Search Results - EGA European Genome-Phenome Archive

Genomic and Transcriptomic Markers Associated with Response to Immune Checkpoint Blockade

The neoantigen presentation score (NEOPS) study was designed to better understand molecular determinants of response to immunotherapies, including pembrolizumab and nivolumab in stage III or IV melanoma patients. From this work, we developed a composite approach to predicting neoantigens (NEOPS), which takes into account additional escape mechanisms, including HLA LOH (human leukocyte antigen loss of heterozygosity) and the impact of deleterious mutations to the antigen presentation machinery (APM), yielding an improved prediction of response to immunotherapy compared to TMB (tumor mutational burden) or neoantigen burden alone.

Study phs002388

Discovery of Novel Melanoma Predisposing Mutations by Exome Sequencing

Melanoma risk shows clear heritability, but the inherited genetic factors remain largely unknown. Rare high risk mutations in CDKN2A, CDK4, BAP1 and TERT have been described but these variants, in aggregate, account for less than 50% of the kindreds reporting a family history of melanoma. This project will seek to identify new genes which may confer melanoma susceptibility. Identifying melanoma predisposing mutations can provide new biological insights and may impact important clinical decision making regarding treatment, surveillance and preventive approaches. Hereditary melanoma patients (defined as those individuals with multiple primary melanomas and those patients with a family history of melanoma) were collected from melanoma clinics at the Massachusetts General Hospital in Boston and the A. Sygrous Hospital in Athens, Greece. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

Study phs000823

Identification of Targetable FGFR Gene Fusions in Diverse Cancers

In this study, patients with advanced cancer across all histologies were enrolled in our IRB approved clinical sequencing program, called MI-ONCOSEQ, to go through an integrative sequencing which includes whole exome sequencing of the tumor and matched normal, and transcriptome sequencing. Four index cases were identified which harbor gene rearrangements of FGFR2 including two cholangiocarcinoma cases, a metastatic breast cancer case, and a metastatic prostate cancer case. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, including TCGA, we identified FGFR gene fusions with intact kinase domains of FGFR1, FGFR2, or FGFR3 in cholangiocarcinoma, breast cancer, prostate cancer, lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins in vitro induced cell proliferation, and bladder cancer cell lines that harbors FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.

Study phs000602

Somatic Mutational Analysis by Exome Sequencing Endometrial Carcinosarcomas

The purpose of this study was to identify somatic (tumor-specific) mutations in endometrial carcinosarcoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 14 de-identified primary tumor DNAs and matched non-tumor DNAs.

Study phs001152

Single Cell Genomic Analysis of Lymphoma

Our study aimed to define the extent of heterogeneity between anatomically separated tumor manifestations in follicular lymphoma at single-cell resolution. We subjected single-cell suspensions derived from nodal, synchronously-acquired fine needle aspirations from two distinct tumor sites to high-throughput microfluidics-based single-cell RNA sequencing. By comparing the relative composition of the tumor subpopulations between the two tumor sites, we found that some patients can exhibit site-to-site differences. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper cell abundance. Our study demonstrates the significant limitations of a solitary biopsy in defining the full scope of a patient's disease.

Study phs002188

DNA Methylation Characterization of Fusion-Positive and Fusion-Negative Rhabdomyosarcoma

Rhabdomyosacoma (RMS) is a common pediatric soft tissue tumor that is associated with the skeletal muscle lineage. RMS comprises two major subtypes: fusion-positive (FP, most commonly PAX3- FOXO1 or PAX7-FOXO1) and fusion-negative (FN, frequently associated with mutations in RAS pathway). Our previous study demonstrated that FP and FN tumors exhibit distinct DNA methylation profiles. In this study, further investigation of genome-wide DNA methylation profiles in RMS tumors revealed DNA methylation differences between AX3-FOXO1 and PAX7-FOXO1 subsets in FP RMS, and between RAS mutation and RAS wild-type subsets in FN RMS. These data provide new insight into the relationship of DNA methylation with mutational changes and transcriptional organization in FP and FN RMS.

