Translational Genomics Research Articles

Engaging community stakeholders in research on best practices for clinical genomic sequencing.

Aim:Maximizing the utility and equity of genomic sequencing integration in clinical care requires engaging patients, their families, and communities. The NCGENES 2 study explores the impact of engagement between clinicians and caregivers of children with undiagnosed conditions in the context of a diagnostic genomic sequencing study.Methods:A Community Consult Team (CCT) of diverse parents and advocates for children with genetic and/or neurodevelopmental conditions was formed.Results:Early and consistent engagement with the CCT resulted in adaptations to study protocol and materials relevant to this unique study population.Discussion:This study demonstrates valuable contributions of community stakeholders to inform the implementation of translational genomics research for diverse participants.

A Robust Method to Quantify Cell Wall Bound Phenolics in Plant Suspension Culture Cells Using Pyrolysis-Gas Chromatography/Mass Spectrometry.

The wide-scale production of renewable fuels from lignocellulosic feedstocks continues to be hampered by the natural recalcitrance of biomass. Therefore, there is a need to develop robust and reliable methods to characterize and quantify components that contribute to this recalcitrance. In this study, we utilized a method that incorporates pyrolysis with successive gas chromatography and mass spectrometry (Py-GC/MS) to assess lignification in cell suspension cultures. This method was compared with other standard techniques such as acid-catalyzed hydrolysis, acetyl bromide lignin determination, and nitrobenzene oxidation for quantification of cell wall bound phenolic compounds. We found that Py-GC/MS can be conducted with about 250 µg of tissue sample and provides biologically relevant data, which constitutes a substantial advantage when compared to the 50–300 mg of tissue needed for the other methods. We show that when combined with multivariate statistical analyses, Py-GC/MS can distinguish cell wall components of switchgrass (Panicum virgatum) suspension cultures before and after inducing lignification. The deposition of lignin precursors on uninduced cell walls included predominantly guaiacyl-based units, 71% ferulic acid, and 5.3% p-coumaric acid. Formation of the primary and partial secondary cell wall was supported by the respective ~15× and ~1.7× increases in syringyl-based and guaiacyl-based precursors, respectively, in the induced cells. Ferulic acid was decreased by half after induction. These results provide the proof-of-concept for quick and reliable cell wall compositional analyses using Py-GC/MS and could be targeted for either translational genomics or for fundamental studies focused on understanding the molecular and physiological mechanisms regulating plant cell wall production and biomass recalcitrance.

Racism and racial inequities in health care rise to the forefront: Amid the country's national reckoning on race, experts are renewing their focus on systemic racism in the health care system.

Racism and racial inequities in health care rise to the forefront: Amid the country's national reckoning on race, experts are renewing their focus on systemic racism in the health care system.

Abstract 5862: NCI Office of Cancer Genomics supports multidisciplinary genomics research initiatives to advance precision oncology

Abstract The National Cancer Institute's (NCI) Office of Cancer Genomics' (OCG) mission is to advance the molecular understanding of cancers to improve clinical outcomes. To accomplish this goal, OCG develops and collaboratively manages molecular characterization and translational genomics research initiatives. OCG currently supports four innovative and complementary initiatives. These programs generate comprehensive genomic datasets, develop bioinformatics tools to analyze these datasets, create biologically-relevant human tumor-derived Next-Generation Cancer Models (NGCMs) and valuable experimental reagents and resources. The Cancer Genome Characterization Initiative (CGCI) (https://ocg.cancer.gov/programs/cgci) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) (https://ocg.cancer.gov/programs/target) are the molecular characterization programs. These programs aim to identify therapeutic targets and biomarkers in understudied, rare, and high-risk adult and pediatric cancers. Clinically annotated tumor and normal matched tissue samples are collected and analyzed by whole-genome, whole-exome, and transcriptome sequencing. The datasets are available to the research community through program-specific Data Matrices: CGCI Data Matrix and TARGET Data Matrix. CGCI and TARGET data are also available through NCI's Genomic Data Commons (GDC)(https://portal.gdc.cancer.gov/). The Pediatric Genomic Data Inventory (PGDI) is a global inventory of pediatric molecular and clinical datasets. The CTD2 Network (https://ocg.cancer.gov/programs/ctd2) aims to understand cancer metastasis, tumor heterogeneity and drug resistance, and develop optimal combinations of pharmacologic and immunological agents. The CTD2 Network develops bioinformatics tools, generates diverse raw/primary datasets that can be accessed through the CTD2 Data Portal and further validates subsets of these data listed at the CTD2 Dashboard. The Human Cancer Models Initiative (HCMI) (https://ocg.cancer.gov/programs/HCMI) is an international consortium that is generating human tumor-derived NGCMs from diverse tumor subtypes including rare and pediatric cancers. The models, together with related clinical and genomic data, are available as a community resource. The HCMI Searchable Catalog allows users to search the list of available models and associated clinical and molecular data. The clinical and molecular data are stored at the NCI's GDC. Data, analytical tools, and resources generated by OCG initiatives are made publicly available to further the collaborative goal of enabling precision oncology to improve patient care. The OCG website (https://ocg.cancer.gov/) also provides data usage policies, guides to access data, experimental methods, standard operating procedures, and educational and helpful links for the community. Citation Format: Cindy W. Kyi, Pamela C. Birriel, Tanja M. Davidsen, Martin L. Ferguson, Patee Gesuwan, Nicholas B. Griner, Yiwen He, Lauren M. Hurd, Subhashini Jagu, Eva Tonsing-Carter, Daniela S. Gerhard. NCI Office of Cancer Genomics supports multidisciplinary genomics research initiatives to advance precision oncology [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 5862.

