A Genome-Wide Assessment of Inherited Genetic Variants and the Risk of Langerhans Cell Histiocytosis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4059-4059
Author(s):  
Erin Peckham ◽  
Philip J Lupo ◽  
Michael E Scheurer ◽  
Rikhia Chakraborty ◽  
John Belmont ◽  
...  

Abstract Introduction: Langerhans cell histiocytosis (LCH) is a disease characterized by inflammatory lesions including pathologic CD207+ dendritic cells. Clinically, LCH is highly variable ranging from single lesions to highly aggressive, disseminated disease involving multiple organs and requiring intensive chemotherapy. Recent data support a model of pathogenesis in which activating somatic mutations in MAPK pathway genes arise in myeloid DC precursors. However, little is known about genetic susceptibility to this condition. Therefore, we conducted a genome-wide association study to characterize the role of inherited genetic variants on disease risk. Methods: We utilized a case-parent trio approach, which is immune to the effects of population stratification bias. Specifically, this allows for the inclusion of individuals regardless of genetic ancestry. LCH case-parent trios (n=134) were recruited from Texas Children's Cancer Center. Genotyping was performed using the Illumina Omni-5 Quad BeadChip. Genetic ancestry was determined using the bioinformatics algorithm STRUCTURE. To inform this algorithm, a set of 12,898 autosomal ancestry informative markers specifically identified to infer population substructure was extracted from the study trios. Estimated genomic ancestral proportions were then used to classify each study participant as either of European ancestry, Amerindian ancestry, or of African ancestry. For the association analysis, we focused on the role of common variants (i.e., minor allele frequency ≥5%). The association analysis was conducted utilizing the PREMIM-EMIM algorithm, an established, multinomial log-likelihood approach for assessing case-parent trios GWAS data. This method allows for the inclusion of "incomplete" trios (e.g., mother-case duos). We applied a genome-wide statistical significance cutoff of p<1.0x10-5. Results: In this GWAS, LCH cases were predominantly male (54%), and based on the genetic ancestry analysis, 60% were of European ancestry, 36% Amerindian ancestry, and 4% African ancestry. Among the 343 individuals included in the analysis, 1,672,105 SNPs autosomal SNPs were assessed and an overview of the results is displayed using a Manhattan plot. We identified five potential inherited genomic regions associated with LCH susceptibility. The strongest associations between inherited SNPs and childhood LCH were seen in SMAD6 on chromosome 15 (p-value = 2.38x10-7) and in ECE1 on chromosome 1 (p-value = 2.15x10-6). Conclusions: In this genome-wide assessment of the role of inherited genetic variation on the risk of LCH, we identified SNPs with significant effects in genes implicated in diverse pathways including embryogenesis and cellular division. Among the proteins encoded by the regions identified, SMAD6and ECE1 have both been reported to impact ERK activation, a critical feature of LCH pathogenesis. These findings support potential for inherited genetic variants to influence risk of developing LCH. Disclosures Allen: NovImmune: Consultancy, Other: unpaid; Roche: Consultancy, Other: unpaid.

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4278-4278
Author(s):  
Erin Peckham-Gregory ◽  
Michael Scheurer ◽  
Rikhia Chakraborty ◽  
Harshal Abhyankar ◽  
Kenneth L. McClain ◽  
...  

