Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies

BACKGROUND

Clinical, molecular, and genetic epidemiology studies displayed remarkable differences between ever- and never-smoking lung cancer.

METHODS

We conducted a stratified multi-population (European, East Asian, and African descent) association study on 44,823 ever-smokers and 20,074 never-smokers to identify novel variants that were missed in the non-stratified analysis. Functional analysis including expression quantitative trait loci (eQTL) colocalization and DNA damage assays, and annotation studies were conducted to evaluate the functional roles of the variants. We further evaluated the impact of smoking quantity on lung cancer risk for the variants associated with ever-smoking lung cancer.

RESULTS

Five novel independent loci, GABRA4, intergenic region 12q24.33, LRRC4C, LINC01088, and LCNL1 were identified with the association at two or three populations (P < 5 × 10-8). Further functional analysis provided multiple lines of evidence suggesting the variants affect lung cancer risk through excessive DNA damage (GABRA4) or cis-regulation of gene expression (LCNL1). The risk of variants from 12 independent regions, including the well-known CHRNA5, associated with ever-smoking lung cancer was evaluated for never-smokers, light-smokers (packyear ≤ 20), and moderate-to-heavy-smokers (packyear > 20). Different risk patterns were observed for the variants among the different groups by smoking behavior.

CONCLUSIONS

We identified novel variants associated with lung cancer in only ever- or never-smoking groups that were missed by prior main-effect association studies.

IMPACT

Our study highlights the genetic heterogeneity between ever- and never-smoking lung cancer and provides etiologic insights into the complicated genetic architecture of this deadly cancer.

Probing the p-type Chemiresistive Response of NiFe2 O4 Nanoparticles for Potential Utilization as Ethanol Sensor

Detection of gas molecules and volatile organic compounds (VOCs) using efficient, low cost sensors has fetched significant attention in environmental monitoring, safety measures and medical diagnosis. In the present work, nickel ferrite (NFO) nanoparticles are explored as p-type semiconducting metal oxide (SMO) sensor for detection of five different organic vapors namely methanol, ethanol, n-propanol, iso-propanol and acetone which often cause severe damage to human body under prolonged exposure. The sensing studies in presence of the aforementioned five vapors are carried out by varying the sensor operating temperature (225-300 °C) and vapor concentrations (10-1000 ppm). Developed NFO sensor demonstrated best performance in terms of sensing (~10 ppm), response time (<10 s), excellent repeatability and selectivity towards ethanol among all other considered gas species. The repeatability of the sensor response is verified and the underlying reasons for the variation in the response of NFO sensor due to the change of operating temperature, analyte type and concentrations has been discussed. The synthesis of NFO through auto combustion method and study on their formation behaviour, oxygen vacancy evolution, band gap calculation, crystalline nature as well as microstructural features provides here the comprehensive information about the potential application of NFO nanoparticles as gas sensor.

Role of ammonium ionic liquid and Pd nanoparticles in cavitation-based graphite decontamination and recycling process

Sonochemical recovery of radioactive contaminants from nuclear graphite has been demonstrated to be quite invaluable in recent studies. However, graphite is a soft material and is prone to erosion and wear. This restricts the recycle of graphite cleaned using ultrasound beyond a few decontamination cycles. Hence, it is an imperative to prevent the surface erosion of graphite in the sonic field. The current work studies the efficacy of ultrasound in decontaminating ceria contaminated graphite coupons using a cocktail of acids (0.25 M HNO3 - 1 M HCOOH - 0.2 M [N2H5][NO3]). Based on the superlative effects of ionic liquids in lubrication and erosion prevention, the effect of adding ionic liquid stabilized Pd nanoparticles to the leachate was also studied. It was observed that the Trioctylmethyl ammonium chloride (TOMAC) ionic liquid prevented the generation of the carbon residue due to a protective viscous layer formation reducing the mechanical effects of cavitation on graphite surface. It also helped in maintaining the porosity change in graphite microstructure around 5% after 15 cycles of decontamination. TOMAC also proved to offer better surface protection on graphite compared to imidazolium-based ILs, based on the change in compressive strength and porosity in different ionic liquids. The palladium nanoparticles, on the other hand, helped in reductive dissolution of ceria layer by acting as a reducing agent due to its lower reduction potential compared to cerium. With the surge in demand of graphite worldwide, a non-destructive decontamination process for graphite with no secondary waste generation is the need of the hour. This study is an attempt in that direction.

A Recurrent ADPRHL1 Germline Mutation Activates PARP1 and Confers Prostate Cancer Risk in African American Families

African American (AA) families have the highest risk of prostate cancer. However, the genetic factors contributing to prostate cancer susceptibility in AA families remain poorly understood. We performed whole-exome sequencing of one affected and one unaffected brother in an AA family with hereditary prostate cancer. The novel non-synonymous variants discovered only in the affected individuals were further analyzed in all affected and unaffected men in 20 AA-PC families. Here, we report one rare recurrent ADPRHL1 germline mutation (c.A233T; p.D78V) in four of the 20 families affected by prostate cancer. The mutation co-segregates with prostate cancer in two families and presents in two affected men in the other two families, but was absent in 170 unrelated healthy AA men. Functional characterization of the mutation in benign prostate cells showed aberrant promotion of cell proliferation, whereas expression of the wild-type ADPRHL1 in prostate cancer cells suppressed cell proliferation and oncogenesis. Mechanistically, the ADPRHL1 mutant activates PARP1, leading to an increased H2O2 or cisplatin-induced DNA damage response for prostate cancer cell survival. Indeed, the PARP1 inhibitor, olaparib, suppresses prostate cancer cell survival induced by mutant ADPRHL1. Given that the expression levels of ADPRHL1 are significantly high in normal prostate tissues and reduce stepwise as Gleason scores increase in tumors, our findings provide genetic, biochemical, and clinicopathological evidence that ADPRHL1 is a tumor suppressor in prostate tissue. A loss of function mutation in ADPRHL1 induces prostate tumorigenesis and confers prostate cancer susceptibility in high-risk AA families.

IMPLICATIONS

This study highlights a potential strategy for ADPRHL1 mutation detection in prostate cancer-risk assessment and a potential therapeutic application for individuals with prostate cancer in AA families.

Genome-wide interaction analysis identified low-frequency variants with sex disparity in lung cancer risk

Differences by sex in lung cancer incidence and mortality have been reported which cannot be fully explained by sex differences in smoking behavior, implying existence of genetic and molecular basis for sex disparity in lung cancer development. However, the information about sex dimorphism in lung cancer risk is quite limited despite the great success in lung cancer association studies. By adopting a stringent two-stage analysis strategy, we performed a genome-wide gene-sex interaction analysis using genotypes from a lung cancer cohort including ~ 47 000 individuals with European ancestry. Three low-frequency variants (minor allele frequency < 0.05), rs17662871 [odds ratio (OR) = 0.71, P = 4.29×10-8); rs79942605 (OR = 2.17, P = 2.81×10-8) and rs208908 (OR = 0.70, P = 4.54×10-8) were identified with different risk effect of lung cancer between men and women. Further expression quantitative trait loci and functional annotation analysis suggested rs208908 affects lung cancer risk through differential regulation of Coxsackie virus and adenovirus receptor gene expression in lung tissues between men and women. Our study is one of the first studies to provide novel insights about the genetic and molecular basis for sex disparity in lung cancer development.

Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer

To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.