The Possible Role of Point Mutations and Activation of the CDC27 Gene in Progression of Multiple Myeloma

Multiple myeloma (MM) is characterized by malignancy of terminally differentiated B-lymphocytes. Identification of mutations in genes and pathways in MM is crucial to elucidate the pathophysiology of this cancer. Genomic profiling of malignant myeloma cells may give unprecedented results, which may eventually lead to the development of novel drugs. MM is a complex disease with a complex interactive system that consists of dysregulation of different pathways that require precise investigation for designing more effective drugs. The recent advances in high throughput sequencing (HTS) and a better understanding of myeloma's genetic architecture provide yet another approach to uncovering the driver mutations in myeloma. In the present study, we aimed to study whether cell division cycle 27 (CDC27) has a role in MM's malignancy and performed Whole Exome Sequencing (WES) in four clinical cases. Given the importance of the CDC27 gene in cell division, various studies demonstrate in different cancers that the CDC27 gene is associated with tumor proliferation and progression. Analysis of our data in the coding region of MM cases revealed that all four cases under study carrying point mutations in multiple sites of the CDC27 gene.Interestingly, CDC27 plays a pivotal role in the anaphase-promoting complex during cell division. Therefore, we opine that CDC27 may also have a role in MM. We concluded that the effective investigation of translational genomics of CDC27 should be screened from the gene level to the functional level of the protein (bench to bedside research) and studying its possible role in MM cell progression, which might be a novel therapeutic approach.

Yellow Mosaic Disease (YMD) of Mungbean (Vigna radiata (L.) Wilczek): Current Status and Management Opportunities.

Globally, yellow mosaic disease (YMD) remains a major constraint of mungbean production, and management of this deadly disease is still the biggest challenge. Thus, finding ways to manage YMD including development of varieties possessing resistance against mungbean yellow mosaic virus (MYMV) and mungbean yellow mosaic India virus (MYMIV) is a research priority for mungbean crop. Characterization of YMD resistance using various advanced molecular and biochemical approaches during plant–virus interactions has unfolded a comprehensive network of pathogen survival, disease severity, and the response of plants to pathogen attack, including mechanisms of YMD resistance in mungbean. The biggest challenge in YMD management is the effective utilization of an array of information gained so far, in an integrated manner for the development of genotypes having durable resistance against yellow mosaic virus (YMV) infection. In this backdrop, this review summarizes the role of various begomoviruses, its genomic components, and vector whiteflies, including cryptic species in the YMD expression. Also, information about the genetics of YMD in both mungbean and blackgram crops is comprehensively presented, as both the species are crossable, and same viral strains are also found affecting these crops. Also, implications of various management strategies including the use of resistance sources, the primary source of inoculums and vector management, wide-hybridization, mutation breeding, marker-assisted selection (MAS), and pathogen-derived resistance (PDR) are thoroughly discussed. Finally, the prospects of employing various powerful emerging tools like translational genomics, and gene editing using CRISPR/Cas9 are also highlighted to complete the YMD management perspective in mungbean.