Abstract Introduction: Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate, and has a median age at diagnosis of 30 months. Approximately 50% of children with LCH relapse, and 40% experience a second relapse event within two years. Sequencing studies have identified activating somatic mutations in MAPK pathway genes in ~85% of LCH lesions. Notably, LCH cases who are carriers of BRAFV600E+ experience a 2-fold increased risk of relapse. However, the role of inherited genetic effects in LCH relapse remains unknown. Therefore, we conducted a genome-wide association study (GWAS) to characterize the role of inherited genetic variants on risk of LCH relapse. Methods: LCH cases (n=117) for this discovery GWAS were recruited from Texas Children's Hospital, of which 52 patients experienced a relapse event and 65 patients did not. Genotyping was performed on the Illumina Omni5 Quad BeadChip. We tested the association between common variants (minor allele frequency >5%) and LCH relapse risk in PLINK. A genome-wide threshold of significance was applied at P-value<5.0x10-8, and threshold of suggestive significance at P-value<1.0x10-5. Principal component analysis was performed to account for genetic ancestry, with the top two principal components (PCs) accounting for 85% of variability. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) controlling for age at diagnosis, sex, and the top two PCs were estimated using logistic regression. An independent replication set of LCH cases (n=124) were recruited from Texas Children's Hospital to validate discovery GWAS findings. Results: High-quality genotype data for 583,173 germline variants were tested for an association with LCH relapse risk in the discovery GWAS stage. We identified a variant in high linkage disequilibrium with a cluster of loci on Chromosome 9 that surpassed our threshold of suggestive significance (non-coding RNA LOC100506532 rs2182640; P-value=6.98x10-6). This intronic variant was associated with a decreased risk of LCH relapse that remained statistically significant after adjusting for age at diagnosis, sex, and the top two PCs (aOR: 0.16; 95% CI: 0.07-0.35). While this non-coding RNA gene is largely uncharacterized, non-coding RNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Results from validation of this risk locus in an independent replication set are forthcoming. Conclusions: In this genome-wide assessment of inherited genetic variation and LCH relapse, we identified a genomic region that may be associated with LCH relapse. It is unclear which variant in the LOC100506532 cluster is a potentially causal allele. One of these variants may be a proxy for the causal locus, or may act through an effect on other genes in the same region or at distal sites. Notably RXRA, a retinoic acid receptor gene, is located in close proximity (~400kb) to LOC100506532 and regulates gene expression in various biologic processes. Risk variants within this gene have been identified to modulate disease-specific survival in melanoma, another BRAF-driven malignancy. While we are in the process of validating the association between LOC100506532 rs2182640 and LCH relapse risk in an independent replication set, our discovery GWAS results provide initial evidence to suggest that inherited risk factors influence LCH disease severity. Disclosures No relevant conflicts of interest to declare.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Caroline M. Nievergelt ◽  
Adam X. Maihofer ◽  
Torsten Klengel ◽  
Elizabeth G. Atkinson ◽  
Chia-Yen Chen ◽  
...  

Abstract The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5–20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson’s disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations.


2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 163-164
Author(s):  
Anastasia Gurinovich ◽  
Kaare Christensen ◽  
Marianne Nygaard ◽  
Jonas Mengel-From ◽  
Stacy Andersen ◽  
...  

Abstract Some cognitive abilities, such as vocabulary, are resilient to brain aging, while others such as conceptual reasoning, memory, and processing speed, decline with age and their rate of decline is genetically regulated. Despite the strong genetic heritability of processing speed assessed by the digit symbol substitution test (DSST), previous studies have failed to identify robust common genetic variants associated with this test. The Long Life Family Study (LLFS) includes long lived individuals and their family members who maintain good DSST scores as they age and who may carry variants associated with better DSST. We therefore conducted a genome-wide association study (GWAS) of DSST in LLFS using ~15M genetic variants imputed to the HRC panel of 64,940 haplotypes with 39,635,008 sites and replicated the findings using genetic data imputed to the 1000 Genomes phase 3 reference panel combining two Danish cohorts: the Middle Aged Danish Twins and the Longitudinal Study of Aging Danish Twins. The GWAS in LLFS discovered 20 rare genetic variants reaching genome-wide significance (p-value &lt; 5x10-8), including 18 variants associated with better processing speed with large effect size. The genetic associations of rs7623455, rs9821776, rs9821587, rs78704059 in chromosome 3 were replicated in the combined Danish cohort. These genetic variants tagged two hormone receptor related genes, THRB and RARB, both related to cognitive aging. Further gene-based tests in LLFS confirmed that these two genes have protective variants associated with better processing speed.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 1010-1010
Author(s):  
Tarah Jean Ballinger ◽  
Guanglong Jiang ◽  
Fei Shen ◽  
Kathy Miller ◽  
Bryan P. Schneider