Study phs001970

High-Risk Breast Cancer GWAS

The GWAS includes High Risk Women from the following epidemiological studies of breast cancer, comprising a total of 3,719 cases and 3,642 controls (cases/controls: MEC, 0/200; ABCFR, 326/418; FCCC, 56/3; BCFR-UT, 66/32; CNIO-BC, 87/92; GESBC, 65/0; LIFE, 164/0; MARIE, 41/105; MAYO, 208/210; MNYR, 293/409; MSKCC, 310/0; NC-BCFR, 234/233; OFBCR, 553/560; POSH, 377/0; HBOC, 47/47; BBCS, 612/1333; UPENN, 280/0 This study was funded by a grant CA165038 to Christopher Haiman (University of Southern California) and John Hopper (University of Melbourne) from the National Cancer Institute, National Institute of Health. The contributing studies: Multiethnic Cohort (MEC). This study was supported by grant UM1 CA164973 from the National Cancer Institute, National Institute of Health. Ontario Familial Breast Cancer Registry, the Ontario site of the Breast Cancer Family Registry Cohort (OFBCR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Utah Breast Cancer Family Registry (BCFR-UT). This study was supported by grant UM1 CA164920 from the National Cancer Institute. New York site of the Breast Cancer Family Registry (MNYR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Northern California site of the Breast Cancer Family Registry (NC-BCFR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Australian Breast Cancer Family Registry (ABCFR). This study was supported by grant UM1 CA164920 from the National Cancer Institute. Breast Cancer Study (CNIO-BC). This study has been partially funded by The Spanish Network on Rare Diseases (CIBERER) and the Spanish National Genotyping Center (CEGEN). Genetic Epidemiologic Study of Breast Cancer (GESBC). The GESBC was supported by the Deutsche Krebshilfe e. V. [70492] and German Cancer Research Center (DKFZ). Mammary Carcinoma Risk Factor Study (MARIE). This study was supported by the Deutsche Krebshilfe e.V. [70-2892-BR I, 106332, 108253, 108419], the Hamburg Cancer Society, the German Cancer Research Center (DKFZ) and the Federal Ministry of Education and Research (BMBF) Germany [01KH0402]. Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH). Funding for the POSH study was provided by Cancer Research UK (grant refs A7572, A11699, C22524), the Breast Cancer Campaign (grant number: 2013MayPR044) and from 2003-2006 by a grant from The Wessex Cancer Trust. Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH). Funding for the POSH study was provided by Cancer Research UK (grant refs A7572, A11699, C22524), the Breast Cancer Campaign (grant number: 2013MayPR044) and from 2003-2006 by a grant from The Wessex Cancer Trust. Hereditary Breast and ovarian Cancer: Genetic and Molecular Studies (HBOC). This study was supported by National Cancer Institute grant CA58860 and The Lon V Smith Foundation: LVSF-44528. Mayo Clinic inherited breast and ovarian cancer study (MAYO). This study was supported by the Breast Cancer Research Foundation, NIH grants CA192393, CA176785, and an NIH CA116201 Specialized Program of Research Excellence (SPORE) in Breast Cancer. British Breast Cancer Study (BBCS); Mammographic oestrogens and growth factor study (MOG). The BBCS and the MOG study are funded by Cancer Research UK and Breakthrough Breast Cancer and acknowledge NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN). Genotyping of non-BRCA1/2 mutation carriers (UPENN). The study is supported by the Basser Research Center at the University of Pennsylvania, Rooney Family Foundation, NIH grants CA176785 and CA192393, the Breast Cancer Research Foundation, the Susan G. Komen Foundation for the Cure and Macdonald Family Foundation. Clinical Significance of Germline BRCA Mutations (MSKCC). The study is supported by the Robert and Kate Niehaus Clinical Cancer Genetics Research Initiative, The Breast Cancer Research Foundation, and the Cancer Center Support Grant from the National Institute of Health, National Cancer Institute 5P30 CA08748-40. Women's Learning the Influence of Family and Environment (LIFE). This study was supported by grants CA17054 and CA74847 from the National Cancer Institute, National Institutes of Health, No. 4PB-0092 from the California Breast Cancer Research Program of the University of California. Philadelphia site of the Breast Cancer Family Registry at Fox Chase Cancer Center (FCCC). This study is supported by NIH grant CA164920.