Volterra filter modelling of non-linear system using Artificial Electric Field algorithm assisted Kalman filter and its experimental evaluation

The main objective of this paper is to improve the identification efficiency of non-linear systems using the Kalman filter (KF), which is optimised with the Artificial Electric Field (AEF) algorithm. The conventional KF suffers from the proper tuning of its parameters, which leads to a divergence problem. This issue has been solved to a great extent by the meta-heuristic AEF algorithm assisted Kalman filter (AEF-KF). This paper proposes three steps for the identification of the systems while solving the problem as mentioned above. Firstly, it converts the identification model to a measurement problem. Next, the AEF algorithm optimises the KF parameters by considering the fitness function with the KF equations. The third step is to identify the model using conventional KF algorithm with the optimised KF parameters. To evaluate the performance of the proposed method, parameter estimation error, mean squared error (MSE), fitness (FIT) percentage, statistical information and percentage improvement are considered as the performance metrics. To validate the performance of the proposed method, five distinct non-linear models are identified with the Volterra model using KF and the AEF-KF techniques under various noisy input conditions. Besides, the practical applicability of the proposed approach is also tested on two non-linear benchmark systems using experimental data sets. The obtained simulation results confirm the efficacy and robustness of the proposed identification method in terms of the convergence speed, computational time and various performance metrics as compared to KF, Kalman smoother (KS) which is optimised using different state-of-the-art evolutionary algorithms and also other existing recently reported similar types of stochastic algorithms based approaches.

Distribution of soil carbon fractions under different bamboo species in northwest Himalayan foothills, India

Soil carbon and its fractions are important in understanding the mechanism of soil carbon sequestration. The present study evaluated the impact of seven commercial bamboo species, viz., Bambusa balcooa, B. bambos, B. vulgaris, B. nutans, Dendrocalamus hamiltonii, D. stocksii, and D. strictus, on labile and non-labile carbon fractions. In the 0-15-cm layer, B. nutans had the highest very labile C (7.65 g kg^-1) followed by B. vulgaris > B. balcooa > D. stocksii > D. hamiltonii > B. bambos > D. strictus > open. The active carbon pool was significantly low under the control plot (i.e. the open) indicating the positive influence of bamboo in soil C build-up in the top 0-15 cm soil layer. Amongst the different species of bamboo evaluated in this study, D. strictus accumulated the highest active C pool in 0-30-cm soil layer followed by B. vulgaris. Of the total organic C in the 0-30 cm soil depth, majority (55-60%) was contributed by the passive C pool comprising the less labile and the non-labile fraction of SOC. A high value of carbon stratification ratio (> 2) was observed for D. strictus, B. bambos, and D. hamiltonii which proves their potential for restoration of the degraded lands. The majority of bamboo species except for B. balcooa and D. stocksii showed a higher carbon management index than open systems, thereby indicating higher rates of soil C rehabilitation. Of the seven bamboo species, B. vulgaris, D. strictus, and B. nutans can be adopted for cultivation in the northwest Himalayas given their ability to positively impact the SOC and its fractions in both surface and sub-surface soil.

Abstract PO-190: Health disparities in high-risk lung cancer families and their association with smoking, environmental exposures, and other etiological factors

Lung cancer (LC) is by far the leading cause of cancer-related deaths worldwide. LC survival has only improved marginally over the last decades with the five-year survival rate for LC being lower than most other leading cancer sites. African Americans (AAs) have a higher incidence rate and lower survival rate for LC in comparison to all other racial and ethnic groups in the United States. In addition, incidence rates among AAs and European Americans (EAs) vary with histology of LC. Although tobacco smoking has been identified as the major risk factor for LC, studies have shown there is a genetic component involved in the development of the disease. About 25% of LC cases have at least one first- or second-degree relative, indicating that family history is a relevant risk factor. The goal of this study is to characterize genetic, clinical, and environmental risk factors among individuals of EA and AA ancestry from the high-risk families with LC that could hold important clinical value to address LC disease disparity. Study participants with LC were recruited from a network of 30 hospitals from Louisiana along with multiple states across the country. Study participants with at least two confirmed cases of primary LC within the family were eligible. Participants were divided into two subgroups: Familial (≥2 LC cases/family) and Hereditary LC (HLC families) (≥3 affected LC cases/family). Medical and pathology reports were obtained from hospitals along with demographic and environmental data from the families. A total of 192 study participants (157 EA and 35 AA) from both familial and HLC families from the years 1992 through 2021 were used in this study. Data abstracted from the pathology, clinical reports, and study questionnaire was entered into spreadsheets and analyzed. Histology of LC diagnosis and clinical reports on mutation analysis were documented. The preliminary analyses of results have found that the average age of onset for AAs is significantly lower than in EA (P value &lt; 0.0001). Additionally, while smoking is commonly referred to as a major contributor to LC disparities, AAs were found to have significantly lower pack years of cigarette use than EAs (P value &lt; 0.05). The average age the AA participants ‘begin to smoke' was also found to be significantly lower than EAs (P value &lt; 0.05). The majority of the study participants with LC were diagnosed with adenocarcinoma irrespective of the number of pack-years for cigarette use. Mutation analysis in the clinical report for a small number of study participants in the EA families provided limited information. Additional analysis is ongoing. Clinical and pathological characterization in association with risk factors from high-risk families with EA and AA ancestry will provide us with a better understanding behind the disproportionate distribution of incidence and survival for LC in the AA population.

Citation Format: Grace L. Brandhurst, Angelle Bencaz, Sarah North, Ellen Jaeger, Diptasri Mandal, Joan Bailey-Wilson. Health disparities in high-risk lung cancer families and their association with smoking, environmental exposures, and other etiological factors [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-190.

Sonocatalytic recovery of ceria from graphite and inhibition of graphite erosion by ionic liquid based platinum nanocatalyst

Use of ultrasound as an intensified non-destructive decontamination technique for processing graphite limits its reusability beyond a few number of decontamination cycles due to the exfoliation of graphite due to cavitation effects. The current work establishes that the use of platinum nanoparticles in the leachant reduces the erosion of graphite substrate due to cavitation. It presents an improved way of sonochemical recovery of ceria using a mixture of nitric acid, formic acid and hydrazinium nitrate in the presence of platinum nanoparticles and ionic liquid. The platinum nanoparticles catalyst in ionic liquid prevented the generation of the carbon residue due to the combined effect of denitration and reduced sonication. The presence of the catalyst showed a fivefold increase in dissolution kinetics of ceria as well as absence of graphite erosion, facilitating better chances of graphite recycling than the decontamination without the catalyst. The catalytic approach offers a better recycle strategy for graphite with reduced exfoliation and NOx generation due to denitration, making it a more sustainable decontamination process. Since ceria is used as a surrogate for plutonium oxide, the results can be extended to decontaminate such deposits clearly establishing the utility of the presented results in the nuclear industry.

Abstract PO-202: Copy number variation (CNV) analysis identifies variants in 1p36 in African American and Caucasian hereditary prostate cancer cases