1010 Background: Both Black race and obesity are associated with worse survival in early stage breast cancer. Obesity disproportionately affects Black women; however, the degree this contributes to racial disparities in breast cancer remains unclear. Prior work evaluated heterogeneous populations or used self- reported race, rather than genetic ancestry. African ancestry is associated with higher BMI and worse survival in breast cancer; however, the intersection between genetic ancestry and obesity on survival outcomes remains unknown. Methods: We analyzed data from the adjuvant trial E5103. Patients with high risk, HER2 negative breast cancer received doxorubicin/cyclophosphamide x 4, followed by weekly paclitaxel x 12, with or without bevacizumab. Genetic ancestry was determined on the 2,854 patients with available germline DNA, BMI, and outcome data using principal components from a genome-wide array. The primary objective assessed impact of BMI on DFS and OS by ancestry. Multivariate Cox proportional hazard models evaluated correlation between continuous or binary BMI and survival in African (AA) and European (EA) Americans. Results: 13.4% of patients were genetically classified as AA and 86.6% as EA. Higher continuous BMI was significantly associated with worse DFS and OS only in AAs (DFS: HR = 1.25 95% CI 1.07-1.46, p = 0.004; OS: HR = 1.38 95% CI 1.10-1.73, p = 0.005); not in EAs (DFS HR = 0.97 95% CI 0.90-1.05, p = 0.50; OS HR = 1.03 95% CI 0.93-1.14, p = 0.52). By disease subtype, BMI was associated with worse outcomes only in AAs with ER+, and not TNBC. By categorical BMI, WHO class III obesity (³ 40) significantly associated with worse DFS and OS only in AAs (DFS HR = 1.98, p = 0.010; OS HR = 2.07, p = 0.064), not in EAs (DFS HR = 0.97, p = 0.86; OS HR = 1.28, p = 0.30). Proportion of African ancestry (proAA) was associated with higher BMI and worse outcomes in the total population; however, within AAs there was no significant interaction between proAA and BMI on DFS (HR = 0.36, p = 0.06) or OS (HR = 0.38, p = 0.24). In AAs, BMI remained associated with DFS (HR = 2.78, p = 0.019), suggesting higher BMI is associated with worse DFS regardless of proAA. Coefficients for the interaction term indicate that as proAA increases the impact of BMI on outcome is lessened. Conclusions: Higher BMI is significantly associated with worse breast cancer outcomes in women of African ancestry in E5103, but not in those of European ancestry. Categorically, this association was significant only for severe obesity, indicating the relationship may depend on the degree of obesity. As proAA increased in AAs, the impact of BMI on outcome was lessened, suggesting other host factors may contribute more to obesity’s influence on outcome than genetics. Determination of the optimal populations for weight loss interventions will advance precision medicine efforts to impact racial disparities and outcomes in early stage breast cancer.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
N Pujol Gualdo ◽  
K Läll ◽  
M Lepamets ◽  
R Arffman ◽  
T Piltonen ◽  
...  