What Have We Learned from GWAS for Atopic Dermatitis?

GWASs have revealed multiple loci associated with atopic dermatitis (AD). Some have confirmed pre-existing knowledge, including the role of skin barrier and type 2 inflammation in AD pathogenesis, whereas others have provided newer insights, including evidence of autoimmunity and previously unrecognized genes controlling epidermal differentiation. The majority of risk loci are in intergenic regions for which functional mechanism(s) remain unknown. These loci require detailed molecular studies carried out in cells and tissues of relevance to AD. Genomic findings to date account for ∼30% of AD heritability, therefore, considerable further work is needed to fully understand individual risk.

Integrating stakeholder feedback in translational genomics research: an ethnographic analysis of a study protocol’s evolution

PurposeThis study describes challenges faced while incorporating sometimes conflicting stakeholder feedback into study design and development of patient-facing materials for a translational genomics study aiming to reduce health disparities among diverse populations. MethodsWe conducted an ethnographic analysis of study documents including summaries of patient advisory committee meetings and interviews, reflective field notes written by study team members, and correspondence with our institutional review board (IRB). Through this analysis, we identified cross-cutting challenges for incorporating stakeholder feedback into development of our recruitment, risk assessment, and informed consent processes and materials. ResultsOur analysis revealed three key challenges: (1) balancing precision and simplicity in the design of study materials, (2) providing clinical care within the research context, and (3) emphasizing potential study benefits versus risks and limitations. ConclusionsWhile involving patient stakeholders in study design and materials development can increase inclusivity and responsiveness to patient needs, patient feedback may conflict with that of content area experts on the research team and IRBs who are tasked with overseeing the research. Our analysis highlights the need for further empirical research about ethical challenges when incorporating patient feedback into study design, and for dialogue with genomic researchers and IRB representatives about these issues.

Abstract C035: Relationship between ancestry fractions and gene expression in triple-negative breast cancer in Hispanic/Latina women

Abstract Background: Breast cancer is the most frequently diagnosed form of invasive cancer in women and the second leading cause of cancer death. Triple-negative breast cancer (TNBC) accounts for 10-20% of the disease. This aggressive subtype lacks receptors for estrogen, progesterone, and human epidermal growth factor receptor 2 (HER2), drastically reducing treatment options. Hispanic/Latinas, who derive ancestry from European, African, and Native origins, are at least 30% more likely to be diagnosed with TNBC compared to non-Hispanic White women. However, little is known about the genomic architecture of TNBCs in Hispanic/Latinas. The goal of our study was to test the association between genetic ancestry and gene expression in TNBC samples from Hispanics/Latinas to help identify potential therapeutic targets. Methods and Results: We obtained 41 TNBC tissues through collaboration with the National Cancer Institute in Colombia along with demographic and clinical information. Genetic ancestry proportions were estimated using a panel of 106 Ancestry Informative Markers (AIMs). RNA was extracted from FFPE tissues, qualified using Agilent chips, and used for RNA sequencing at the Translational Genomics Core at the Stanley S. Scott Cancer Center. We used an online tool (http://cbc.mc.vanderbilt.edu/tnbc/) to validate TNBC status, and 33 of the 41 samples were confirmed. Quality control procedures ensured that the samples were of acceptable quality for further analysis. Individuals were classified as having high or low genetic ancestry proportions for each of the ancestral components, based on mean ancestry proportions overall. Differential gene expression between individuals in each ancestry category was estimated utilizing DESeq2 in R-Studio. Average genetic ancestry proportions for the 33 samples analyzed were 0.52 European (18 individuals were in the high European ancestry group, 14 in the low European ancestry group), 0.36 Indigenous American (15 high, 17 low) and 0.1 African (8 high, 24 low). We observed that 91 genes were differentially expressed between high vs. low European ancestry, 21 for the Native and 12 for the African. Interestingly, 5 genes were common between the European and Native ancestries. LGALS9C and MESP1 had significant differences in normalized counts between high and low ancestry for both the Europeans and Natives, though the subgroups displayed opposite correlation patterns. These results were validated by real-time PCR. Using cBioPortal, we found that MESP1 and LGALS9C were associated with amplification in 2.8% and 1.5% of breast cancer cases, respectively. LGALS9C expression displays an inverse correlation with disease outcome in several cancers, including breast. Conclusions: Our data suggest that expression levels of several genes, most notably MESP1 and LGALS9C, may be ancestry specific in TNBC patients from Colombia. Confirmation and further understanding of these findings are of outmost importance given that they could be therapeutic targets. Citation Format: Laura Carrasquilla, Jone Garai, Silvia J. Serrano-Gomez, Maria C. Sanabria-Salas, Melody C. Baddoo, Laura Fejerman, Jovanny Zabaleta. Relationship between ancestry fractions and gene expression in triple-negative breast cancer in Hispanic/Latina women [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C035.

