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• An_exome_sequencing_study_of_the_HIV_elite_long_term_non_progressors_and_rapid_progressors__CASCADE_cohorts_

  Background: A rare subgroup of HIV infected individuals naturally controls infection withouttreatment. These ?elite controllers? constitute an important model for the natural control ofHIV infection. Indeed, the study of these individuals may provide insights into strategies forthe development of HIV vaccines. Although several HLA and chemokine alleles are knownto be over-represented in elite controllers, only a small portion of HIV phenotypic variation isexplained by known genetic variants. The elite controller phenotype is rare and distinct,representing the extreme of an infectious disease trait. As such, this phenotype may be partlyexplained by variation in host immune control, which may be characterized by differences inrare functional genetic variants. Genomic regions underlying elite control can be potentiallyidentified by comparing the presence or frequency of variants in this group to thatrepresenting the opposite extreme. In this context, ?rapid progressors? is a group defined byits rapid immunological and clinical disease progression.Aim: To extend an existing study, in order to identify DNA sequence variants involved in thecontrol of HIV infection with greater statistical resolution. Specifically, we aim to sequence upto 200 exomes from multiple cohort studies within the EuroCoord CASCADE collaboration (acollaboration of 25 HIV seroconversion cohort studies across Europe).

  Study EGAS00001000522

• H3Africa - An integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasis

  The objective of the TrypanoGEN project is to discover genetic variants associated with different responses to sleeping sickness infection. The project was designed in two phases:Phase 1) Variant discovery; 222 samples were sequenced to approximately 10X coverage on an Illumina 2500 with 2x150bp reads, at the University of Liverpool Center for Genomic Research. In addition, 77 samples from Cameroon and Zambia were sequenced to approximately 30X Coverage at Baylor College of Medicine. The sequenced reads were mapped onto the 1000 genomes project human_g1k_v37_decoy reference genome using BWA. The SNP calling on all the samples was done using the genome analysis tool kit GATK v3.4. Samples were selected from seven populations where Trypanosomiasis is endemic: Nilo-Saharan speakers from North-West Uganda and Niger-Congo speakers from South-East Uganda, DRC, Ivory Coast, Guinea, Cameroon and Zambia. The samples included 182 controls, 97 cases, 17 latent infections and 3 suspect cases. Phase 2) Variants discovered in Phase 1 will be used in the development of the H3Africa SNP chip. This chip will then be used in a GWAS study to identify variants associated with trypanosomiasis.

  Study EGAS00001002602

• Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer

  Bevacizumab is an approved anti-angiogenic drug for patients with metastasized colorectal cancer (mCRC) targeting VEGF. The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months and acquired resistance mechanisms are greatly unknown. Using plasma DNA, we studied the evolution of tumor genomes in a cohort of patients with mCRC (n=150) and observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of TCGA data (n=619) suggested an association with later stages, which we confirmed by longitudinal plasma analyses. We defined the minimally amplified region and studied the mechanistic consequences of copy number gain of the involved genes. The amplification of one gene, POLR1D, impacted cell proliferation, resulting in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab. In several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with evolution of therapy resistance. Hence, we describe a novel resistance mechanism against a widely applied treatment in mCRC patients which will impact clinical management

  Study EGAS00001003791

• Genetic Basis of Developmental Disabilities

  Developmental disabilities are birth defects that cause lifelong problems with how a body part or system works. Developmental disabilities include nervous system insults affecting how the brain, spinal cord and nervous system function; they cause intellectual disability, including Down syndrome and fragile X syndrome; and they also cause learning and behavioral disorders, such as autism spectrum disorders. At the Kennedy Krieger Institute, approximately 450 inpatients and 13,000 outpatients are seen per year (involving 114,000 visits). For most of these disorders, the underlying molecular cause has not been identified. Some, such as chromosomal disorders, have a strongly genetic basis while others, such as traumatic brain injury, are caused by environmental insults but are nonetheless influenced by the genetic background. The purpose of the present study is to identify chromosomal abnormalities underlying a variety of developmental disabilities. The approach is to obtain blood and saliva from children, and from one or both biological parents (and in some cases from siblings and/or additional relatives). Genomic DNA is purified and assayed on single nucleotide polymorphism (SNP) microarrays and/or by sequencing, including whole genome sequencing. These technologies provide high resolution information about chromosomal changes, and the information provided by the parental (and other relatives') DNA allows an interpretation of whether changes in a child are inherited or occur de novo. The study design includes multiple data analysis procedures to interpret the biological significance of findings of chromosomal changes relative to a child's parents, relative to children with similar diagnoses, relative to children with other chromosomal anomalies, and (in some cases) relative to the chromosomal status of siblings. We will further interpret the significance of the findings relative to the general (apparently normal) population by obtaining publicly available data from apparently normal individuals.