Study phs000929

Single-cell RNA-Seq of human lymphoma reveals malignant B cell diversity and patterns of T cell immune checkpoint co-expression

Follicular lymphoma (FL) is a generally incurable B-cell malignancy which has the potential to transform into highly aggressive lymphomas. Genomic studies indicate it is often a small subpopulation rather than the dominant population in the FL that gives rise to the more aggressive subtype. To resolve the underlying transcriptional networks of follicular B-cell lymphomas at single molecule and cell resolution, we leveraged droplet-based barcoding technology for highly parallel single cell RNA-Seq. We analyzed the transcriptomes from tens of thousands of cells derived from five primary FL tumors. Simultaneously, we conducted multi-dimensional flow cell sorting to validate our characterizing of cellular lineages and critical expressed proteins. For each tumor, we identified multiple cellular subpopulations, matching known hematopoietic lineages. Comparison of gene expression by matched malignant and normal B cells from the same patient revealed tumor-specific features. Malignant B cells exhibited restricted immunoglobulin light chain expression (either Ig Kappa or Ig Lambda), as well the expected upregulation of the BCL2 gene, but also down-regulation of the FCER2, CD52 and MHC class II genes. By leveraging the single-cell resolution on large numbers of cells per patient, we were able to examine tumor-resident T cells. We identified pairs of immune checkpoint molecules that were co-expressed, providing a potentially useful strategy for selection of patient-tailored combination immunotherapies. In summary, massively parallel measurement of single-cell expression in thousands of tumor cells and tumor-resident lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development.

Study phs001378

Germline Sequencing for Aggressive Prostate Carcinoma

This study aims to elucidate the genetic determinants of susceptibility to aggressive prostate carcinoma. To this end, germ line whole exome sequence has been generated from patients with aggressive prostate cancer. Whole genome sequence for a representative subset of tumors from patients whose cancer was resistant to primary therapy is included as well. This deep genomic interrogation will allow the identification of rare, functionally disruptive variants that may play a role in disease progession and response to treatment.

Study phs000661

Aspirin and Inflammation: Mutations, Genes, Pathways and Prevention in Barrett's Esophagus

Background: Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett's esophagus (BE) and to lower the incidence and mortality of esophageal adenocarcinoma (EA). The esophagus is exposed to both intrinsic and extrinsic mutagens resulting from gastric reflux, chronic inflammation and exposure to environmental carcinogens such as those found in cigarettes. Here we test the hypothesis that NSAID use inhibits accumulation of point mutations/indels during somatic genomic evolution in BE. Methods: Whole exome sequences were generated from 82 purified epithelial biopsies and paired blood samples from a cross-sectional study of 41 NSAID users and 41 nonusers matched by sex, age, smoking, and continuous time using or not using NSAIDs. Results: NSAID use reduced overall frequency of point mutations across the spectrum of mutation types, lowered the frequency of mutations even when adjusted for both TP53 mutation and smoking status, and decreased the prevalence of clones with high variant allele frequency. Never smokers who consistently used NSAIDs had fewer point mutations in signature 17, which is commonly found in EA. NSAID users had on average a 50% reduction in functional gene mutations in nine cancer-associated pathways and also had less diversity in pathway mutational burden compared to nonusers. Conclusions: These results indicate NSAID use functions to limit overall mutations on which selection can act and supports a model in which specific mutant cell populations survive or expand better in the absence of NSAIDs. Galipeau PC, et al. Genome Med. 2018 Feb 27;10(1):17. PMID: 29486792.

Study phs001654

Transcriptomic Profiling of Oropharyngeal Squamous Cell Carcinoma

The study is a retrospective transcriptomic profiling of oropharyngeal squamous cell carcinoma. The pathologic database was queried for squamous cell carcinoma tumors originating from the anatomic oropharynx (tonsil or tongue base) with available samples from surgical archives. This retrospective RNA sequencing cohort included cases dating prior to the routine implementation of p16 immunohistochemistry (IHC) testing at our institution, therefore, p16 status was not required for inclusion in this study. Formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center (LCCC) Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer's protocol (Promega 9FB167). After a pathology review of a hematoxylin and eosin (H&E) stained slides to identify tumor area, RNA was extracted from unstained slides using macrodissection. Total RNA quality was measured using a NanoDrop spectrophotometer (Thermo Scientific ND-2000C) and a TapeStation 4200 (Agilent G2991AA). Total RNA concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies Q33216). Libraries were prepared with Illumina TruSeq Stranded Total RNA with Ribo-Zero protocol. Libraries were sequenced on an Illumina HiSeq2500 sequencer. Paired end read data, with read lengths of 75 were collected.