Prostate cancer (PCa) is a common malignancy which affects 1 in 8 men. There is a significant racial disparity and African American (AA) males are more at risk for developing such cancers, at a rate of almost double compared to the males of European ancestry (EA). So far, not much is known about the role of germline copy number variations (CNVs) in this health disparity. Our previous work has shown several genetic regions with CNVs in both AA and EA hereditary prostate cancer (HPC) cases. The goal of this project was to detect germline CNVs in the targeted resequencing data spanning 9 Mb region in 1p36, that was previously identified by microarray and whole exome sequencing analyses. For this study, a total of 50 individuals were used, 25 AA and 25 EA men from HPC families. We have used three CNV calling algorithms: XHMM, CANOES, and GATK4. First, we focused on four PCa associated genes: NBPF1, NBL1, SRSF10, and RHD, that were previously identified in our study. In the current CNV analysis, XHMM identified deletions in NBPF1 in several samples in both AA and EA cases. GATK4 was unable to call any CNVs in this gene. NBL1 had no identified deletions in any tool, despite previous microarray data to the contrary. XHMM identified full deletions of SRSF10 in most of the cases, while GATK4 identified partial deletion in several cases from both ancestries, but more frequently in AA cases. Finally, a deletion was detected in RHD in only a few cases, and the deletion was confirmed by both XHMM and GATK4 algorithms. Deletion in RHD was more common in the EA population than the AA population. CANOES was unable to identify any variants within our regions of interest. We then expanded our search to other identified variants to identify regions commonly detected by the CNV calling algorithms. A region of deletion was detected in the CELA3A gene (reported to be downregulated in pancreatic and prostate cancer) and a region between AKR7L and AKR7A3 both of which are found to be frequently mutated in cancer cells. XHMM called the deletion of both of these regions at a much higher rate than GATK4: nearly in all our cases from the two ancestries, compared to only a few in GATK4 and CANOES. The few PCa cases who had deletions across all tools were always in the AA population. Altogether, this new analytical strategy establishes the usefulness of applying multiple CNV callers in identifying regions of potential interest, as well as verifying the results from previous studies of PCa. Results from this study may hold valuable information in finding potential biomarkers to address PCa health disparity in the future. Further validation of the identified variants is ongoing.

Citation Format: Alan F. Williams, Kirsten W. Termine, John Waldron, Oliver Sartor, Joan Bailey-Wilson, Diptasri Mandal. Copy number variation (CNV) analysis identifies variants in 1p36 in African American and Caucasian hereditary prostate cancer cases [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-202.

Comparative Study of Common Bile Duct Diameter between Normal and Post Cholecystectomy Cases Using Trans-abdominal Ultrasonography

Background Increase in common bile duct diameter can occur because of different causes. Post cholecystectomy status is one of the potential causes. Many studies done in the past show different results and are hence inconclusive. Objective To see if the post cholecystectomy cases would have a statistically significant change in common bile duct diameter. Method We carried out a study in 100 cases (46 post cholecystectomy cases and 54 cases with intact gall bladder, measuring their common bile duct diameters and performing an unpaired t test to see if the mean in common bile duct among these two groups of cases was statistically significant. Result One hundred cases, 46 post cholecystectomy cases and 54 cases with intact gall bladder were included in our study. An unpaired t-test was used to compare the common bile duct diameters in these two groups. Our findings showed that the difference in common bile duct diameter between the cases with intact gall bladder and those who underwent cholecystectomy was significant for both one tailed and two tailed studies (p < 0.001). Hence, it can be stated that post cholecystectomy status increases the common bile duct diameter. Conclusion An increased Common bile duct diameter in post cholecystectomy case could be because of the post cholecystectomy status itself and not due to some other obstructive cause. So careful decision is necessary before subjecting the patient to further invasive/non-invasive investigations and treatments.

Performance of radio-iodine discharge control methods of nuclear reprocessing plants

It is imperative to control radio-iodine discharges to atmosphere from nuclear reprocessing plants. Inhalation and ingestion of radio-iodine cause its concentration in the thyroid gland leading to risk of thyroid cancer in humans. Two isotopes of iodine viz. iodine-131 (¹³¹I) and iodine-129 (¹²⁹I) are generated in considerable quantities in the nuclear fuel as fission products in the nuclear reactors. From nuclear reactors, no iodine is released to the atmosphere during normal operations, whereas from spent fuel reprocessing plants, during normal operation, iodine is discharged to the atmosphere, mainly through gaseous discharges. Shortly after the initial periods of reprocessing in 1944, iodine emission control methods were incorporated in the design of reprocessing plants. At the time of spent fuel discharge from reactor, quantity of ¹³¹I is high and can contribute radiation dose to humans during reprocessing operations. A delay or cooling period of spent fuel, before reprocessing for a definite number of days can reduce the quantities to below the permissible limits of discharge due to its short half-life of 8 days. ¹²⁹I has a very long half-life, and is only significant for reprocessing plants of large throughput and high fuel burn-ups. Minimum required de-contamination factor (DF) for iodine for a reprocessing plant can be estimated from the limits of discharge of iodine stipulated by regulatory authority of each country. Though many processes were developed and demonstrated extensively in lab and pilot scale, only a few of these processes were found to be suitable for commercial deployment. This paper reviews systematically the operation experiences and performance characteristics of iodine control methods implemented so far. The review also focus on the effect of integrating various iodine control methods on the main reprocessing operations and thereby facilitate selection of the optimum iodine control method.

Sonochemical recovery of uranium from nanosilica-based sorbent and its biohybrid

Use of nanomaterials to remove uranium by adsorption from nuclear wastewater is widely applied, though not much work is focused on the recovery of uranium from the sorbents. The present work reports the recovery of adsorbed uranium from the microstructures of silica nanoparticles (SiO2M) and its functionalized biohybrid (fBHM), synthesized with Streptococcus lactis cells and SiO2M, intensified using ultrasound. Effects of temperature, concentration of leachant (nitric acid), sonic intensity, and operating frequency on the recovery as well as kinetics of recovery were thoroughly studied. A comparison with the silent operation demonstrated five and two fold increase due to the use of ultrasound under optimum conditions in the dissolution from SiO2M and fBHM respectively. Results of the subsequent adsorption studies using both the sorbents after sonochemical desorption have also been presented with an aim of checking the efficacy of reusing the adsorbent back in wastewater treatment. The SiO2M and fBHM adsorbed 69% and 67% of uranium respectively in the second cycle. The adsorption capacity of fBHM was found to reduce from 92% in the first cycle to 67% due to loss of adsorption sites in the acid treatment. Recovery and reuse of both the nuclear material and the sorbent (with some make up or activation) would ensure an effective nuclear remediation technique, catering to UN's Sustainable Development Goals.

Assessment of eco-hydrological parameters for important sympodial bamboo species in Himalayan foothills

Bamboos due to high soil water conservation potential are gaining increased attention in plantation programs across the globe. Large-scale plantation of fast-growing bamboo, however, can have important hydrological consequences. The study aims to quantify the eco-hydrological parameters, viz., throughfall (TF), stemflow (SF), and interception (I) in seven important sympodial bamboo species in north western Himalayan foothills of India. The species selected include Bambusa balcooa, Bambusa bambos, Bambusa vulgaris., Bambusa nutans, Dendrocalamus hamiltonii, Dendrocalamus stocksii, and Dendrocalamus strictus. Throughfall versus gross rainfall (GR) relationship in different species indicated high throughfall production during high rainfall events with r² > 0.90. Average throughfall was lowest (62.1%) in D. hamiltonii and highest in B. vulgaris (74.6%). SF ranged from 1.32% in B. nutans to 3.39% in D. hamiltonii. The correlation coefficient (r) between leaf area index (LAI), number of culms, and crown area with the interception were 0.746, 0.691, and 0.585, respectively. The funneling ratio (F) was highest (27.0) in D. hamiltonii and least in B. nutans. Canopy storage capacity was highest in D. strictus (3.57 mm) and least in D. hamiltonii (1.09 mm). Interception loss was highest (34.4%) in D. hamiltonii and lowest in B. vulgaris (23.5%) and D. strictus (23.6%). Higher interception in bamboos make them suitable for soil conservation, but careful selection of species is required in low rainfall areas.

