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Journal articles on the topic 'Exome chip association analysis'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

van 't Hof, Femke N. G., Dongbing Lai, Jessica van Setten, et al. "Exome-chip association analysis of intracranial aneurysms." Neurology 94, no. 5 (2019): e481-e488. http://dx.doi.org/10.1212/wnl.0000000000008665.

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ObjectiveTo investigate to what extent low-frequency genetic variants (with minor allele frequencies <5%) affect the risk of intracranial aneurysms (IAs).MethodsOne thousand fifty-six patients with IA and 2,097 population-based controls from the Netherlands were genotyped with the Illumina HumanExome BeadChip. After quality control (QC) of samples and single nucleotide variants (SNVs), we conducted a single variant analysis using the Fisher exact test. We also performed the variable threshold (VT) test and the sequence kernel association test (SKAT) at different minor allele count (MAC) thr

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2

Jaworek, Thomas, Kathleen A. Ryan, Brady J. Gaynor, et al. "Exome Array Analysis of Early-Onset Ischemic Stroke." Stroke 51, no. 11 (2020): 3356–60. http://dx.doi.org/10.1161/strokeaha.120.031357.

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Background and Purpose: The genetic contribution to ischemic stroke may include rare- or low-frequency variants of high-penetrance and large-effect sizes. Analyses focusing on early-onset disease, an extreme-phenotype, and on the exome, the protein-coding portion of genes, may increase the likelihood of identifying such rare functional variants. To evaluate this hypothesis, we implemented a 2-stage discovery and replication design, and then addressed whether the identified variants also associated with older-onset disease. Methods: Discovery was performed in UMD-GEOS Study (University of Maryl

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3

Zhou, Xu-jie, Lam C. Tsoi, Yong Hu, et al. "Exome Chip Analyses and Genetic Risk for IgA Nephropathy among Han Chinese." Clinical Journal of the American Society of Nephrology 16, no. 2 (2021): 213–24. http://dx.doi.org/10.2215/cjn.06910520.

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Background and objectivesIgA nephropathy is the most common form of primary GN worldwide. The evidence of geographic and ethnic differences, as well as familial aggregation of the disease, supports a strong genetic contribution to IgA nephropathy. Evidence for genetic factors in IgA nephropathy comes also from genome-wide association patient-control studies. However, few studies have systematically evaluated the contribution of coding variation in IgA nephropathy.Design, setting, participants, & measurementsWe performed a two-stage exome chip–based association study in 13,242 samples, incl

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Chen, Ming-Huei, Lisa R. Yanek, Joshua D. Backman, et al. "Exome-chip meta-analysis identifies association between variation in ANKRD26 and platelet aggregation." Platelets 30, no. 2 (2017): 164–73. http://dx.doi.org/10.1080/09537104.2017.1384538.

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5

Miller, Peter G., Dandi Qiao, Joselyn Rojas-Quintero, et al. "Association of clonal hematopoiesis with chronic obstructive pulmonary disease." Blood 139, no. 3 (2022): 357–68. http://dx.doi.org/10.1182/blood.2021013531.

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Abstract Chronic obstructive pulmonary disease (COPD) is associated with age and smoking, but other determinants of the disease are incompletely understood. Clonal hematopoiesis of indeterminate potential (CHIP) is a common, age-related state in which somatic mutations in clonal blood populations induce aberrant inflammatory responses. Patients with CHIP have an elevated risk for cardiovascular disease, but the association of CHIP with COPD remains unclear. We analyzed whole-genome sequencing and whole-exome sequencing data to detect CHIP in 48 835 patients, of whom 8444 had moderate to very s

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Zhu, Qianqian, Li Yan, Qian Liu, et al. "Exome chip analyses identify genes affecting mortality after HLA-matched unrelated-donor blood and marrow transplantation." Blood 131, no. 22 (2018): 2490–99. http://dx.doi.org/10.1182/blood-2017-11-817973.

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Key Points We conducted the first exome-wide association study between germ line variant genotype and survival outcomes after unrelated-donor BMT. A number of novel genes were found to significantly affect survival outcomes.

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Wu, Hsin-Ta, Ekaterina Kalashnikova, Samay Mehta, et al. "Characterization of clonal hematopoiesis of indeterminate potential mutations from germline whole exome sequencing data." Journal of Clinical Oncology 38, no. 15_suppl (2020): 1525. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.1525.