Study phs002935

Integrative Analysis of Lung Adenocarcinoma in EAGLE (Version 2)

We performed a comprehensive analysis of intratumor heterogeneity of somatic mutations in cancer driver genes, copy number aberrations and DNA methylation in 292 tumor samples from 84 lung adenocarcinoma (LUAD) patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. SNVs of 37 established lung cancer driver genes were profiled by deep target sequencing in 180 tumor samples and 55 blood samples and 1 buccal sample from 56 subjects. Somatic copy number alterations were profiled using SNP arrays in 268 tumor samples from 80 subjects. DNA methylation levels were profiled with methylation arrays in 205 tumor samples and 74 normal tissue samples from 68 subjects.

Study phs001169

Functional Multiomics of Cellular Therapy and Immune Checkpoint Blockade Therapy for Solid Tumors

Tumor samples were collected from a patient with synovial sarcoma, which acquired resistance to ACT targeting NY-ESO-1. Biopsies (n=3; primary, metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Bulk tumor whole exome and RNA sequencing corresponding to all three tumor specimens and whole exome sequencing from patient-matched normal blood are made available through this accession.

Study phs002762

Rare germline sequence variants, copy number variations, expression alterations, methylation variations and disease susceptibility in familial melanoma

Although a number of high-risk melanoma genes have been identified, they account for melanoma risk in less than 40% of melanoma-prone families. The major goals of our research are to identify novel high-penetrance genes for familial melanoma in melanoma-prone families without known mutations and to identify modifier factors, including genetic and epigenetic, in melanoma-prone families with and without known major mutations. We are using whole exome sequencing to identify additional high-risk susceptibility genes and using targeted sequencing to follow up on the top genes in additional family members and in population-based melanoma cases and controls. We are also using RNASeq to investigate genome-wide allele-specific expression and eQTLs in these families to identify genes with expression alteration, which will provide additional information for gene discovery. In addition, we also conducted genome-wide copy number variation (CNV), methylation, and miRNA expression profiling analyses in our melanoma families with the goal of identifying genetic and epigenetic factors as disease modifiers.

Study phs001177

Whole-Genome Sequencing Analysis of Extrachromosomal DNA with Amplicon Architect

The study is related to our manuscript entitled "Single-cell genetic heterogeneity linked to immune infiltration in glioblastoma". Using multiplexed FISH analysis of 3-4 tumor cores from 17 glioblastoma formalin-fixed paraffin-embedded (FFPE) tumors, we identified two classes of tumors based on single cell co-occurrence of EGFR and CDK4 amplification. Tumors with a low odds ratio for finding EGFR and CDK4 amplified in the same cell (ORlow tumors) had higher EGFR copy number and higher diversity of copy number in cells harboring EGFR amplification. This suggested that in ORlow tumors EGFR is likely present on extrachromosomal DNA. To test this hypothesis, we performed whole genome sequencing on DNA extracted from FFPE slides from 3 ORlow samples and 3 ORhigh samples and used AmpliconArchitect to investigate the structure of the EGFR amplicon. We found multiple breakpoints and high complexity structure in the 3 tested ORlow samples, but not in the ORhigh samples, supporting the possibility of an extrachromosomal nature of EGFR amplification in the first group.