Cavitation-assisted decontamination of yttria from graphite of different densities

Yttria coated graphite crucibles are widely used to handle molten refractory and radioactive metals like uranium and plutonium. However, the coated layer suffers damages like cracking and peeling off owing to thermal cycles. As a result, removal of the yttria layer from the graphite surface is essential to ensure reuse of the crucible and minimization of radioactive waste. The present work investigates intensified dissolution of yttria from the coated graphite samples using ultrasound as a non-destructive decontamination technique to recycle the graphite substrate. The optimum conditions established for maximum dissolution were 8 M as acid strength, frequency of 30 kHz, temperature of 45 °C and power density of 8 W cm^-2 that resulted in maximum dissolution of 52% in 30 min. Use of an oxidant H₂O₂ to the acid, did not yield any improvement in the dissolution kinetics, instead, increased oxidation of the graphite substrate was observed, leading to the anomalous weight gain of the graphite substrate despite surface erosion. Effect of ultrasound on the dissolution was pronounced, with almost a threefold increase compared to dissolution performed under silent conditions. Rates of dissolution of yttria from the substrate of different densities and pore size distribution were also studied. The dissolution was slowest from graphite of density 1.82 g cm^-3 as the pore size distribution was conducive to accommodate the yttria particles. The dissolution in nitric acid followed ash layer diffusion controlled kinetics. The study has demonstrated the efficacy of application of ultrasound for accelerated decontamination of graphite substrates.

Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer

Although lung cancer is known to be caused by environmental factors, it has also been shown to have genetic components, and the genetic etiology of lung cancer remains understudied. We previously identified a lung cancer risk locus on 6q23-25 using microsatellite data in families with a history of lung cancer. To further elucidate that signal, we performed targeted sequencing on nine of our most strongly linked families. Two-point linkage analysis of the sequencing data revealed that the signal was heterogeneous and that different families likely had different risk variants. Three specific haplotypes were shared by some of the families: 6q25.3-26 in families 42 and 44, 6q25.2-25.3 in families 47 and 59, and 6q24.2-25.1 in families 30, 33, and 35. Region-based logarithm of the odds scores and expression data identified the likely candidate genes for each haplotype overlap: ARID1B at 6q25.3, MAP3K4 at 6q26, and UTRN (6q24.1) and PHACTR2 (6q24.2). Further annotation was used to zero in on potential risk variants in those genes. All four genes are good candidate genes for lung cancer risk, having been linked to either lung cancer specifically or other cancers. However, this is the first time any of these genes has been implicated in germline risk. Functional analysis of these four genes is planned for future work. SIGNIFICANCE: This study identifies four genes associated with lung cancer risk, which could help guide future lung cancer prevention and treatment approaches.

Rare deleterious germline variants and risk of lung cancer

Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.

Numerical approach to minimize mercury contamination by geometric and parametric optimization

Due to high vapour pressure at ambient conditions, exposed mercury contributes significant vapour concentration in working atmosphere. Ventilation is a conventional, cheap and very effective method to bring down the concentration of hazardous materials like mercury vapour below permissible limit. In this work a numerical model was developed to obtain intuitive understandings of the spatial distribution of mercury vapors from an exposed surface. The model was validated with experimental data generated using a precinct ventilation system with 8.14% absolute average error. a Validated model was used to study the effect of air flow rate (100–1200 LPM) and impact of architectural design of the containment for fixed exposed mercury surfaceon the final (diluted) mercury concentration. Comparative analysis shows that modification in structural design offers a reduced volume averaged exit mercury concentration and also the reduced peak mercury concentration(C_peak) in the computational domain. Computational approach outlined in this work can be used to estimate spatial variation of mercury vapor concentration and to locate and quantify regions of high local concentration of mercury in various geometries.

A Germline Variant at 8q24 Contributes to Familial Clustering of Prostate Cancer in Men of African Ancestry

Although men of African ancestry have a high risk of prostate cancer (PCa), no genes or mutations have been identified that contribute to familial clustering of PCa in this population. We investigated whether the African ancestry-specific PCa risk variant at 8q24, rs72725854, is enriched in men with a PCa family history in 9052 cases, 143 cases from high-risk families, and 8595 controls of African ancestry. We found the risk allele to be significantly associated with earlier age at diagnosis, more aggressive disease, and enriched in men with a PCa family history (32% of high-risk familial cases carried the variant vs 23% of cases without a family history and 12% of controls). For cases with two or more first-degree relatives with PCa who had at least one family member diagnosed at age <60 yr, the odds ratios for TA heterozygotes and TT homozygotes were 3.92 (95% confidence interval [CI] = 2.13-7.22) and 33.41 (95% CI = 10.86-102.84), respectively. Among men with a PCa family history, the absolute risk by age 60 yr reached 21% (95% CI = 17-25%) for TA heterozygotes and 38% (95% CI = 13-65%) for TT homozygotes. We estimate that in men of African ancestry, rs72725854 accounts for 32% of the total familial risk explained by all known PCa risk variants. PATIENT SUMMARY: We found that rs72725854, an African ancestry-specific risk variant, is more common in men with a family history of prostate cancer and in those diagnosed with prostate cancer at younger ages. Men of African ancestry may benefit from the knowledge of their carrier status for this genetic risk variant to guide decisions about prostate cancer screening.

Abstract 3517: A germline variant at 8q24 contributes to familial clustering of prostate cancer in men of African ancestry

Germline variation at 8q24 is the strongest risk factor for prostate cancer (PCa) across all racial and ethnic populations. While most 8q24 associations have been observed across populations, rs72725854 [T risk allele frequency ~6%] is only found in men of African ancestry and is the strongest known genome-wide association signal for PCa in this population. We investigated whether the T allele of rs72725854 is associated with PCa family history and age at diagnosis, characteristics known to have a strong genetic component. Analyses were performed using a sample of 9,052 cases and 8,595 controls from the African Ancestry Prostate Cancer (AAPC) GWAS Consortium and the ELLIPSE/PRACTICAL OncoArray Consortium. Participants were unselected for PCa family history. Among cases, 23.7% carried at least one copy of the T allele versus 11.6% of controls. The OR was 2.29 (95% CI=2.10–2.49) for TA heterozygotes and 5.04 (95% CI=3.36–7.55) for TT homozygotes. The percentage of cases carrying the T allele was significantly greater for men with a PCa family history (27.4% vs. 22.7% without a family history, p=0.002) and for men diagnosed &lt;60 (28.2% vs. 21.6% if over ≥60, p=0.002). The mean age at diagnosis for men with the TT genotype was 61.1 years (sd=8.7), compared to 62.7 (sd=9.1) for TA heterozygotes and 64.3 (sd=8.9) for AA homozygotes (p=5.7E-14). Carrier frequency was highest among men with both a positive family history and an early diagnosis (30.8%). The T allele was also over-represented in cases with more advanced PCa, with carrier frequencies ranging from 26% for lethal PCa (metastatic disease, PSA&gt;100 ng/ml or death from PCa), 25.4% for high-risk disease (stage T3/T4, Gleason 8-10, or PSA=20-100 ng/ml), 24.6% for intermediate-risk disease (Gleason=7, stage T1/T2, and PSA=10-20 ng/ml), and 21.4% for low-risk disease (Gleason&lt;7, stage T1/T2, and PSA&lt;10 ng/ml) (p=0.026). We also examined whether the risk allele is over-represented in 144 men from PCa families, with multiple first- and/or second-degree relatives with PCa or men diagnosed with PCa ≤55 years old. Among affected probands, 32.7% carried the risk allele, with 3.5% being homozygous carriers. The OR for TA heterozygotes and TT homozygotes was 3.41 (95% CI=2.33–4.98) and 11.06 (95% CI=3.92–31.18), respectively. Among men without a family history, the absolute risk for PCa by age 60 for non-risk allele carriers was 4.3%, compared to 9.0% and 15.6% for TA heterozygotes and TT homozygotes, respectively. Absolute risks by age 60 were higher among men with a family history of prostate cancer, reaching 9.0% for non-risk allele carriers, compared to 20.8% and 37.7% for TA heterozygotes and TT homozygotes, respectively. Given the high PCa risk conveyed by rs72725854 and the greater frequency of the allele in men with more aggressive and lethal disease, carriers of the risk allele would benefit from earlier and more regular PSA screening.