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1525 Background: Clonal hematopoiesis of Indeterminate Potential (CHIP) is an age-related phenomenon where somatic mutations accumulate in cells of the blood or bone marrow. It is a source of biological noise that causes false-positives in ctDNA analysis and is present in up to 20% of individuals over the age of 70. The presence of CHIP has been linked to an increased risk of hematologic cancers and cardiovascular disease. The Signatera assay filters CHIP mutations through tumor tissue and germline sequencing thereby reducing false-positive results and focuses on tumor-specific mutations for e

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Kunkle, Brian W., Badri N. Vardarajan, Adam C. Naj, et al. "O1-03-03: Identification of Novel Candidate Genes for Early-Onset Alzheimer's Disease Through Integrated Whole-Exome Sequencing and Exome Chip Array Association Analysis." Alzheimer's & Dementia 12 (July 2016): P177—P178. http://dx.doi.org/10.1016/j.jalz.2016.06.306.

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Zon, Becky, Aswin Sekar, Katharine Clapham, et al. "Clonal Hematopoiesis and Venous Thromboembolism in the UK Biobank." Blood 142, Supplement 1 (2023): 568. http://dx.doi.org/10.1182/blood-2023-180764.

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Background: Patients with myeloid malignancies have an increased risk of thrombosis, but less is known about the risk of thrombosis in clonal hematopoiesis of indeterminate potential (CHIP). We evaluated genotype-specific associations between CHIP and both prevalent and incident venous thromboembolism (VTE) in the largest such analysis to date of the UK Biobank. Methods: We examined 425,573 individuals without a prevalent hematologic malignancy diagnosis from the UK Biobank. Whole exome sequencing and single nucleotide polymorphism array data were analyzed to identify individuals with CHIP and

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Torres, Guillermo G., Marianne Nygaard, Amke Caliebe, et al. "Exome-Wide Association Study Identifies FN3KRP and PGP as New Candidate Longevity Genes." Journals of Gerontology: Series A 76, no. 5 (2021): 786–95. http://dx.doi.org/10.1093/gerona/glab023.

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Abstract Despite enormous research efforts, the genetic component of longevity has remained largely elusive. The investigation of common variants, mainly located in intronic or regulatory regions, has yielded only little new information on the heritability of the phenotype. Here, we performed a chip-based exome-wide association study investigating 62 488 common and rare coding variants in 1248 German long-lived individuals, including 599 centenarians and 6941 younger controls (age &lt; 60 years). In a single-variant analysis, we observed an exome-wide significant association between rs1046

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Cheung, Chloe Y. Y., Clara S. Tang, Aimin Xu, et al. "An Exome-Chip Association Analysis in Chinese Subjects Reveals a Functional Missense Variant of GCKR That Regulates FGF21 Levels." Diabetes 66, no. 6 (2017): 1723–28. http://dx.doi.org/10.2337/db16-1384.

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Hiitola, Emil, Juuso Korhonen, Jukka Koskela, et al. "Clonal Hematopoiesis Associated with Rheumatoid Arthritis." Blood 142, Supplement 1 (2023): 2698. http://dx.doi.org/10.1182/blood-2023-173664.

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Introduction: Clonal hematopoiesis (CH) becomes common with age and can play a role in the pathophysiology of inflammatory diseases by modifying immune cell function. CH is characterized by the presence of somatic mutations in genes such as DNMT3A and TET2 (CH of indeterminate potential, CHIP), and as mosaic chromosomal alterations (mCAs). While CHIP, particularly in the context of TET2 mutations, can promote inflammation in cardiovascular diseases, the association between clonal hematopoiesis and autoimmunity has not been comprehensively studied to date. Rheumatoid arthritis (RA) is one of th

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Agrawal, Mridul, Abhishek Niroula, Pierre Cunin, et al. "The Association between Clonal Hematopoiesis and Gout." Blood 138, Supplement 1 (2021): 595. http://dx.doi.org/10.1182/blood-2021-153639.

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Abstract Background: Gout is a highly prevalent arthritis associated with debilitating joint pain and functional impairment. It is caused by elevated serum uric acid levels (hyperuricemia) and triggered by precipitation of urate crystals in and around joints. Urate crystals are ingested by macrophages and provoke an innate immune response with subsequent secretion of inflammatory cytokines including interleukin 1 beta (IL-1B). Clonal hematopoiesis of indeterminate potential (CHIP) is a precursor to hematologic malignancies defined by somatic mutations in hematopoietic cells that drive clonal e

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Cheung, Chloe Y. Y., Chi-Ho Lee, Clara S. Tang, et al. "Genetic Regulation of Pigment Epithelium-Derived Factor (PEDF): An Exome-Chip Association Analysis in Chinese Subjects With Type 2 Diabetes." Diabetes 68, no. 1 (2018): 198–206. http://dx.doi.org/10.2337/db18-0500.

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Cheung, Chloe Y. Y., Clara S. Tang, Aimin Xu, et al. "Exome-chip association analysis reveals an Asian-specific missense variant in PAX4 associated with type 2 diabetes in Chinese individuals." Diabetologia 60, no. 1 (2016): 107–15. http://dx.doi.org/10.1007/s00125-016-4132-z.