Study phs003100

The Primary Open-Angle Glaucoma Genes and Environment (GLAUGEN) Study

Background Information: Primary open-angle glaucoma (POAG) is an age-related, intraocular pressure (IOP)-dependent progressive optic neuropathy that ultimately leads to irreversible blindness. Vision loss from POAG is a condition of public health significance. Current evidence suggests that POAG is a polygenetic disease modified by environmental influences. Despite the fact that a positive family history of disease is an important risk factor for POAG, conventional linkage and candidate gene approaches have revealed less than 5% of the genetic component of the disease. Furthermore, there is no consensus on environment risk factors for POAG. Elevated IOP is the only modifiable risk factor for POAG; yet, lowering IOP slows, but does not halt the disease process. Study Objectives: The overall goal of our research is to elucidate the pathogenesis of POAG so that cost-effective disease detection and primary prevention strategies can be implemented. The primary aim of the Glaucoma Gene Environment Initiative (GLAUGEN), funded by the Human Genome Research Institute (NHGRI), is to discover genetic loci associated with POAG. The secondary aim of GLAUGEN, funded by NHGRI and the National Eye Institute, is to discover gene environment interactions in POAG. Methods and study populations: For this study, we have assembled cases and controls from three studies: the Nurses' Health Study (NHS), the Health Professionals Follow-up Study (HPFS) and the Genetic Etiologies of POAG (GEP) project based at Massachusetts Eye and Ear Infirmary (MEEI). This case-control group includes 1057 unrelated cases and 1272 controls. Members of the NHS and HPFS also have repeated environmental exposure data collected prior to a diagnosis of POAG. NHS - The Nurses Health Study started in 1976 under the direction of Dr. Frank E. Speizer. With funding from the NIH, registered nurses from 11 US states were invited to complete a detailed questionnaire regarding lifestyle and health biennially. Initially, 121,000 women responded to the baseline questionnaire. Currently, Dr. Susan Hankinson serves as the program director for the NHS. HPFS - The Health Professionals Follow-up Study began in 1986 under the direction of Drs. Walter Willett and Meir Stampfer. Under the auspices of the NIH, they enlisted 51,529 male health professionals from throughout the US to complete similarly designed biennial questionnaires. Beginning in 1990, questions regarding ocular health were added to biennial questionaires completed by health professionals participating in the NHS and HPFS. This allowed us to formulate (PI: S. Hankinson; NEI) and maintain (PI: L. Pasquale; NEI) a cohort at risk for POAG derived from the respective general cohorts who were under ophthalmic care. We then developed a definition of POAG that allowed us to identify cases from a population that was geographically dispersed. The centerpiece of this definition is the presence of reproducible visual field loss consistent with nerve fiber layer (NFL) dropout (the NFL contains the axons that comprise the optic nerve) on reliable tests. Reproducible visual field loss occurred in the context of anterior segment findings that did not suggest a secondary cause of elevated IOP and posterior segment findings that did not suggest a secondary cause of visual field loss. We selected controls from the cohort at risk for POAG on the basis of age, gender and time period when cases were identified. GEP - The Genetic Etiologies of POAG was initiated in 1996 with funding from the National Eye Institute under the direction of Dr. Janey Wiggs. The purpose of this work was to discover novel genetic loci associated with POAG. In the GEP, cases were derived predominantly from the Glaucoma Service at MEEI. The majority of cases had an examination by a glaucoma specialist and met the definition for POAG used in NHS and HPFS. Cases with only one reliable visual field consistent with NFL dropout were included if there was a cup-disc ratio of 0.7 or more. The majority of controls were patients who presented to the MEEI comprehensive ophthalmology service for routine eye examination or from spouses of MEEI patients with secondary forms of glaucoma. Other controls were identified from regional glaucoma screenings held throughout Massachusetts. Members of GEP have detailed ocular phenotype data but limited information on environmental exposures. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to primary open-angle glaucoma through large-scale genome-wide association studies of three well-characterized cohorts of cases and controls, some in matched pairs. Genotyping was performed at the Broad Institute of MIT and Harvard, a GENEVA genotyping center. Data cleaning and harmonization were performed at the GEI-funded GENEVA Coordinating Center at the University of Washington.

Study phs000308

National Institutes of Health H3Africa African Collaborative Center for Microbiome and Genomics Research (ACCME)

The African Collaborative Center for Microbiome and Genomics Research is a multi-institutional collaborative research project. The objectives of the project are to collaborate and implement high impact integrative epidemiology and genomics research into discovery of biomarkers associated with cervical carcinogenesis. Specifically ACCME links and leverages existing funded research and program activities at the collaborating institutions to study the interaction between vaginal microbiome, host genetic factors and molecular variants of Human Papilloma Virus (HPV) to determine correlates of viral persistence in the causal pathway of cervical cancer, a major cause of preventable mortality in Nigeria and other parts of sub-Saharan Africa. This research offers several opportunities to advance understanding of cervical carcinogenesis, viral oncogenesis, new biomarker discovery and risk stratification by genotype in a cohort of African women. Sponsorship: This project is sponsored by the National Institutes of Health (NIH)