Citation Format: Burcu F. Darst, Jeannette T. Bensen, Sue A. Ingles, Benjamin A. Rybicki, Barbara Nemesure, Esther M. John, Jay H. Fowke, Victoria L. Stevens, Sonja I. Berndt, Chad D. Huff, Jong Y. Park, Wei Zheng, Elaine A. Ostrander, Shiv Srivastava, John Carpten, Thomas A. Sellers, Maureen Sanderson, Dana C. Crawford, Olivier Cussenot, Jennifer Cullen, Rick A. Kittles, Jianfeng Xu, Zsofia Kote-Jarai, Luc Multigner, Marie-Elise Parent, Florence Menegaux, Geraldine Cancel-Tassin, Adam S. Kibel, Eric A. Klein, Phyllis J. Goodman, Jennifer J. Hu, Graham Casey, Anselm J. Hennis, Ian M. Thompson, Robin Leach, James L. Mohler, Elizabeth T. Fontham, Gary J. Smith, Jack A. Taylor, Rosalind A. Eeles, Laurent Brureau, Stephen J. Chanock, Stephen Watya, Janet L. Stanford, Diptasri Mandal, William B. Isaacs, Kathleen A. Cooney, William J. Blot, David V. Conti, Christopher A. Haiman. A germline variant at 8q24 contributes to familial clustering of prostate cancer in men of African ancestry [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3517.

Abstract 37: Highly aggregated lung cancer families reveal a heterogeneous cause for a previous linkage signal on 6q

More Americans die every year of lung cancer than any other cancer. While the environmental risks for lung cancer are well understood, the genetic risk factors for this disease are not, even though it has been shown that lung cancer risk aggregates in families. Segregation analyses have confirmed the likelihood of rare, highly penetrant variants affecting lung cancer. Family studies offer a unique opportunity to identify such rare risk variants. We have previously identified a genome-wide significant risk locus for lung cancer using multipoint linkage analysis in highly aggregated lung cancer families. In this study, we performed targeted sequencing on this 6q23-6q27 region on 75 individuals from the 9 most strongly linked families. Parametric two-point linkage analysis using an autosomal dominant model with 10% penetrance for carriers and a 1% phenocopy rate and disease allele frequency of 1% was performed for each family. While we did not find any genome-wide significant results in any of the individual families, we did observe several interesting potential rare risk variants. First, we observed that the significant signal previously observed on 6q is recapitulated in these data but the location of the peak LOD is highly heterogeneous across families and it is likely that each family has a different risk gene. While most of the highest LOD scores were in noncoding variants, we did observe exonic variants with the highest LOD scores in two families (44 and 42). Both variants were rare, with a minor allele frequency (MAF) of approximately 1% and were in LPA and GPR126 respectively. Both these genes have been implicated somatically in lung cancer, however this is the first time that they have been implicated in the germline. While the other families have their highest LOD scores in noncoding variants, some of these genes are also good potential candidate genes including PARK2 (family 30), GRM1 (family 47), and PDE10A (family 102). All three genes have been implicated in lung cancer in some capacity, and this is the first time that GRM1 and PDE10A have been implicated as germline mutations. Again, all these variants are rare (MAF ⇐ 0.01) in the general population, which makes sense for a potential highly penetrant risk variant. In this study, we have elucidated that a previously identified risk locus on 6q25 is heterogeneous in the nine most strongly linked families, with different families appearing to be carrying different risk variants. Many of the top variants in each family are rare variants that are in good potential causal genes that have been identified for the first time here as germline risk variants for lung cancer. Further functional annotation is underway for these variants and some additional linkage analyses using other penetrance matrices may also be performed.

Citation Format: Anthony M. Musolf, Claire L. Simpson, Bilal A. Moiz, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Ming You, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Joan E. Bailey-Wilson. Highly aggregated lung cancer families reveal a heterogeneous cause for a previous linkage signal on 6q [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 37.

Two-stage Study of Familial Prostate Cancer by Whole-exome Sequencing and Custom Capture Identifies 10 Novel Genes Associated with the Risk of Prostate Cancer

BACKGROUND

Family history of prostate cancer (PCa) is a well-known risk factor, and both common and rare genetic variants are associated with the disease.

OBJECTIVE

To detect new genetic variants associated with PCa, capitalizing on the role of family history and more aggressive PCa.

DESIGN, SETTING, AND PARTICIPANTS

A two-stage design was used. In stage one, whole-exome sequencing was used to identify potential risk alleles among affected men with a strong family history of disease or with more aggressive disease (491 cases and 429 controls). Aggressive disease was based on a sum of scores for Gleason score, node status, metastasis, tumor stage, prostate-specific antigen at diagnosis, systemic recurrence, and time to PCa death. Genes identified in stage one were screened in stage two using a custom-capture design in an independent set of 2917 cases and 1899 controls.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Frequencies of genetic variants (singly or jointly in a gene) were compared between cases and controls.

RESULTS AND LIMITATIONS

Eleven genes previously reported to be associated with PCa were detected (ATM, BRCA2, HOXB13, FAM111A, EMSY, HNF1B, KLK3, MSMB, PCAT1, PRSS3, and TERT), as well as an additional 10 novel genes (PABPC1, QK1, FAM114A1, MUC6, MYCBP2, RAPGEF4, RNASEH2B, ULK4, XPO7, and THAP3). Of these 10 novel genes, all but PABPC1 and ULK4 were primarily associated with the risk of aggressive PCa.

CONCLUSIONS

Our approach demonstrates the advantage of gene sequencing in the search for genetic variants associated with PCa and the benefits of sampling patients with a strong family history of disease or an aggressive form of disease.

PATIENT SUMMARY

Multiple genes are associated with prostate cancer (PCa) among men with a strong family history of this disease or among men with an aggressive form of PCa.

Intensified dissolution of uranium from graphite substrate using ultrasound

Decontamination of graphite structural elements and recovery of uranium is crucial for waste minimization and recycle of nuclear fuel elements. Feasibility of intensified dissolution of uranium-impregnated graphite substrate using ultrasound has been studied with objective of establishing the effect of operating parameters and the kinetics of sonocatalytic dissolution of uranium in nitric acid. The effect of operating frequency and acoustic intensity as well as the acid concentration and temperature on the dissolution of metal has been elucidated. It was observed that at lower acid concentrations (6 M-8 M), the dissolution ratio increases by 15% on increasing the bath temperature from 45 to 70 °C. At higher acid concentration (>10 M), the increase was only around 5-7% for a similar change in temperature. With 12 M HNO₃, pitting was also observed on the graphite surface along with erosion due to high local reaction rates in the presence of ultrasound. For higher frequency of applied ultrasound, lower dissolution rate of uranium was observed though it also leads to high rates of erosion of the substrate. It was thus established that suitable optimization of frequency is required based on the nature of the substrate and the choice of recycling it. The dissolution rate was also demonstrated to increase with acoustic intensity till it reaches to the maximum at the observed optimum (1.2 W/cm² at 33 kHz). Comparison with silent conditions revealed that enhanced rate was obtained due to the use of ultrasound under optimum conditions. The work has demonstrated the effective application of ultrasound for intensifying the extent of dissolution of metal.

