic, transcriptomic, and epigenomic changes in 50 different tumour types or subtypes that are of clinical and societal importance across the globe (International network of cancer genome projects. Nature 464, 993-998 (15 April 2010)).

As of December 2014, the ICGC has received commitments from researchers and funding organizations in Asia, Australia, Europe, North America and South America for 77 project teams in 17 jurisdictions to study more than 25,000 tumour genomes.

More than 27,000 tumours that meet ICGC requirements for consent have been obtained and research pathologists have approved over 27,000 samples as meeting ICGC standards.

Processed data is available via the Data Coordination Centre (http://dcc.icgc.org) based at the Ontario Institute for Cancer Research and is updated quarterly. The data release (Version 17) in October 2014 included datasets from 42 ICGC members. The ICGC Data Portal has been improved to provide enhanced support to the research community browsing this vast dataset.

The ICGC and The Cancer Genome Atlas (TCGA) PanCancer Analysis of Whole Genomes (PCAWG) project is committing more than 2,500 tumour-normal whole genome pairs from 23 different tumour types to uniform alignment and variant calling. More than 600 researchers will contribute to the interpretation of the data and writing of papers that will focus on specific analyses covering: Identification of driver mutations outside coding regions, including those that affect cis-regulatory regions and non-coding RNAs; and identification of gene regulatory pathways altered by non-coding mutations. Because the projected size of the pan-cancer dataset for 5,000 WGS is very large, PCAWG is using a distributed compute cloud environment (at different computing centres in the USA, Europe and Asia) that meet technical requirements of the project and the bioethical framework of ICGC and its member projects. More information can be found on www.icgc.org.

Citation Format: Jennifer L. Jennings, Thomas J. Hudson. International cancer genome consortium (ICGC). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2988. doi:10.1158/1538-7445.AM2015-2988