Study phs001945

Molecular Determinants of Tumor Behavior in Early Lung Adenocarcinoma

Lung adenocarcinoma is the leading cause of cancer death worldwide and a heterogeneous disease with poor survival in the advanced stage. Given that the frequency of early diagnosis is increasing, the investigation of the molecular determinants of disease progression is paramount. Prediction of whether the tumor is indolent or aggressive has been the subject of recent investigations. Yet, the molecular underpinnings explaining the difference in tumor behavior remains largely unknown and is directly relevant to the efficacy and cost-effectiveness of lung cancer screening, including the risks of over-diagnosis and overtreatment. To gain insights into the molecular pathogenesis and the underlying molecular determinants of clinical behavior of early adenocarcinoma, we investigated genetic alterations in 102 surgically resected early adenocarcinomas. We hypothesized that the behavior of early adenocarcinoma can be predicted based on genomic underpinnings. To identify the type of genomic alterations associated with resected indolent and aggressive early lung ADC, the DNA samples from 21 adenocarcinoma in situ (AIS), 27 minimally invasive adenocarcinoma (MIA) and 54 fully invasive adenocarcinoma were collected and subjected to a deep next generation sequencing, targeting a custom 347 cancer gene panel. Our study provides new insights into cancer genomic evolution, helps to elucidate the interplay of somatic mutation and the adaptation of clones, and brings new insights into the key distinction between indolent and aggressive tumor behavior.

Study phs001811

Loss of IFN-gamma Signaling in Tumor Cells Associates with Primary Resistance to Anti-CTLA-4 Therapy

Antibody blockade of the inhibitory CTLA-4 pathway has led to clinical benefit in a subset of patients with metastatic melanoma. Anti-CTLA-4 enhances T cell responses, including production of IFN-γ, which is a critical cytokine for host immune responses. However, the role of IFN-γ signaling in tumor cells in the setting of anti-CTLA-4 therapy remains unknown. Here we demonstrate that, based upon exome sequencing data, patients identified as non-responders to anti-CTLA-4 (ipilimumab) harbor a much higher genomic defects in the IFN-γ pathway genes than melanoma patients who had clinical response to ipilimumab therapy.

Study phs001257

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

Cancer-associated fibroblasts (CAFs) are major players in the progression and drug resistance of pancreatic ductal adenocarcinoma (PDAC). CAFs constitute a diverse cell population consisting of several recently described subtypes, although the extent of CAF heterogeneity has remained undefined. Here we employ single-cell RNA-sequencing to thoroughly characterize the neoplastic and tumor microenvironment content of human PDAC tumors. Six human PDAC tumor specimens from six patients were collected, and processed for single-cell RNA-sequencing analysis. Adjacent-normal pancreas tissue was also collected from two of the patients. Tumor samples were digested, and fluorescence-activated cell sorting was used to isolate viable cells. For one tumor sample, viable, CD45-negative, CD31-negative, and EpCAM-negative cells were also isolated to enrich for CAFs. The 10X Chromium platform was then used to isolate single cells for RNA-sequencing analysis. This work has demonstrated the differences in immune cell populations between adjacent-normal and tumor tissues, and identified subpopulations of epithelial cells and CAFs present in PDAC tumors. This high-throughput analysis is a resource to better understand the cell populations present in PDAC, and may ultimately aid in the development of more effective therapies for this deadly malignancy.

Study phs001840

National Cancer Institute Clinical and Laboratory Analysis of Familial Cancer

The purpose of this study is to continue the analysis begun on 09C0079 which was focused on identification of the genetic mutation associated with a new gastric polyposis syndrome, Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS). GAPPS, first described in 2012, is an autosomal dominant gastric polyposis syndrome that confers a substantial risk for gastric adenocarcinoma. The GAPPS phenotype consists of a carpeting of greater than 100 fundic gland polyps (FGPs) in the oxyntic mucosa of the gastric body and fundus, with antral sparing with some FGPs displaying high-grade dysplasia. This is in contrast to sporadic FGPs that are benign, most often are not associated with high-grade dysplasia though low-grade dysplasia has been reported, and are fewer in number. Gastric FGPs have been found to be associated with Familial Adenomatous Polyposis (FAP) and attenuated FAP, which is an autosomal dominant condition associated with germ line mutations in APC which confers a phenotype consisting of multiple (>100) adenomatous polyps in the colon and rectum developing after the first decade of life. FGPs are reported to occur in 12-84% of patients with FAP, whereas sporadic FGPs are identified in ~5% of patients undergoing upper gastrointestinal endoscopy. Gastric adenocarcinoma arising from FGPs in individuals with FAP have been reported. Other manifestations of FAP and AFAP include polyps in the upper gastrointestinal tract, congenital hypertrophy of retinal pigment epithelium, osteomas and epidermoid cysts, supernumerary teeth, desmoid formation, and other malignancies such as thyroid, small bowel cancer, hepatoblastoma, and medulloblastoma. Thus far there are no reports in GAPPS of polyposis arising in the esophagus, gastric antrum, pylorus, small intestine, or colon.