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Weng, Lu-Chen, Amelia Weber Hall, Seung Hoan Choi, et al. "Genetic Determinants of Electrocardiographic P-Wave Duration and Relation to Atrial Fibrillation." Circulation: Genomic and Precision Medicine 13, no. 5 (2020): 387–95. http://dx.doi.org/10.1161/circgen.119.002874.

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Background: The P-wave duration (PWD) is an electrocardiographic measurement that represents cardiac conduction in the atria. Shortened or prolonged PWD is associated with atrial fibrillation (AF). We used exome-chip data to examine the associations between common and rare variants with PWD. Methods: Fifteen studies comprising 64 440 individuals (56 943 European, 5681 African, 1186 Hispanic, 630 Asian) and ≈230 000 variants were used to examine associations with maximum PWD across the 12-lead ECG. Meta-analyses summarized association results for common variants; gene-based burden and sequence

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Cho, Seong-Beom, and Jinhwa Jang. "A Genome-Wide Association Study of a Korean Population Identifies Genetic Susceptibility to Hypertension Based on Sex-Specific Differences." Genes 12, no. 11 (2021): 1804. http://dx.doi.org/10.3390/genes12111804.

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Genome-wide association studies have expanded our understanding of the genetic variation of hypertension. Hypertension and blood pressure are influenced by sex-specific differences; therefore, genetic variants may have sex-specific effects on phenotype. To identify the genetic factors influencing the sex-specific differences concerning hypertension, we conducted a heterogeneity analysis of a genome-wide association study (GWAS) on 13,926 samples from a Korean population. Using the Illumina exome chip data of the population, we performed GWASs of the male and female population independently and

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Shi, Xiaolei, Abderrahman Day, Hannah E. Bergom, et al. "Molecular correlates of high B7-H3-expressing metastatic castrate-resistant prostate cancers (mCRPC) via exome, transcriptome, and epigenome analyses." Journal of Clinical Oncology 40, no. 16_suppl (2022): 5045. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.5045.

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5045 Background: mCRPC is a lethal condition with limited effective treatment options. B7-H3, a transmembrane protein of the B7 checkpoint superfamily is overexpressed in prostate cancer (PC) and is associated with poor prognosis. While several novel approaches target B7-H3 in prostate cancer, lack of knowledge about the molecular features and regulatory mechanisms of B7-H3 expression in mCRPC prevents the optimal design of these interventions. We aimed to characterize B7-H3 in mCRPC with the purpose to reveal the roles of B7-H3 in mCRPC pathogenesis, and stratify the patient population optima

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Corvigno, Sara, Amma Asare, Jun Yao, et al. "Abstract 6407: Identification of novel chemotherapy-related CHIP variations in patients with high-grade serous ovarian cancer." Cancer Research 84, no. 6_Supplement (2024): 6407. http://dx.doi.org/10.1158/1538-7445.am2024-6407.

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Abstract Background: Hematopoietic lineage differentiation is subjected to genetic mutations that, due to fitness advantages, might give rise to clonally expanded populations. Clonal hematopoiesis of indeterminate potential (CHIP) is defined as the outgrowth of a single clone driven by acquired somatic mutations in hematopoietic stem cells (HSCs), in the absence of hematological abnormalities. Previous studies have shown the association of CH with aging and a higher risk of developing secondary hematologic malignancies in cancer patients treated with chemotherapy agents. It is therefore of gre

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Samatkyzy, D., S. Rakhimova, U. Kozhamkulov, et al. "CLONAL HEMATOPOIESIS AND ITS ROLE IN THE DEVELOPMENT OF CARDIOVASCULAR DISEASES." Eurasian Journal of Applied Biotechnology, no. 3S (September 12, 2024): 58. http://dx.doi.org/10.11134/btp.3s.2024.46.

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Clonal hematopoiesis (CH) is the increase in somatic clones carrying mutations in hematopoietic stem cells. This biological condition can lead to cancer and is implicated in the development of atherosclerosis and cardiovascular diseases. CH of indeterminate potential (CHIP) refers to somatic mutations in genes that are associated with the development of Coronary heart disease (CHD) and leukemia. Now, with next-generation sequencing, we can detect mutations even if they are present in only a small number of cells in the tissue sample being studied. Consequently, numerous studies have shown that

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Patel, Sagar A., Angelo Marra, Jeffrey M. Switchenko, et al. "Clonal hematopoiesis of indeterminate potential (CHIP) and cardiovascular toxicity from androgen deprivation therapy in men with prostate cancer." Journal of Clinical Oncology 42, no. 4_suppl (2024): 312. http://dx.doi.org/10.1200/jco.2024.42.4_suppl.312.