Abstract Study question Can genome-wide association analysis unravel the biological underpinnings of PP and facilitate personalized risk assessment via genetic risk scores construction? Summary answer We unravel novel links with urogenital development and vascular health in PP and present polygenic risk score as a tool to stratify PP risk. What is known already Prolapse is characterized by a descent of the pelvic organs into the vaginal cavity. PP affects around 40% of women after menopause and is the main indication for major gynecological surgery, having an important health, social and economic burden. Although the etiology and biological mechanisms underlying PP remain poorly understood, prior studies suggest genetic factors might play a role. Recently, a genome-wide association study (GWAS) identified seven genome-wide significant loci, located in or near genes involved in connective tissue metabolism and estrogen exposure in the etiology of PP. Study design, size, duration We conducted a three-stage case-control genome-wide association study. Firstly, in the discovery phase, we meta-analyzed Icelandic, UK Biobank and the FinnGen R3 datasets, comprising a total of 20118 cases and 427426 controls of European ancestry. For replication we used an independent dataset from Estonian Biobank (7968 cases and 118895 controls). Finally, we conducted a joint meta-analysis, containing 28086 cases and 546321 controls, which is the largest GWAS of PP to date. Participants/materials, setting, methods We performed functional annotation on genetic variants unraveled by GWAS and integrated these with expression quantitative trait loci and chromatin interaction data. In addition, we looked at enrichment of association signal on gene-set, tissue and cell type level and analyzed associations with other phenotypes both on genetic and phenotypic level. Colocalisation analyses were conducted to help pinpoint causal genes. We further constructed polygenic risk scores to explore options for personalized risk assessment and prevention. Main results and the role of chance In the discovery phase, we identified 18 genetic loci and 20 genetic variants significantly associated with POP (p &lt; 5 × 10−8) and 75% of the variants show nominal significance association (p &lt; 0.05) in the replication. Notably, the joint meta-analyses detected 20 genetic loci significantly associated with POP, from which 13 loci were novel. Novel genetic variants are located in or near genes involved in gestational duration and preterm birth (rs2687728 p = 2.19x10-9, EEFSEC), cardiovascular health and pregnancy success (rs1247943 p = 5.83x10-18, KLF13), endometriosis (rs12325192 p = 3.72x10-18, CRISPLD2), urogenital tract development (rs7126322, p = 4.35x10-15, WT1 and rs42400, p = 4.8x10-10, ADAMTS16) and regulation of the oxytocin receptor (rs2267372, p = 4.49x10-13, MAFF). Further analyses demonstrated that POP GWAS signals colocalise with several eQTLS (including EEFSEC, MAFF, KLF13, etc.), providing further evidence for mapping associated genes. Tissue and cell enrichment analyses underlined the role of the urogenital system, muscle cells, myocytes and adipocytes (p &lt; 0.00001, FDR&lt;0.05). Furthermore, genetic correlation analyses supported a shared genetic background with gastrointestinal disorders, joint and musculoskeletal disorders and cardiovascular disease. Polygenic risk scores analyses included a total of 125551 people in the target dataset, with 5379 prevalent patients and 2517 incident patients. Analyzing the best GRS as a quintile showed association with incident disease (Harrell c-statistic= 0.603, SD = 0.006). Limitations, reasons for caution This GWAS meta-analyses focused on European ancestry populations, which challenges the generalizability of GWAS findings to non-European populations. Moreover, this study included women with PP from population-based biobanks identified using the ICD-10 code N81, which limits analyses considering different disease stages and severity. Wider implications of the findings Our study provides genetic evidence to improve the current understanding of PP pathogenesis and serves as basis for further functional studies. Moreover, we provide a genetic tool for personalized risk stratification, which could help prevent PP development and improve the quality of a vast quantity of women. Trial registration number not applicable


2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1280-1280
Author(s):  
Kenneth Westerman ◽  
Ye Chen ◽  
Han Chen ◽  
Jose Florez ◽  
Joanne Cole ◽  
...  

Abstract Objectives Gene-diet interaction analysis can inform the development of precision nutrition for diabetes by uncovering genetic variants whose effects on glycemic traits vary across dietary behaviors. However, due to noise in dietary datasets and the low statistical power inherent in interaction analysis, there is a lack of confident, well-replicated gene-diet interactions for glycemic traits. Emerging computationally-efficient software tools have made it feasible to conduct well-powered, genome-wide interaction analysis in hundreds of thousands of individuals. Here, our objective was to conduct a genome-wide gene-diet interaction analysis for glycated hemoglobin (HbA1c; a measure of hyperglycemia), leveraging the large sample size of the UK Biobank cohort and data-driven dietary patterns to discover genetic variants whose effect is modulated by diet. Methods Food frequency questionnaires were previously used to derive empirical dietary patterns using principal components analysis (FFQ-PCs) in the UK Biobank. FFQ-PCs were used in genome-wide interaction analysis for HbA1c levels in unrelated, non-diabetic individuals of European ancestry (N = 331,610), adjusting for age, sex, and 10 genetic principal components. P-values were calculated for both the interaction (P-int) and a joint test (significance of the variant-HbA1c association combining the main and interaction effects) and the MAGMA tool was used to calculate gene-level enrichment statistics. Results Preliminary results from the first two FFQ-PCs confirmed known genetic loci for HbA1c using the joint test, such as at G6PC2 and GCK. Though no interaction tests reached genome-wide significance, suggestive signals (P-int &lt; 1e-5) emerged at the variant level (including one near TPSD1, which codes for a tryptase and has been linked to red blood cell traits) and the gene level (such as for GTF3C2, which has previously been shown to interact with sleep in impacting lipid traits). Conclusions We have conducted the largest genome-wide study of gene-diet interactions for glycemic traits to-date and identified regions in the genome whose effect on HbA1c may be modulated by dietary intake, suggesting that this approach has the potential to reveal new insights into the genetics of glycemic traits and inform individualized dietary guidelines for diabetes prevention and management. Funding Sources NHLBI.