Abstract C092: Immune characteristics of triple-negative breast cancer (TNBC) in Latin American women from Colombia

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive form of the disease with limited treatment options and poor survival. A series of retrospective studies established the presence of tumor-infiltrating lymphocytes (TILs) in most primary breast cancers, the number of which affect the response rate to chemotherapy in both neoadjuvant and adjuvant treatment contexts. A subset of TNBC is highly immunogenic, and recent studies have shown that understanding the specific immune profiles of tumors has implications both for treatment and prognosis. Most studies have been conducted in samples of women of European origin, and little is known about the immune profile of TNBCs in Hispanic/Latinas. The specific goal of our study was to test the association between immune characteristics of TNBC from Colombian patients and genetic ancestry proportions, to determine if genetic ancestry could be a relevant factor in defining the immune characteristics of TNBC. Methods: We obtained 41 TNBC tissues through collaboration with the National Cancer Institute in Colombia along with demographic and clinical information. Genetic ancestry was estimated with a panel of 106 ancestry informative markers and the program STRUCTURE. RNA was extracted from FFPE tissues, qualified using Agilent chips, and used for sequencing at the Translational Genomics Core at the Stanley S. Scott Cancer Center. Using the TNBCtype program we confirmed 33 samples as TNBC. The program xCell was used for cell-signature identification based on RNAseq data. We explored associations between genetic ancestry and scores obtained for different immune cell-types and an overall immune score using linear regression. We analyzed the association for the following specific cells: Th1 cells, Th2 cells, Treg, CD4 T cells, CD4 TEM, CD4 memory T cells, CD8 T cells, CD8 TCM, CD8 TEM, CD8 naive T cells, macrophages, macrophages M1, macrophages M2, and mast cells. Results: The overall immune score was positively associated with the proportion of African ancestry (p=0.049). Interestingly, we observed that Indigenous American ancestry was inversely associated with the Treg cell score while African ancestry was positively associated with it. Levels of these regulatory cells have been correlated with prognosis in ER- and triple-negative disease. We also found that CD4 T cell and CD4 memory T-cell scores were positively associated with African ancestry (P=0.006 and P=0.049 respectively). Conclusions: Our results suggest that genetic ancestry among Latina women from Colombia is associated with certain immune characteristics of breast cancer. We need to further test these associations in a larger sample to confirm the findings, obtain additional insights, and understand their implications for TNBC treatment and prognosis among Latin American women. Citation Format: Valentina A. Zavala, Laura C. Carrasquilla, Silvia J. Serrano-Gomez, Maria C. Sanabria-Salas, Melody C. Baddoo, Jone Garai, Jovanny Zabaleta, Laura Fejerman. Immune characteristics of triple-negative breast cancer (TNBC) in Latin American women from Colombia [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C092.

Abstract C034: Differential gene expression according to ancestry in Hispanic/Latina women with luminal B breast cancer