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312 Background: Androgen deprivation therapy (ADT) with agonists of the gonadotropin releasing hormone (GnRH) receptor (e.g. leuprolide) is associated with coronary artery disease and major adverse cardiovascular (CV) events. CHIP, an age-related expanded somatic blood cell clone without other hematologic abnormalities, is associated with inflammation and accelerated atherosclerosis. Whether CHIP is associated with adverse CV outcomes in patients receiving ADT is unknown. Methods: Twenty-five men with localized prostate cancer pursuing radiotherapy plus ≥ 6 months of leuprolide were enrolled o

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Bouzid, Hind, Julia Belk, Max Jan, et al. "Clonal Hematopoiesis is Associated with Reduced Risk of Alzheimer's Disease." Blood 138, Supplement 1 (2021): 5. http://dx.doi.org/10.1182/blood-2021-151064.

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Abstract Clonal hematopoiesis of indeterminate potential (CHIP) occurs when hematopoietic stem cells (HSCs) acquire a mutation, most commonly a null variant in TET2 or DNMT3A, that confers a selective advantage. Blood cancers may result if additional cooperating mutations are acquired. However, CHIP may also cause atherosclerosis and other inflammatory diseases because these mutations alter the function or development of effector immune cells derived from the HSCs. Genome-wide association studies have implicated microglia, the resident myeloid cells in the brain, as key players in the biology

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Malek, Ehsan, Petra Martin, Paolo F. Caimi, et al. "Presence of Chip-Mutated Autologous Hematopoietic Cells in Mobilized Peripheral Blood Products Is Associated with Shorter Progression-Free Survival after Autologous Transplants for Multiple Myeloma." Blood 134, Supplement_1 (2019): 515. http://dx.doi.org/10.1182/blood-2019-127335.

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Multiple Myeloma (MM) remains a cancer of terminally-differentiated plasma cells that reside predominantly within the bone marrow. Malignant plasma cells are nurtured by a permissive microenvironment that favors tumor progression, drug resistance and disease relapse. Recurrent somatic mutations in hematopoietic stem cells, the source of major components in bone marrow niche, lead to age-associated clonal hematopoiesis of indetermined potential (CHIP) and has been associated with inferior survivals among individuals without malignant hematologic disorders. It is possible that these mutations in

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Aguilar, Jeff Justin, Vikram Dhillon, Sandhya Dhiman, et al. "Racial Disparities in Clonal Hematopoiesis Among Solid Cancer Patients with Cardiovascular Diseases." Blood 144, Supplement 1 (2024): 5636. https://doi.org/10.1182/blood-2024-204416.

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Introduction Clonal hematopoiesis of indeterminate potential (CHIP) is associated with an increased risk of cardiovascular disease, higher all-cause mortality, and elevated likelihood of developing hematological malignancies. Prior studies reported CHIP at a higher prevalence in solid cancer patients (~25-30%), possibly due to increased exposure to mutagenic/epigenetic stressors inherent in this population, common risk factors shared between solid cancers and CHIP or the oncogenic therapies they receive. Environmental factors may influence the epigenetic landscape, impacting the progression of

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Ignatieva, E. V., and E. A. Matrosova. "Disease-associated genetic variants in the regulatory regions of human genes: mechanisms of action on transcription and genomic resources for dissecting these mechanisms." Vavilov Journal of Genetics and Breeding 25, no. 1 (2021): 18–29. http://dx.doi.org/10.18699/vj21.003.

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Whole genome and whole exome sequencing technologies play a very important role in the studies of the genetic aspects of the pathogenesis of various diseases. The ample use of genome-wide and exome-wide association study methodology (GWAS and EWAS) made it possible to identify a large number of genetic variants associated with diseases. This information is accumulated in the databases like GWAS central, GWAS catalog, OMIM, ClinVar, etc. Most of the variants identified by the GWAS technique are located in the noncoding regions of the human genome. According to the ENCODE project, the fraction o

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Selionova, M. I., L. V. Evstaf’eva, E. N. Konovalova, and E. V. Belaya. "Marker-assisted and Genomic Selection of Beef Cattle." Timiryazev Biological Journal, no. 2 (August 10, 2023): 37–48. http://dx.doi.org/10.26897/2949-4710-2023-2-37-48.

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This article provides an overview of modern genetic technologies for improving production traits and predicting breeding value in beef cattle. In particular, in marker-assisted selection the most promising is the selectionby desirable genotypes in the genes of myostatin (MSTN), calpain (CAPN), calpastatin (CAST), growth hormone (GH), leptin (LEP), thyroglobulin (TG), fatty acid binding protein (FABP), retinoic acid C-receptor (RORC), diacyl-glycerol acyltransferase (DGATI), sterol-Co desaturase (SCD). A modern and much more advanced approach is the Single Step Genomic Best Linear Unbiased Pred

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Boddicker, Nicholas J., Daniel R. O'Brien, Esteban Braggio, et al. "Clonal Hematopoiesis of Indeterminate Potential (CHIP) and Chronic Lymphocytic Leukemia (CLL) Driver Genes: Risk of CLL and Monoclonal B-Cell Lymphocytosis (MBL)." Blood 132, Supplement 1 (2018): 3116. http://dx.doi.org/10.1182/blood-2018-99-117044.