Rooting behaviour and soil properties in different bamboo species of Western Himalayan Foothills, India

Due to extensive root system, connected rhizome bamboos are considered suitable for improving soil properties within a short period, though most of the claims are anecdotal and need to be supported with quantified data. The study evaluates seven bamboo species viz., Bambusa balcooa, Bambusa bambos, Bambusa vulgaris, Bambusa nutans, Dendrocalamus hamiltonii, Dendrocalamus stocksii and Dendrocalamus strictus for their rooting pattern and impact on soil health properties. Coarse and fine root intensity was maximum in B. vulgaris. Coarse root biomass ranged from 0.6 kg m⁻³ in B. nutans to 2.0 kg m⁻³ in B. vulgaris and B. bambos. Fine root biomass ranged from 1.1 kg m⁻³ in B. nutans to 4.5 kg m⁻³ in D. hamiltonii. Contribution of fine roots in terms of intensity and biomass was much higher than coarse roots. Fine root biomass showed declining trend with increase in soil depth in all the species. During sixth year, the litter fall ranged from 8.1 Mg ha⁻¹ in D. stocksii to 12.4 Mg ha⁻¹ in D. hamiltonii. Among soil physical properties significant improvement were recorded in hydraulic conductivity, water stable aggregates and mean weight diameter. Soil pH, organic carbon and available phosphorus under different species did not reveal any significant changes, while significant reduction was observed in total nitrogen and potassium. Significant positive correlation was observed between WSA and iron content. Soil microbial population and enzyme activities were higher in control plot. Considering root distribution, biomass, soil hydraulic conductivity and water stable aggregates, B. bambos, B. vulgaris and D. hamiltonii are recommended for rehabilitation of degraded lands prone to soil erosion.

Whole Exome Sequencing of Highly Aggregated Lung Cancer Families Reveals Linked Loci for Increased Cancer Risk on Chromosomes 12q, 7p, and 4q

BACKGROUND

Lung cancer kills more people than any other cancer in the United States. In addition to environmental factors, lung cancer has genetic risk factors as well, though the genetic etiology is still not well understood. We have performed whole exome sequencing on 262 individuals from 28 extended families with a family history of lung cancer.

METHODS

Parametric genetic linkage analysis was performed on these samples using two distinct analyses-the lung cancer only (LCO) analysis, where only patients with lung cancer were coded as affected, and the all aggregated cancers (AAC) analysis, where other cancers seen in the pedigree were coded as affected.

RESULTS

The AAC analysis yielded a genome-wide significant result at rs61943670 in POLR3B at 12q23.3. POLR3B has been implicated somatically in lung cancer, but this germline finding is novel and is a significant expression quantitative trait locus in lung tissue. Interesting genome-wide suggestive haplotypes were also found within individual families, particularly near SSPO at 7p36.1 in one family and a large linked haplotype spanning 4q21.3-28.3 in a different family. The 4q haplotype contains potential causal rare variants in DSPP at 4q22.1 and PTPN13 at 4q21.3.

CONCLUSIONS

Regions on 12q, 7p, and 4q are linked to increased cancer risk in highly aggregated lung cancer families, 12q across families and 7p and 4q within a single family. POLR3B, SSPO, DSPP, and PTPN13 are currently the best candidate genes.

IMPACT

Functional work on these genes is planned for future studies and if confirmed would lead to potential biomarkers for risk in cancer.

Abstract 4176: Familial lung cancer exhibits multiple novel linked haplotypes within pedigrees

Lung cancer (LC) kills more people in the United States each year than any other cancer. While it is well known that a variety of environmental factors (particularly tobacco smoke) strongly increase the risk of LC, there are multiple associated genetic variants with small contributions to risk. High aggregation of LC within rare individual families suggest that there are high-risk genetic variants as well. However, these genetic risk factors for LC are under studied due to the rapid fatality of LC. We studied 28 highly aggregated extended high-risk familial lung cancer (HRFLC) families collected from eight different sites across the US. Whole exome sequencing was performed on 290 individuals from these families to identify potential risk variants for HRFLC using genetic linkage analysis. Quality control was performed on the sequence data, filtering on parameters such as read depth, genotype quality, missingness, and Mendelian inconsistencies. Identity-by-descent (IBD) values were also calculated to verify correct familial relationships. Quality control procedures left approximately 400,000 SNVs and indels for analysis.Parametric two-point linkage analysis was performed assuming an autosomal dominant mode of inheritance. Disease allele frequency was set to 1% with a penetrance of 80% for carriers and 1% phenocopy rate. While we did not identify any genome-wide significant variants across the 28 families, multiple suggestive variants were identified. The largest cluster of suggestive variants was located at 14q32 in the CATSPERB gene. Given the likely locus heterogeneity in LC (combined with the lack of power in some families), it is not surprising that none of the variants were significant across the families; looking at the individual family results proved more informative. Long haplotypes linked to LC risk were identified in multiple families. These long runs of positive linkages, which have little to no negative linkage evidence across them, are characteristic of true linkage signals in these types of analysis. Two of the most interesting linked regions were at 7p36.1 and 4q21.23-28.23. The 7p signal (observed in a single family) was genome-wide suggestive and located within the SSPO gene. SSPO has been implicated in breast and skin cancer (melanoma); it is a novel lung cancer signal. The 4q linkage (again observed in a single family) covers a large chunk of 4q and contains multiple potential candidate genes, however, the best candidate gene is PTPN13, a gene implicated in lung cancer but never in familial lung cancer. We are currently evaluating the individual family results of several other pedigrees and plan to perform additional analyses to confirm these linkages.

Citation Format: Anthony Musolf, Haiming Sun, Bilal A. Moiz, Claudio W. Pikielny, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Richard K. Wilson, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Ramaswamy Govindan, Joan E. Bailey-Wilson. Familial lung cancer exhibits multiple novel linked haplotypes within pedigrees [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 4176.

Abstract LB-053: Familial studies identify variants in the E2A transcription factor as putative risk factors for lung cancer

Lung cancer (LC) is the primary cause of cancer-related deaths in the United States. Whereas smoking and other environmental factors strongly increase LC risk, multiple genetic variants also contribute to risk in smokers. Furthermore, among smokers, some families have been identified with an abnormally high prevalence of LC, suggesting that unknown genetic factors can greatly increase LC risk in smokers. The typically short survival after LC diagnosis impedes collection of detailed genotypic information on any single large family pedigree, impairing the identification of putative high-risk factors. Therefore, the Genetic Epidemiology of LC Consortium has collected epidemiological and genetic data from a number of families with high numbers of LC cases from eight different sites across the US. In this study, we have obtained whole exome sequences (WES) from 290 members of 28 families, including 66 LC cases. We used a gene-based approach to allow for the possibility that different families may contain different variants of the same gene. Variants were filtered for i) allele frequency, ii) functional effect using combined annotation-dependent depletion (CADD), and, iii) affecting a gene with either a known or suspected role in cancer. We further selected variants based on their segregation in family pedigrees in a pattern consistent with a large effect on LC risk. Candidate LC risk genes were then identified as those represented in at least two families by the same or different variants. We further culled the list of genes by requiring the presence of at least one rare, functional variant enriched in the WES of 1060 cases relative to 899 controls from the Transdisciplinary Research on Cancer of the Lung consortium. This analysis narrowed our results to two genes, one being E2A, a member of the E family of bHLH transcription factors. Whereas loss-of-function mutations in E2A drive lymphoid cancers, the E2A protein also participates in an oncogenic heterodimer with TWIST1 that promotes the epithelial-mesenchymal transition and is implicated in multiple cancer types. Furthermore, the E2A/TWIST1 heterodimer is the primary TWIST1-containing complex implicated in oncogenesis, and silencing of E2A in KRAS-mutant non-small cell lung cancer (NSCLC) cell lines results in oncogene-stimulated senescence and apoptosis. Our data identified three distinct E2A variants present in all 10 sequenced LC cases in the 5 families in which those variants are found. Finally, two of these E2A variants are located only 57 nucleotides from each other, immediately adjacent to sequences encoding a transcription activation domain, suggesting that both variants alter the same specific protein function. These data identify E2A variants as likely high risk factors for LC in smokers and validate our general approach for identifying genetic factors with a large impact on LC risk.