Abstract Background: Breast cancer (BC) is the second leading cause of cancer-related death in women. There is a lack of breast cancer studies showing the differential gene expression in minorities. We have previously found differences in gene expression according to ancestry in Hispanic/Latina women with BC. The goal of our study was to determine the differential gene expression between high and low European, African, and Native ancestries of Hispanic/Latina women with luminal B BC. Methods: Breast cancer tissue samples were collected from the Moffitt Cancer Center (MCC) in Tampa, FL, and had been analyzed for ancestry informative markers (AIMs) as part of a collaboration between MCC and the University of Puerto Rico. The RNA was quantified, qualified, and used to prepare genomic libraries using regents and protocols from Illumina at the Translational Genomics Core, Stanley S. Scott Cancer Center, LSUHSC-New Orleans. Quality assessment showed close to 50% alignment in coding regions. Raw counts were normalized and used to perform differential gene expression analysis (p<0.05 and fold change >2.0) using DESeq2 in R-Studio between individuals with high and low European, African, and Native ancestral fractions. Heatmaps were used to compare the distribution of the samples visually based on ancestry fraction and the level of gene expression. We used the online tool Venny (http://bioinfogp.cnb.csic.es/tools/venny/) to identify significantly different genes that were uniquely expressed in each ancestral group or shared between them. In addition, we used online tools (http://xcell.ucsf.edu/) for cell infiltration analysis and the software MetaCore to identify possible pathways in which the differentially expressed genes may be involved. Results: We found a significant inverse correlation between European and both African and Native American ancestries, and these clearly separated based on high and low ancestral fraction. Eighteen genes were shared between European and Native American ancestries, showing opposite expression between the ancestries, suggesting an ethnicity-associated expression. The expression of these genes was validated by real-time PCR. Interestingly, cBioportal analysis showed that ANO1, EPN3, PLAT, and TRPA1 genes are frequently amplified in breast cancer. Furthermore, one gene SPAG6 was commonly expressed among all ancestries with a positive correlation in Native ancestry and negative correlation in European ancestry. We found that African ancestry was associated with the infiltration on lymphocyte progenitors and type 2 macrophages. Meanwhile, European and Native ancestries correlated with type 2 lymphocytes and monocytes, respectively. Pathway analysis revealed possible activation of immune responses driven by genes significant in European and Native ancestries. Conclusions: Overall, our data suggest that patients with luminal B breast cancer may have differential gene expression associated to ancestry, to gene abnormalities and differential immune responses. Citation Format: Joussette I. Alvarado, Jone Garai, Li Li, Adam J. Boe, Doug Cress, Teresita Antonia, Jamie Teer, Lucio Miele, Jovanny Zabaleta. Differential gene expression according to ancestry in Hispanic/Latina women with luminal B breast cancer [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C034.

Translational genomics and beyond in bipolar disorder.

Genome-wide association studies (GWAS) have revealed multiple genomic loci conferring risk of bipolar disorder (BD), providing hints for its underlying pathobiology. However, there are still remaining questions to answer. For example, discordance exists between BD heritability estimated with earlier epidemiological evidence and that calculated based on common GWAS variations. Where is the "missing heritability"? How can we explain the biology of the disease based on genetic findings? In this review, we summarize the accomplishments and limitations of current BD GWAS, and discuss potential reasons for the "missing heritability." In addition, progresses of research for the biological mechanisms underlying BD genetic risk using brain tissues, reprogrammed cells, and model animals are reviewed. While our knowledge of BD genetic basis is significantly promoted by these efforts, the complexities of gene regulation in the genome, the spatial-temporal heterogeneity during brain development, and the limitations of different experimental models should always be considered. Notably, several genes have been widely studied given their relatively well-characterized involvement in BD (e.g., CACAN1C and ANK3), and findings of these genes are summarized to both outline possible biological mechanisms of BD and describe examples of translating GWAS discoveries into the pathophysiology.

Lessons learned about harmonizing survey measures for the CSER consortium.

Implementation of genome-scale sequencing in clinical care has significant challenges: the technology is highly dimensional with many kinds of potential results, results interpretation and delivery require expertise and coordination across multiple medical specialties, clinical utility may be uncertain, and there may be broader familial or societal implications beyond the individual participant. Transdisciplinary consortia and collaborative team science are well poised to address these challenges. However, understanding the complex web of organizational, institutional, physical, environmental, technologic, and other political and societal factors that influence the effectiveness of consortia is understudied. We describe our experience working in the Clinical Sequencing Evidence-Generating Research (CSER) consortium, a multi-institutional translational genomics consortium. A key aspect of the CSER consortium was the juxtaposition of site-specific measures with the need to identify consensus measures related to clinical utility and to create a core set of harmonized measures. During this harmonization process, we sought to minimize participant burden, accommodate project-specific choices, and use validated measures that allow data sharing. Identifying platforms to ensure swift communication between teams and management of materials and data were essential to our harmonization efforts. Funding agencies can help consortia by clarifying key study design elements across projects during the proposal preparation phase and by providing a framework for data sharing data across participating projects. In summary, time and resources must be devoted to developing and implementing collaborative practices as preparatory work at the beginning of project timelines to improve the effectiveness of research consortia.

Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications.

SummarySpatio‐temporal and developmental stage‐specific transcriptome analysis plays a crucial role in systems biology‐based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA‐seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired‐end filtered reads were generated followed by identification of 81 901 transcripts from an early‐maturing, high‐yielding, drought‐tolerant groundnut variety, ICGV 91114. Further, 57 344 genome‐wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in‐depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer‐friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.

A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer.

Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples). We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction. By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.

Translational Genomics in Neurocritical Care: a Review.

Translational genomics represents a broad field of study that combines genome and transcriptome-wide studies in humans and model systems to refine our understanding of human biology and ultimately identify new ways to treat and prevent disease. The approaches to translational genomics can be broadly grouped into two methodologies, forward and reverse genomic translation. Traditional (forward) genomic translation begins with model systems and aims at using unbiased genetic associations in these models to derive insight into biological mechanisms that may also be relevant in human disease. Reverse genomic translation begins with observations made through human genomic studies and refines these observations through follow-up studies using model systems. The ultimate goal of these approaches is to clarify intervenable processes as targets for therapeutic development. In this review, we describe some of the approaches being taken to apply translational genomics to the study of diseases commonly encountered in the neurocritical care setting, including hemorrhagic and ischemic stroke, traumatic brain injury, subarachnoid hemorrhage, and status epilepticus, utilizing both forward and reverse genomic translational techniques. Further, we highlight approaches in the field that could be applied in neurocritical care to improve our ability to identify new treatment modalities as well as to provide important information to patients about risk and prognosis.Electronic supplementary materialThe online version of this article (10.1007/s13311-020-00838-1) contains supplementary material, which is available to authorized users.

Abstract P4-07-07: Establishing whole-exome sequencing for breast cancer patient care

Abstract Background. Next-generation sequencing (NGS) technology enables profiling of individual tumours and to measure the increasing number of biomarkers relevant to the management of breast cancer patients. The Australian Translational Genomics Centre (ATGC) is a collaboration between the healthcare sector (Metro South Hospital and Health Service), higher education sector (Queensland University of Technology) and a government-run pathology service (Pathology Queensland) to provide genomic profiling of breast cancer patients at the Princess Alexandra Hospital. The program was developed to integrate the ordering, processing and interpretation of large-scale NGS into clinical practice. Methods. Patients were consented for somatic testing and ordering was integrated into the hospital’s electronic ordering system. Samples were derived from fresh tissue biopsies after surgeries (47%) or from FFPE histology sections. No selection criteria were applied during the initial phase and the cohort was representative of newly presenting patients at the hospitals breast cancer clinic. Patients were sequenced using a NATA-accredited ISO15189 program using whole-exome sequencing (WES) combined with a high-coverage spike-in panel of known cancer genes. Clinical reports included the calculation of tumour purity, tumour mutational burden (TMB), the assessment of copy number events and somatic mutations down to 3% allele frequency. Standard molecular testing in Australia includes ER, PR and HER2 status, and additional testing included testing of Tier 1-2 somatic variants in the genes ABCC3, AKT1, CCND1, CCNE1, CDKN2A, ERBB2, ESR1, FGF3, FGFR1, FGFR2, MTOR, NCOA3, NF2, PIK3CA, PIK3R1, PTEN, RB1, RSF1, SF3B1, TP53. Results. Seventy-one patients were tested by WES/panel, and an average of 1.5 clinically significant Tier 1- 2 mutations were detected per patient. In 77% of cases, the molecular profiling could stratify patients to those with either PI3K/Akt/mTOR pathway activation (by PIK3CA activating mutations, AKT, MTOR mutations or PTEN loss) or CDK4/6 activation (by CCND1 expansion or CDKN2A loss). The most frequently observed mutations were PIK3CA activation (40%) and CCND1 copy number expansions (24%). A small proportion (n=3) were found to have mTOR or TCS1/2 mutations reported to have association with a durable response to mTOR inhibitors. Additionally, 11 patients (15%) had a high TMB (TMB, &amp;gt;6.8 mutations/megabase) with 6 having &amp;gt;10 mutations/Mb. Within this high-TMB cohort, 3 were found to be ER-PR-HER-, however, the majority (n=7) were ER+PR+HER2- patients. Calculation of the tumour purity indicated that, despite expert resection of the biopsies to isolate the most tumour dense regions, tumour purity was not significantly enriched. In 58% of cases, the tumour purity was less than 50%, and in 13% of samples, it was less than 25%, indicating that in clinical practice the method of sequencing must be robust, as many samples have significant amounts of contaminating stroma. Conclusion. We demonstrate that integration of WES/panel testing into clinical practice is practical and provides multiplexed testing of current and emerging biomarkers in a significant number of tested patients. While a high proportion of patients had mutations that could stratify them to targeted therapies in the event of metastatic disease, the somatic molecular profiles did not modify first line therapy decision-making. Training of clinical staff for patient consent and the dissemination of findings, the development of a dedicated molecular tumour board, and decision protocols to identify patients of metastatic risk were identified as key developments in this clinical program. The program identified previously unidentified subsets of patients including a subset of ER+ patients with high TMB for which for there are no effective treatments option in Australia. Citation Format: Kate Roberts, Paul J Leo, Jeremy Khoo, Alice Febery, Jonathan Ellis, Mhairi Clout, Lawrie Wheeler, Lisa Anderson, Matthew Brown, Ian Bennett. Establishing whole-exome sequencing for breast cancer patient care [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-07.