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Abstract Clonal hematopoiesis of indeterminate potential (CHIP) is defined as somatic mutations in clonal blood cells of individuals without any other hematological abnormalities and have been identified using whole exome sequencing (WES) from pre-specified genes. CHIP is reportedly associated with aging, reduced overall survival, cardiovascular disease, and hematologic disease, mainly myeloid cancers. Additionally, whole genome sequencing and WES studies in CLL cases have identified putative CLL driver genes with recurrent somatic variants or copy number alterations. Here, we investigate the

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Cole, John W., Taiwo Adigun, Rufus Akinyemi, et al. "The copy number variation and stroke (CaNVAS) risk and outcome study." PLOS ONE 16, no. 4 (2021): e0248791. http://dx.doi.org/10.1371/journal.pone.0248791.

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Background and purpose The role of copy number variation (CNV) variation in stroke susceptibility and outcome has yet to be explored. The Copy Number Variation and Stroke (CaNVAS) Risk and Outcome study addresses this knowledge gap. Methods Over 24,500 well-phenotyped IS cases, including IS subtypes, and over 43,500 controls have been identified, all with readily available genotyping on GWAS and exome arrays, with case measures of stroke outcome. To evaluate CNV-associated stroke risk and stroke outcome it is planned to: 1) perform Risk Discovery using several analytic approaches to identify C

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Asare, Amma, Sara Corvigno, Jun Yao, et al. "Abstract 5070: Landscape of clonal hematopoiesis prior to PARP inhibitor treatment in patients with ovarian cancer." Cancer Research 84, no. 6_Supplement (2024): 5070. http://dx.doi.org/10.1158/1538-7445.am2024-5070.

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Abstract Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) are an important tool for treatment of ovarian and other cancers, particularly for those with mutations in BRCA1 or 2 genes or homologous recombination deficiency. The risk of developing secondary hematologic malignancy, particularly myelodysplastic syndrome or acute myeloid leukemia (MDS/AML), is substantially higher (4-12%) after PARPi maintenance or treatment in the second line and beyond in patients with ovarian cancer. This elevated risk necessitates additional investigation into the pathogenesis of PARPi-related seconda

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Clay, Alyssa I., Theresa Hahn, Qianqian Zhu, et al. "Exome Array Analyses Identify Low-Frequency Germline Variants Associated with Increased Risk of AML in a HLA-Matched Unrelated Donor Blood and Marrow Transplant Population." Blood 128, no. 22 (2016): 42. http://dx.doi.org/10.1182/blood.v128.22.42.42.

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Abstract Both genome wide association studies (GWAS) of common variation and exome wide association studies (EXWAS) of rare variation have successfully identified disease susceptibility variants for a variety of diseases. One GWAS of inherited susceptibility to Acute Myeloid Leukemia (AML) has been conducted, but no EXWAS have been performed to measure risk of AML attributable to low-frequency constitutional genetic variation. We performed the first EXWAS of risk of AML as a nested case-control study in the DISCOVeRY-BMT (Determining the Influence of Susceptibility Conveying Variants Related t

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Melroy-Greif, Whitney E., Ian R. Gizer, Kirk C. Wilhelmsen, and Cindy L. Ehlers. "Genetic Influences on Evening Preference Overlap with Those for Bipolar Disorder in a Sample of Mexican Americans and American Indians." Twin Research and Human Genetics 20, no. 6 (2017): 499–510. http://dx.doi.org/10.1017/thg.2017.62.

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Diurnal preference (e.g., being an owl or lark) has been associated with several psychiatric disorders including bipolar disorder (BP), major depressive disorder, and substance use disorders. Previous large-scale genome-wide association studies (GWAS) aimed at identifying genetic influences on diurnal preference have exclusively included subjects of European ancestry. This study examined the genetic architecture of diurnal preference in two minority samples: a young adult sample of Mexican Americans (MAs), and a family-based sample of American Indians (AIs). Typed or imputed variants from exom

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Ravi, Arvind, Justin Gainor, Monica Arniella, et al. "Abstract 3580: Integrative genomics of checkpoint blockade response in advanced non-small cell lung cancer." Cancer Research 82, no. 12_Supplement (2022): 3580. http://dx.doi.org/10.1158/1538-7445.am2022-3580.