Study phs001935

Clonally selected lines after CRISPR/Cas editing are not isogenic

The CRISPR-Cas9 system has enabled researchers to precisely modify/edit the sequence of a genome. A typical editing experiment consists of two steps: (i) editing cultured cells and (ii) selection of clones, which are presumed to be isogenic, with and without the intended edit. The application of the CRISPR-Cas9 system may result in off-target edits, while cloning would reveal culture-acquired mutations. We analyzed the extent of the former and of the latter by whole genome sequencing (WGS) involving separate genomic loci in three experiments conducted by three independent laboratories. In all experiments we hardly found any off-target edits, while we detected hundreds to thousands of single nucleotide mutations unique to each clone after relatively short culture of 10-20 passages. Notably, clones also differed in copy number alterations that were several kb to several mb in size, representing the largest source of genomic divergence among clones. This study in dbGaP includes data from experiments carried out by investigators at the Oklahoma Medical Research Foundation and Baylor College of Medicine (OMRF/BCM) involving an iPSC line derived from fibroblasts of a female patient (line c7) carrying a constitutional heterozygous variant (chr1:1,464,679 C>T; GRCh37) in exon 15 of the ATPase family, AAA domain containing 3A (ATAD3A) gene. The parental line was edited by introducing a double stranded break at the variant allele to correct the variant by homology directed repair. Two unedited control clones (clone7 and clone8) and one edited clone (SC20) were selected for WGS.

Study phs003110

Melanoma Brain Metastasis Single-Cell RNA Sequencing Atlas

Melanoma brain metastasis (MBM) frequently occurs in patients with advanced melanoma, yet our understanding of the underlying salient biology is rudimentary. Here, we performed single-cell/nucleus RNA-seq in 22 treatment-naive MBM (scRNA-seq n=5; snRNA-seq n=17) and 10 extracranial melanoma metastases (ECM; all snRNA-seq), and matched spatial single-cell transcriptomics (n=16) and T cell receptor (TCR)-seq (n=5). Key observations were validated in matched bulk RNA- and ATAC-seq of isogenic MBM/ECM cell culture models (n=24; including triplicates (labeled as *-A, -B and -C) of 4 MBM- and 4 ECM-derived patient cell lines with 2 matched pairs). This work provides comprehensive insights into MBM biology and serves as a foundational resource for further discovery and therapeutic exploration.

Study phs002944

Genome-wide Association Study and Meta-Analysis of Ewing Sarcoma

We combined a set of 122 French Ewing sarcoma (EWS) cases from the Institut Curie, 19 EWS cases from the National Cancer Institute (NCI) Center for Cancer Research (CCR), and 29 EWS cases from the NCI Bone Disease and Injury Study. All EWS cases were confirmed by medical record review and the presence of a specific EWSR1-ETS translocation were noted when data was available. Each participant provided informed consent and each participating study was approved by the Institutional Review Boards of their study center. DNA was extracted using standard methods from blood, saliva (Oragene), or buccal cells. All de novo genotyping of EWS cases was performed at the NCI CGR on the Illumina OmniExpress-24 v1.1 array. Genotyping was performed according to manufacturer's guidelines using the Infinium HD Assay automated protocol.

Study phs001549

Whole Exome Characterization of Squamous Cell Lung Cancers (Lung SQCC) from Appalachian Kentucky (APPKY)

This is a pilot study of squamous cell lung cancer and matched normal tissue pairs collected (convenience sample) from patients from Central Appalachia, in Southeastern Kentucky. This study performed whole exome sequencing on tumor and matched normal DNA samples from 51 lung squamous cell carcinoma (SQCC) subjects from Appalachian Kentucky (AppKY). Somatic genomic alteration profiles were compared between the AppKY and TCGA SQCC cohorts. We found that IDH1 and PCMTD1 had higher mutation rates in AppKY versus TCGA. These findings suggest population differences in the genetics of lung SQCC between AppKY and US populations that have implications for personalized treatment for this disease.

Study phs001651

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