Citation Format: Claudio W. Pikielny, Anthony M. Musolf, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, yafang Li, Ming You, Richard Wilson, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Ambrose I. Granizo-Mackenzie, Yanhong Liu, Ramaswamy Govindan, James McKay, Rayjean Hung, John K. Field, David C. Christiani, Joan E. Bailey-Wilson, Christopher I. Amos. Familial studies identify variants in the E2A transcription factor as putative risk factors for lung cancer [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 LB-053.

Rare Variants in Known Susceptibility Loci and Their Contribution to Risk of Lung Cancer

BACKGROUND

Genome-wide association studies are widely used to map genomic regions contributing to lung cancer (LC) susceptibility, but they typically do not identify the precise disease-causing genes/variants. To unveil the inherited genetic variants that cause LC, we performed focused exome-sequencing analyses on genes located in 121 genome-wide association study-identified loci previously implicated in the risk of LC, chronic obstructive pulmonary disease, pulmonary function level, and smoking behavior.

METHODS

Germline DNA from 260 case patients with LC and 318 controls were sequenced by utilizing VCRome 2.1 exome capture. Filtering was based on enrichment of rare and potential deleterious variants in cases (risk alleles) or controls (protective alleles). Allelic association analyses of single-variant and gene-based burden tests of multiple variants were performed. Promising candidates were tested in two independent validation studies with a total of 1773 case patients and 1123 controls.

RESULTS

We identified 48 rare variants with deleterious effects in the discovery analysis and validated 12 of the 43 candidates that were covered in the validation platforms. The top validated candidates included one well-established truncating variant, namely, BRCA2, DNA repair associated gene (BRCA2) K3326X (OR = 2.36, 95% confidence interval [CI]: 1.38-3.99), and three newly identified variations, namely, lymphotoxin beta gene (LTB) p.Leu87Phe (OR = 7.52, 95% CI: 1.01-16.56), prolyl 3-hydroxylase 2 gene (P3H2) p.Gln185His (OR = 5.39, 95% CI: 0.75-15.43), and dishevelled associated activator of morphogenesis 2 gene (DAAM2) p.Asp762Gly (OR = 0.25, 95% CI: 0.10-0.79). Burden tests revealed strong associations between zinc finger protein 93 gene (ZNF93), DAAM2, bromodomain containing 9 gene (BRD9), and the gene LTB and LC susceptibility.

CONCLUSION

Our results extend the catalogue of regions associated with LC and highlight the importance of germline rare coding variants in LC susceptibility.

Genome-wide association study of familial lung cancer

To identify genetic variation associated with lung cancer risk, we performed a genome-wide association analysis of 685 lung cancer cases that had a family history of two or more first or second degree relatives compared with 744 controls without lung cancer that were genotyped on an Illumina Human OmniExpressExome-8v1 array. To ensure robust results, we further evaluated these findings using data from six additional studies that were assembled through the Transdisciplinary Research on Cancer of the Lung Consortium comprising 1993 familial cases and 33 690 controls. We performed a meta-analysis after imputation of all variants using the 1000 Genomes Project Phase 1 (version 3 release date September 2013). Analyses were conducted for 9 327 222 SNPs integrating data from the two sources. A novel variant on chromosome 4p15.31 near the LCORL gene and an imputed rare variant intergenic between CDKN2A and IFNA8 on chromosome 9p21.3 were identified at a genome-wide level of significance for squamous cell carcinomas. Additionally, associations of CHRNA3 and CHRNA5 on chromosome 15q25.1 in sporadic lung cancer were confirmed at a genome-wide level of significance in familial lung cancer. Previously identified variants in or near CHRNA2, BRCA2, CYP2A6 for overall lung cancer, TERT, SECISPB2L and RTEL1 for adenocarcinoma and RAD52 and MHC for squamous carcinoma were significantly associated with lung cancer.

Abstract 3276: Whole exome sequencing identifies significantly linked regions on multiple chromosomes in families with a history of lung cancer

Lung cancer is the deadliest cancer in the United States, contributing approximately 25% of all cancer deaths. Lung cancer risk is well-documented to increase in response to environmental factors, particularly tobacco smoking. As one might expect for a complex trait, there is also a significant genetic risk component in lung cancer, though it is not very well studied. We obtained whole exome sequencing (WES) genotype data from Washington University on 204 subjects from 25 extended families. These individuals were recruited from families with a history of lung cancer and previous analyses showed these 25 families be informative. The purpose of this study is to identify potential risk variants for lung cancer by performing genetic linkage analysis. Quality control was performed on the sequence data, filtering on parameters such as depth (less than 10), genotype quality (less than 10), missingness, and Mendelian inconsistencies. Identity-by-descent (IBD) values were also calculated to verify correct familial relationships. Quality control procedures left approximately 500,000 SNVs and indels for analysis.

We performed two-point parametric linkage analysis assuming an autosomal dominant mode of inheritance with a disease allele frequency of 1%, a 10% penetrance for carriers and a 1% penetrance for non-carriers. Two discrete sets of linkage analyses were performed. One was a variant-based analysis, which evaluated linkage between the phenotype and individual SNVs or indels. The second was gene-based analysis, which created a multi-allelic pseudomarker corresponding to a gene from haplotypes of rare variants (minor allele frequency &lt;= 0.01) located within that particular gene. Two-point linkage analysis was then performed on the pseudomarkers.

While the variant-based analysis did not identify any genome-wide significant results, several were identified by the gene-based analysis. The highest HLOD scores were both greater than the genome-wide significance level of HLOD = 3.3 and were located on two regions of chromosome 1q: 1q42.13-43 and 1q21.2-21.1. In both regions, the significant HLOD scores clustered around known cancer genes. At the 1q42.13-43 region, signals centered on the cancer-implicated genes OBSCN and RYR2 (also a known mesothelioma gene), while at 1q21.2-21.1 the signals centered on five genes in the neuroblastoma breakpoint family (NBPF) genes, a cluster of recently duplicated genes. NBPF genes have previously been implicated in a variety of different cancers including lung cancer. We are currently performing additional analyses to corroborate the significant results, as well as examining the individual families to determine which families are driving the significant signals.

Citation Format: Anthony M. Musolf, Haiming Sun, Bilal A. Moiz, Diptasri Mandal, Mariza de Andrade, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Joan E. Bailey-Wilson. Whole exome sequencing identifies significantly linked regions on multiple chromosomes in families with a history of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3276.

Parametric Linkage Analysis Identifies Five Novel Genome-Wide Significant Loci for Familial Lung Cancer

OBJECTIVE

One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease.

METHODS

197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array. Parametric linkage analyses were performed using an affected-only phenotype model with an autosomal dominant inheritance using a disease allele frequency of 0.01. Three types of analyses were performed: single variant two-point, collapsed haplotype pattern variant two-point, and multipoint analysis.

RESULTS

Five novel genome-wide significant loci were identified at 18p11.23, 2p22.2, 14q13.1, 16p13, and 20q13.11. The families most informative for linkage were also determined.

CONCLUSIONS

The 5 novel signals are good candidate regions, containing genes that have been implicated as having somatic changes in lung cancer or other cancers (though not in germ line cells). Targeted sequencing on the significant loci is planned to determine the causal variants at these loci.