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Abstract The introduction of checkpoint blockade therapy, specifically anti-PD-1/PD-L1 agents, has transformed the treatment landscape of advanced Non-Small Cell Lung Cancer (NSCLC). While our understanding of the biology underlying immunotherapy in NSCLC is still incomplete, studies to date have established central roles for Tumor Mutation Burden (TMB) and PD-L1 Tumor Proportion Score (PDL1-TPS). In order to expand our understanding of the molecular features underlying response in NSCLC, we describe here the first joint analysis of the Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort, a c

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Zhang, Na, Rongbin Zheng, and Myles Brown. "Abstract 3894: The role of ELF3 in acquired resistance to endocrine therapy in ER-positive breast cancer." Cancer Research 83, no. 7_Supplement (2023): 3894. http://dx.doi.org/10.1158/1538-7445.am2023-3894.

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Abstract Endocrine therapies targeting the estrogen receptor (ER) are the major treatments of ER+ breast cancer, however acquired resistance to endocrine therapy is almost unavoidable and is the main cause of death with breast cancer. The only FDA-approved selective estrogen receptor degrader (SERD) fulvestrant has been used in the second line treatment to overcome aromatase inhibitor- or tamoxifen-resistance. However, fulvestrant has poor pharmacokinetic properties, which has inspired the development of a new generation of oral SERDs including amcenestrant and giredestrant. To understand the

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Ko, Jihoon, Sujin Hyung, Minae An, Noo Li Jeon, and Jeeyun Lee. "Abstract 3206: Three-dimensional tumor angiogenesis mapping in metastatic gastric cancer patients." Cancer Research 82, no. 12_Supplement (2022): 3206. http://dx.doi.org/10.1158/1538-7445.am2022-3206.

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Abstract Background: Patients with gastric cancer (GC) develop malignant ascites as the disease progresses due to peritoneal metastasis. The presence of malignant ascites is a critical prognostic sign of tumor progression. With an understanding of these patient subsets, better optimized treatment strategies are needed. Method: We analyzed whole exome and transcriptome sequences of ascites or primary tumor samples obtained from 46 patients with advanced gastric cancer. In addition, we engineered a microfluidic-based gastric cancer patient-on-a-chip (GRASP) to develop a tumor-induced patient-spe

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Birla, Bhagyashree S., Andrea O'Hara, Elizabeth Louie, et al. "Abstract 6611: Harnessing the power of multiomics from a single sample to explore tumor heterogeneity and advancing immuno-oncology research." Cancer Research 83, no. 7_Supplement (2023): 6611. http://dx.doi.org/10.1158/1538-7445.am2023-6611.

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Abstract The omics era has greatly expanded the repertoire of approaches available for researchers and clinicians to unravel the complexity behind cancer onset in humans: Next Generation Sequencing (NGS) approaches can characterize genomes, epigenomes, transcriptomes and proteomes of patient samples. Advanced DNA barcoding and automated microfluidics can take this to the next level, enabling multiomic characterization of single cells. Peripheral blood mononuclear cells (PBMCs) offer a window into the immune system that, when combined with these omics tools, can provide an insight into immune c

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Karol, Seth E., Wenjian Yang, Leonard A. Mattano, et al. "Genetic Risk Factors for the Development of Osteonecrosis in Children Under Age 10 Treated for Acute Lymphoblastic Leukemia." Blood 126, no. 23 (2015): 250. http://dx.doi.org/10.1182/blood.v126.23.250.250.

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Abstract Background: Therapy induced osteonecrosis has become a limiting toxicity in the intensification of treatment for pediatric acute lymphoblastic leukemia (ALL), particularly among patients 10 to 20 years of age. Prior studies on the genetic determinants of osteonecrosis have focused primarily on patients older than 10 years, leaving the genetic risk factors for the larger group of children with ALL less than 10 years old incompletely understood. It is hypothesized that genetic risk factors may account for a greater proportion of risk of osteonecrosis or involve differing mechanisms in y

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Shea, Patrick R., David B. Goldstein, Veerendra Munugalavadla, et al. "Genome-Wide Association Study of the Human Genetic Factors Influencing the Risk of Adverse Events during Idelalislib Therapy in Patients with Relapsed Indolent Lymphoma." Blood 128, no. 22 (2016): 5284. http://dx.doi.org/10.1182/blood.v128.22.5284.5284.

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Abstract Introduction: Idelalisib (IDELA) is a selective inhibitor of PI3Kδ that has demonstrated efficacy in indolent lymphoma. In the NCT01659021 (101-09) study in patients (pts) with previously treated iNHL, the ORR was 57%. However, in this heavily-treated and refractory population, 27.2% (34/125 pts) discontinued the study due to reported ≥ grade 3 adverse events (AEs). This analysis aims to investigate an underlying genetic molecular mechanism(s) that may contribute to IDELA associated AEs. Methods: We performed a genome-wide association study (GWAS) to determine if common genetic factor

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Yudina, Anastasiya, Alexey Efremov, Danielle Sookiasian, et al. "Abstract 1042: Analytical validation of a liquid biopsy test using cell-free circulating tumor DNA for mutational profiling." Cancer Research 83, no. 7_Supplement (2023): 1042. http://dx.doi.org/10.1158/1538-7445.am2023-1042.