2022 ◽  
Author(s):  
Zeyuan Song ◽  
Anastasia Gurinovich ◽  
Marianne Nygaard ◽  
Jonas Mengel-From ◽  
Stacy Andersen ◽  
...  

We conducted a genome-wide association study (GWAS) of Digit Symbol Substitution Test (DSST) scores administered in 4207 family members of the Long Life Family Study (LLFS). Genotype data were imputed to the HRC panel of 64,940 haplotypes resulting in ~15M genetic variants with quality score > 0.7. The results were replicated using genetic data imputed to the 1000 Genomes phase 3 reference panel from two Danish twin cohorts: the study of Middle Aged Danish Twins and the Longitudinal Study of Aging Danish Twins. The GWAS in LLFS discovered 20 rare genetic variants (minor allele frequency (MAF) < 1.0%) that reached genome-wide significance (p-value < 5x10-8). Among these, 18 variants had large protective effects on the processing speed, including rs7623455, rs9821776, rs9821587, rs78704059 on chromosome 3, which were replicated in the combined Danish twin cohort. These SNPs are located in/near two genes, THRB and RARB, that belonged to thyroid hormone receptors family that may influence speed of metabolism and cognitive aging. The gene-level tests in LLFS confirmed that these two genes are associated with processing speed.


2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Hang-Rai Kim ◽  
Sang-Hyuk Jung ◽  
Jaeho Kim ◽  
Hyemin Jang ◽  
Sung Hoon Kang ◽  
...  

Abstract Background Genome-wide association studies (GWAS) have identified a number of genetic variants for Alzheimer’s disease (AD). However, most GWAS were conducted in individuals of European ancestry, and non-European populations are still underrepresented in genetic discovery efforts. Here, we performed GWAS to identify single nucleotide polymorphisms (SNPs) associated with amyloid β (Aβ) positivity using a large sample of Korean population. Methods One thousand four hundred seventy-four participants of Korean ancestry were recruited from multicenters in South Korea. Discovery dataset consisted of 1190 participants (383 with cognitively unimpaired [CU], 330 with amnestic mild cognitive impairment [aMCI], and 477 with AD dementia [ADD]) and replication dataset consisted of 284 participants (46 with CU, 167 with aMCI, and 71 with ADD). GWAS was conducted to identify SNPs associated with Aβ positivity (measured by amyloid positron emission tomography). Aβ prediction models were developed using the identified SNPs. Furthermore, bioinformatics analysis was conducted for the identified SNPs. Results In addition to APOE, we identified nine SNPs on chromosome 7, which were associated with a decreased risk of Aβ positivity at a genome-wide suggestive level. Of these nine SNPs, four novel SNPs (rs73375428, rs2903923, rs3828947, and rs11983537) were associated with a decreased risk of Aβ positivity (p < 0.05) in the replication dataset. In a meta-analysis, two SNPs (rs7337542 and rs2903923) reached a genome-wide significant level (p < 5.0 × 10−8). Prediction performance for Aβ positivity increased when rs73375428 were incorporated (area under curve = 0.75; 95% CI = 0.74–0.76) in addition to clinical factors and APOE genotype. Cis-eQTL analysis demonstrated that the rs73375428 was associated with decreased expression levels of FGL2 in the brain. Conclusion The novel genetic variants associated with FGL2 decreased risk of Aβ positivity in the Korean population. This finding may provide a candidate therapeutic target for AD, highlighting the importance of genetic studies in diverse populations.


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