Abstract 4268: Familial lung cancer is significantly linked to cancer-associated genes on five chromosomes

Lung cancer (LC) is the leading cancer killer of Americans; an estimated 158,000 people will die in the U.S. from LC in 2016. While it is well-known that LC risk is affected by the environment, particularly tobacco smoking, there is a substantial genetic risk to LC also. We examined genotype data from Illumina HumanCore-12v1-0 array (297,000 SNPs) on 175 individuals in 25 extended families with a strong history of LC recruited by the Genetic Epidemiology of Lung Cancer Consortium. The purpose of this study is to determine which families are segregating a high-penetrance genetic risk haplotype so that the most informative families can be selected for DNA sequencing studies. Quality control was performed to remove SNPs and individuals with greater than 1% missingness as well as monomorphic SNPs. SNPs with Mendelian errors in more than one family were dropped. Identity-by-descent values were calculated to confirm correct familial relationships; 1 individual was dropped. After quality control we were left with approximately 245,000 SNPs for analysis. We performed three types of parametric linkage analyses using an autosomal dominant model with 40% penetrance in carriers and 1% penetrance in non-carriers. A disease allele frequency of 0.01 was used. Standard single variant two-point analysis between the disease and each marker was performed using TwoPointLods. Multipoint linkage analysis was performed using SimWalk2. We also performed regional-based linkage analyses using SEQLinkage and MERLIN. SEQLinkage builds a multiallelic regional marker (similar to a microsatellite) that corresponds to a gene or a portion of a gene. Two-point linkage analyses were then performed on the regional markers using MERLIN. We identified five loci that were genome-wide significant (HLOD score ≥ 3.3) from the regional-based linkage analyses on 18p11.23 (HLOD = 4.1), 2p22.2 (3.9), 14q13.1 (3.7), 16p13.1 (3.4), and 20q13.11 (3.4). It is particularly exciting that the scores centered on prospective cancer genes. Our highest score was centered on PTPRM, a protein tyrosine phosphatase on chromosome 18 that has been implicated as a LC oncogene. The signal on 20q13 also centered on another protein tyrosine phosphatase (PTPRT) that has been shown to be mutated in LC cells. The source of the signal on 16p13 was RNA binding protein RBFOX1, which has been shown to be deleted in LC cell lines and the source of the signal on 2p22 was LRP1B, a LDL receptor-related protein that is often inactivated in LC cells. The source of the final signal on 14q13 was NPAS3, a transcription factor that is a tumor suppressor in brain tumors. It should be noted that all previous evidence linking these genes to cancer was based on somatic mutations; this is the first time any of these genes has been shown to be significantly linked to germline disease risk in a family-based study. We plan to perform targeted sequencing on the linked regions to elucidate the exact causal variant.

Citation Format: Joan E. Bailey-Wilson, Anthony M. Musolf, Claire L. Simpson, Mariza de Andrade, Diptasri Mandal, Colette G. Gaba, Ping Yang, Ming You, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos. Familial lung cancer is significantly linked to cancer-associated genes on five chromosomes [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 4268. doi:10.1158/1538-7445.AM2017-4268

Abstract 4290: A study in locus heterogeneity: Targeted sequencing analysis of 6q reveals multiple significant loci as the source of a previous linkage peak in familial lung cancer

Lung cancer is the leading cancer-related cause of death in the United States. We had previously performed multipoint linkage analysis on families with a strong family history of lung cancer and found significant linkage to the 6q25 region. In order to find the source of that linkage signal, we performed targeted sequencing 6q23-6q27 on 75 individuals from the 9 most highly linked families. We performed two types of parametric linkage analysis, using an autosomal dominant mode of inheritance with 10% penetrance for carriers and a 1% phenocopy rate using a disease allele frequency of 1%. The first type was a two-point analysis using an Elston-Stewart algorithm. This approach did not lead to any genome-wide significant results but demonstrated significant heterogeneity throughout the nine families.In an effort to recover the power from the original multipoint analysis, we performed a regional linkage analysis using SEQLinkage and MERLIN. SEQLinkage built regional haplotypes that corresponded to a gene or an intergenic region - the regions were based on a customized map of our design. The regional markers were multiallelic which allowed for greater information content and were similar to the microsatellites that were used in the original multipoint analysis. The regional markers were then analyzed in a two-point linkage analysis via MERLIN. This allowed us to identify two genome-wide significant signals at PACRG-AS1 at 6q26 (HLOD = 3.4) and SAMD5 at 6q24 (3.3). The PACRG-AS1 is novel, though it is associated with the known lung cancer gene PARK2. SAMD5 may be involved in lung cancer cell proliferation. The heterogeneity of the two signals was particularly interesting. The PACRG-AS1 was driven primarily by two families. The SAMD5 marker was not being strongly driven by any of the families and appears to be a small cumulative effect across the nine families. In addition, several families have large, but non-significant LOD scores at other loci across the region. This further reinforces the locus heterogeneity within the region, and it is likely that our two significant signals here are not the only variants affecting the phenotype. We further attempted to localize the signals by running SEQLinkage using a custom map where genes are broken into exons and introns. Though this resulted in no significant markers, the highest signal was located in the intronic region of SAMD5 (HLOD = 3) and several other suggestive signals were localized to intronic regions of good candidate genes like SASH1 and ARID1B. Examination of predicted effects of the candidate regulatory variants using eQTL databases is ongoing. This is a region full of promising candidates, and it is likely that the two significant signals found here are just part of many that could be affecting lung cancer risk. We plan to do further analysis within the individual families to elucidate any more genes affecting this signal.

Citation Format: Anthony M. Musolf, Claire L. Simpson, Bilal A. Moiz, Candace Middlebrooks, Mariza de Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li, Ming You, Elena Y. Kupert, Marshall W. Anderson, Ann G. Schwartz, Susan M. Pinney, Christopher I. Amos, Joan E. Bailey-Wilson. A study in locus heterogeneity: Targeted sequencing analysis of 6q reveals multiple significant loci as the source of a previous linkage peak in familial lung 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 4290. doi:10.1158/1538-7445.AM2017-4290

Evidence of linkage in MSH6-associated region exclusive to high-risk African-American families with prostate cancer

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Background: The significance of germline variants and their implications for prostate cancer (PCa) patients has gained prominence. Mismatch repair (MMR) genes such as MSH6 and MSH2, along with DNA repair genes, may be more important in PCa than previously appreciated. In the present study, we compared linkage results between African American (AA) and Caucasian (CA) PCa families with multiple affected family members. Methods: Study subjects were from 15 large, high-risk, clinically homogenous AA families and 4 CA families from Southern Louisiana. All families had at least ≥ 3 members with family member diagnosed with PCa. Genotyping for linkage analyses was done using Illumina Infinium II SNP HumanLinkage-12 panel. 6,068 SNPs were released for linkage analyses. Parametric linkage analyses were performed using Merlin software, version 1.1.2. An HLOD score > 1.86 was considered suggestive of linkage. Results: A total of 129 individuals from 15 AA families were genotyped including 45 affected men, 44 unaffected men, and 40 women. The average age at diagnosis was 61; 8 of 15 families had more than 4 affected individuals. 50 CA individuals from similar families were genotyped including 12 affected men, 26 presently unaffected men, and 12 women. For CA families, the average age of onset was 66, with at least 5 affected individuals in each family. In AAs, we identified a peak of suggestive linkage at chromosome 2p16 (HLOD = 1.97). Similarly, in CA families, the strongest linkage signal was observed on chromosome 2q14.1 with an HLOD score of 1.94. At the2 q14 linkage region, there was no linkage in AA PCa families (HLOD = 0.0004). Similarly, on 2p16, there was no linkage in the CA cohort (HLOD = 0). Conclusions: The MSH6 gene is located in 2p16 region. MMR gene mutations have been shown to have evidence of microsatellite instability in PCa as well as hereditary nonpolyposis colorectal cancer. MSH6 gene may represent a genetic variant contributing to risk of PCa in high risk AA families. This potentially has therapeutic implications for use of PD1 inhibitors in this population.

gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels

Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results.