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Abstract Minimally invasive next-generation sequencing-based (NGS) liquid biopsy (LB) tests using cell-free DNA (cfDNA) are increasingly becoming an important tool for the clinical management of cancer patients. The ability to accurately detect molecular alterations from a single plasma sample is valuable for biomarker discovery, diagnostics, and disease monitoring. However, challenges for this assay include low concentrations of circulating tumor DNA (ctDNA) within the cfDNA plasma fraction and PCR and sequencing errors, which can lead to decreased sensitivity in variant calling. Further, som

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Nylén, Miro, Svetlana Vakkilainen, Emil Hiitola, et al. "Clonal Hematopoiesis in Cartilage-Hair Hypoplasia." Blood 142, Supplement 1 (2023): 5667. http://dx.doi.org/10.1182/blood-2023-174194.

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Background: Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder characterized by short stature, hypotrichosis, combined immunodeficiency, and macrocytic anemia. CHH is caused by germline mutations in the RMRP gene encoding the RNA component of the mitochondrial RNA processing endoribonuclease. CHH is heavily enriched in the Finnish (1 in 23000 births) and the Amish (1 in 1340 births) populations. Transient macrocytic anemia is common in children with CHH, whereas severe hypoplastic macrocytic anemia is only present in 10% of pediatric CHH patients and can be treated with allogen

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Park, Tae-Joon, Lyong Heo, Sanghoon Moon, et al. "Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population." International Journal of Genomics 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/421715.

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Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clusterin

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Pissinis, Jeronimo I., Oliver Mazariegos, Marcin Pilarczyk, et al. "Abstract 1081: Sylvester Data Portal: Streamlined access to standardized clinicogenomic data." Cancer Research 85, no. 8_Supplement_1 (2025): 1081. https://doi.org/10.1158/1538-7445.am2025-1081.

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The Sylvester Data Portal (SDP), developed at the University of Miami (UM) Sylvester Comprehensive Cancer Center, is an advanced multi-omics platform that streamlines the management of real-world and research data. SDP facilitates the standardization and integration of data from major genomic profiling vendors, including Caris Life Sciences, Foundation Medicine, and NeoGenomics. SDP utilizes an event-driven ETL pipeline to process, validate, and standardize genomic reports (XML, PDF) and files (FASTQ, BAM, VCF, TSV) from Whole Exome Sequencing (WES), Targeted Sequencing (TS), and Whole Transcr

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Garrett, Melanie E., Karen L. Soldano, Blair R. Anderson, et al. "Genome-Wide Association Study of Glomerular Filtration Rate in a Cohort of Sickle Cell Disease Patients." Blood 124, no. 21 (2014): 1381. http://dx.doi.org/10.1182/blood.v124.21.1381.1381.

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Abstract BACKGROUND: Nephropathy is a common and devastating complication of sickle cell disease (SCD) associated with mortality (Elmariah et al, 2014). However, early detection of SCD nephropathy (SCDN) has proven difficult. Discovery of genetic markers associated with SCDN could greatly improve our ability to identify patients at risk for renal decline. To that end, we have performed a genome-wide association study (GWAS) of glomerular filtration rate (GFR) in our adult SCD cohort. METHODS: Medical history, laboratory values and DNA for genotyping were collected as part of a multicenter stud

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Naranbhai, Vivek, Arvind Ravi, Matthew Hellmann, et al. "Abstract 3468: Immunoproteasome expression and checkpoint blockade response in advanced non-small cell lung cancer." Cancer Research 83, no. 7_Supplement (2023): 3468. http://dx.doi.org/10.1158/1538-7445.am2023-3468.

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Abstract Responders to checkpoint blockade in Non Small Cell Lung Cancer (NSCLC) often feature an inflamed microenvironment prior to therapy. However, the complete set of molecular drivers connecting this histologic observation to enhanced tumor clearance remain enigmatic. In updated analysis of the Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort - a collection of 393 patients with whole exome and/or RNA sequencing along with matched checkpoint blockade response annotation - we identify a prominent predictive role for inducible components of the immunoproteasome, a non-canonical peptide p

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Nittu, Satyavardhan Rao, Richard J. Marrero, Xueyuan Cao, et al. "Genome-Wide Association Study Identifies Variants Predictive of Febrile Neutropenia during Induction I in Newly Diagnosed Pediatric Acute Myeloid Leukemia Patients." Blood 144, Supplement 1 (2024): 6110. https://doi.org/10.1182/blood-2024-208130.