Gastric Cancer Registry: A comprehensive patient-reported resource for multidisciplinary and translational genomic approaches to gastric cancer.

432 Background: Gastric cancer (GC) is the fifth leading cancer diagnosis and third frequent cause of cancer death globally. GC results from a cascade of molecular and genetic changes owing to environmental and genetic factors. While there are known risks to GC, more is to be learned about its development so to establish effective screens for early stages of cancer. Methods: The Gastric Cancer Registry (GCR) was built to investigate GC and discover informative genomic biomarkers. The GCR comprises medical, family, and social history and genomics data from patients with GC, a family history of GC, and/or a known mutation in the gene CDH1. Samples of saliva and gastric tumors are collected when available. The GCR allows us to leverage several genome sequencing datasets to construct a complete molecular landscape of GC. Early analysis of GC tissue includes whole exome sequencing (WES) to identify mutations, whole genome sequencing (WGS) for copy number variation, and RNA sequencing (RNAseq) for expression profiling. Results are used to inform of clonal neoantigens, microbiome, and immune cell populations. Saliva will be analyzed with linked reads sequencing to unearth germline mutations not picked up in standard clinical gene panels. Results: Datasets from 455 patients and samples from 159 patients have been collected. In a pilot study, we pinpointed specific mutations using WES and revealed extensive changes in genome copy number involving clinically actionable genes through WGS. Most tumors had a high degree of genomic instability and exhibited candidate markers for treatment decisions and response. Additionally, we found that RNAseq revealed tumor subgroups through gene expression signatures. Conclusions: The GCR is an informative resource enabling the identification of biomarkers for GC. With the GCR we are integrating expertise in translational cancer genomics with molecular biology, statistics, and bioinformatics to build a platform for discovery and the development of tools that will ultimately improve the detection, treatment, and prevention of GC.

Translational genomics of malignant rhabdoid tumours: Current impact and future possibilities.

Malignant Rhabdoid Tumours (MRT) are the quintessential example of an epigenetic cancer. Mutation of a single gene, SMARCB1 or more rarely SMARCA4, is capable of causing one of the most aggressive and lethal cancers of early childhood and infancy. SMARCB1 encodes a core subunit of the SWI/SNF complex and its mutation evokes genome-wide downstream effects which may be counteracted therapeutically. Here we review and discuss the use of translational genomics in the study of MRT biology and the ways in which this has impacted clinical practice or may do so in the future. First, the diagnosis and definition of MRT and the transition from a histopathological to a molecular definition. Second, epigenetic and transcriptomic subgroups within MRT, their defining features and potential prognostic or therapeutic significance. Third, functional genomic studies of MRT by mouse modelling and forced re-expression of SMARCB1 in MRT cells. Fourth, studies of underlying epigenetic mechanisms (e.g. EZH2, HDACs) or deregulated kinases (e.g. PDGFR, FGFR1) and the potential therapeutic opportunities these provide. Finally, we discuss likely future directions and proffer opinion on how future translational genomics should be integrated into future biological/clinical studies to select and evaluate the best anti-MRT therapeutic agents.

Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia.

We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.