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Background: Febrile neutropenia (FN) is common in acute myeloid leukemia (AML) patients and can significantly impact their morbidity and mortality. The incidence of infectious complications in patients with severe FN is notably high, with a significant proportion of patients experiencing grade 3 or more toxicity (PMID: 38961525). One of the most severe complications is bloodstream infections (), which can lead to severe sepsis and significantly contribute to treatment-related mortality (TRM) specifically in patients with severe FN (≥ grade 3). Following induction chemotherapy, which often incl

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Edwards, T. L., K. E. Hartmann, and D. R. Velez Edwards. "Exome chip evaluation of genetic variants for association with uterine fibroids." Fertility and Sterility 102, no. 3 (2014): e88. http://dx.doi.org/10.1016/j.fertnstert.2014.07.297.

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Darabi, Sourat, Joanne Xiu, Daniel Magee, et al. "Capicua (CIC) mutations in gliomas in association with MAPK activation for exposing a potential therapeutic target." Journal of Clinical Oncology 40, no. 16_suppl (2022): 2056. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.2056.

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2056 Background: Capicua (CIC) Gene is a tumor suppressor, transcriptional repressor, and a member of the high mobility (HMG)-box protein family. CIC is a negative regulator of MAPK and RTK pathways; inactivating CIC mutations (mut) occur in approximately 40% of oligodendrogliomas (OLIG) and less frequently in other gliomas putatively activating downstream signaling. With a goal to identify potential novel treatment options for various gliomas, we explored key signaling pathways associated with CIC mut. Methods: Consecutive glioma tumors were analyzed using Next-Gen DNA sequencing (NextSeq, 59

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Darabi, Sourat, Joanne Xiu, Daniel Magee, et al. "Capicua (CIC) mutations in gliomas in association with MAPK activation for exposing a potential therapeutic target." Journal of Clinical Oncology 40, no. 16_suppl (2022): 2056. http://dx.doi.org/10.1200/jco.2022.40.16_suppl.2056.

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2056 Background: Capicua (CIC) Gene is a tumor suppressor, transcriptional repressor, and a member of the high mobility (HMG)-box protein family. CIC is a negative regulator of MAPK and RTK pathways; inactivating CIC mutations (mut) occur in approximately 40% of oligodendrogliomas (OLIG) and less frequently in other gliomas putatively activating downstream signaling. With a goal to identify potential novel treatment options for various gliomas, we explored key signaling pathways associated with CIC mut. Methods: Consecutive glioma tumors were analyzed using Next-Gen DNA sequencing (NextSeq, 59

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Bergom, Hannah E., Abderrahman Day, Ashraf Shabaneh, et al. "ALAN as an omic tool to build gene signatures and to stratify patients." Journal of Clinical Oncology 41, no. 16_suppl (2023): 1563. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.1563.

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1563 Background: Understanding aberrant gene behavior is critical towards devising clinical therapeutics or gene based diagnostic panels. Clustering and AI/ML have clinical utility, but they do not contextualize changes in gene behavior that result from differences in cell type, microenvironment, or prior treatments. Here, we developed the Algorithm for Linking Activity Networks (ALAN), an informatics algorithm that allows rapid functional comparisons of all detectable genes between clinically annotated patient cohorts. ALAN outputs quantify gene behavior without any additional inputs and can

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Uribe, Laura Reyes, Charles M. Bowen, Kyera Evans, et al. "Abstract 721: Epigenetic intervention in the prevention of Lynch Syndrome Colorectal Cancer." Cancer Research 82, no. 12_Supplement (2022): 721. http://dx.doi.org/10.1158/1538-7445.am2022-721.

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Abstract Introduction: Lynch Syndrome (LS) is the most common cause of hereditary colorectal cancer (CRC) affecting &gt;1 million Americans. LS is caused by germline mutations in one of four DNA mismatch repair (MMR) genes, generating several hundreds of mutations in microsatellite coding sequences. Although defects in the MMR machinery are the principal mechanism driving LS carcinogenesis, the role of the epigenome through histone and DNA methylation remains unexplored. Hypermethylation of MLH1 is detected in 15% of sporadic MMR-deficient CRC and also in LSCRC, indicating a pivotal role o

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Parsons, Heather A., Conor Messer, Katheryn Santos, et al. "Abstract 3874: Genomic mechanisms of resistance to tyrosine kinase inhibitors (TKIs) in HER2+ metastatic breast cancer (HER2+ MBC)." Cancer Research 83, no. 7_Supplement (2023): 3874. http://dx.doi.org/10.1158/1538-7445.am2023-3874.

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Abstract Background. Despite substantial progress in the treatment of HER2+ MBC, most patients (pts) still experience disease progression and cancer-related death. HER2-directed TKIs are highly effective therapies for pts with HER2+ MBC; however, an understanding of resistance mechanisms is needed. Pts receiving HER2-directed TKIs with cell-free DNA (cfDNA) sampling across the treatment spectrum present a unique opportunity to examine genomic alterations. Methods. Pts with biopsy-proven HER2+ MBC were selected from DF/HCC approved protocols for ultra-low pass whole genome sequencing if ≥1 cfDN

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