  Study phs000337

• Systems Analysis of the PfSPZ Vaccine in Kenyan Infants

  The PfSPZ vaccine is a candidate vaccine targeting the Plasmodium falciparum parasite, which is the cause of the most lethal type of human malaria. This study used de-identified blood samples collected from 316 infants aged 5 to 12 months (inclusive) enrolled in a Phase 2, randomized, placebo-controlled trial (NCT02687373) of the PfSPZ malaria vaccine, conducted in a region of western Kenya where malaria transmission is high and perennial. The study began in July, 2016, after peak malaria transmission, and was completed in August, 2018. In this study, three doses of the PfSPZ Vaccine (4.5x105 PfSPZ, 9.0x105 PfSPZ, and 1.8x106 PfSPZ) were tested against a normal saline placebo comparator. In all four groups, doses were administered in 3 doses at 0, 8, and 16 weeks by direct venous inoculation. Vaccine efficacy was determined at 3, 6, and 12 months of follow-up after the third immunization. RNA was extracted from whole blood collected in PAXgene tubes before PfSPZ immunization, and two weeks after the third (final) dose, from 262 children for which sufficient material was available at both time points (82% of 316 enrolled children; 525 samples). RNA was depleted of globin and ribosome transcripts before library generation and sequencing on the Illumina NovaSeq platform. RNA-seq expression data was analyzed to determine blood transcriptional signatures, before and after PfSPZ vaccine immunization, that predicts sterile protection from naturally occurring P. falciparum infection or delayed parasitemia at 3 months post-immunization. Gene expression data will also be correlated to P. falciparum-specific IgG antibody and cellular responses to identify possible molecular correlates of vaccine-induced immunogenicity

  Study phs002196

• Kids First Pediatric Research Study in Familial Predisposition to Hematopoietic Malignancies (SJFAMILY-HM)

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Acute lymphoblastic leukemia (ALL) is the commonest childhood tumor and a leading cause of cancer death in children, adolescents and young adults. Hodgkin and non-Hodgkin lymphoma are also important hematologic malignancies (HM) that occur in children. Each are genetic diseases with growing evidence for a germline predisposition of both familial and sporadic cases, however the inherited genetic basis of ALL/lymphoma are poorly understood. Such knowledge is essential to gain mechanistic insight into the basis of tumor formation, and to guide genetic counseling and genetic management. Here we have assembled a large collection of familial HM kindreds, and extended recurrence cohorts of ALL and HL which will be used to identify the genetic basis of familial HM, examine the frequency of germline variants in sporadic ALL and HL, and to integrate inherited and somatic genomic data. These studies have high potential to provide fundamental new insights into the inherited genetic basis of HM, to provide important information to guide clinical management, and to provide an invaluable public resource of genomic data.

  Study phs001738

• Columbia University Study of Caribbean Hispanics with Familial and Sporadic Late Onset Alzheimer's disease

  Compared to Caucasians residing in the same community the incidence rate of Alzheimer's disease is approximately twice as high in Caribbean Hispanics. Moreover, Caribbean Hispanics represent a homogenous population with only a few founders. Replication of genetic associations in other ethnic groups provides supporting evidence that a putative gene is involved in the disease pathogenesis, and when different allelic variants within the same genes are associated with disease it can help to localize the pathogenic variant. SORL1 is an example of a candidate gene that was first identified in Hispanics and then confirmed in multiple ethnic and racial groups in a meta-analysis. For this project, we are genotyping 704 individuals in families multiply affected by Alzheimer's disease (166 families). These families were recruited in the United States, Puerto Rico and the Dominican Republic. In addition, we are genotyping 2491 individuals (960 patients with sporadic Alzheimer's disease and 1531 unrelated controls) phenotyped in a similar fashion totaling 3195 individuals. Both cohorts are followed at regular intervals of 18 to 24 months, and potential phenotypes available other than those related to Alzheimer's disease include body mass index, measured blood pressure, neurological history and examinations. More importantly, both studies are funded through 2014 and additional phenotypes could be added in successive waves. We propose a genome wide association (GWA) study of Alzheimer's disease and longitudinal changes in cognition and other age-related neurological and medical phenotypes. The goal will be to identify the chromosomal locations of genes underlying this disease and its related endophenotypes.

  Study phs000496

• Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

  Background:Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. This study focuses on molecular intra-tumor heterogeneity using the largest series to date in MPM and is the first to report on the multi-omics profiling of a substantial series of multi-site tumor samples. Methods:Intra-tumor heterogeneity was investigated in 16 patients from whom biopsies were taken at distinct anatomical sites. The paired biopsies collected from apex, side wall, costo-diaphragmatic or highest metabolic sites as well as 5 derived cell lines were screened using targeted sequencing. Whole exome sequencing, RNA sequencing, and DNA methylation were performed on a subset of the cohort for deep characterization. Molecular classification, recently defined histo-molecular gradients, and cell populations of the tumor microenvironment were assessed. Results:Sequencing analysis identified heterogeneous variants notably in NF2, a key tumor suppressor gene of mesothelial carcinogenesis. Subclonal tumor populations were shared among paired biopsies, suggesting a polyclonal dissemination of the tumor. Transcriptome analysis highlighted dysregulation of cell adhesion and extracellular matrix pathways, linked to changes in histo-molecular gradient proportions between anatomic sites. Methylome analysis revealed contribution of epigenetic mechanisms in two patients. Finally, significant changes in the expression of immune mediators and genes related to immunological synapse, as well as differential infiltration of immune populations in the tumor environment were observed and led to a switch from a hot to a cold immune profile in three patients. Conclusions:This comprehensive analysis reveals patient-dependent spatial intra-tumor heterogeneity at the genetic, transcriptomic and epigenetic levels and in the immune landscape of the tumor microenvironment. Results support

  Study EGAS00001005328

• Exploiting immune cell receptor information to quantify index switching in single cell transcriptome sequencing experiment

  By offering high sequencing speed and ultra-high-throughput at a low price, Illumina next-generation sequencing platforms has been widely adopted in recent years. However, an experiment with multiplexed library could be at risk of molecular recombination, known as “index switching”, which causes certain amount of reads to be assigned to an incorrect library. It is reported that a new advance, exclusion amplification (ExAmp) in conjunction with the patterned flow cell technology introduced on HiSeq 3000/HiSeq 4000/HiSeq X sequencing systems, potentially suffers from a higher rate of index switching than conventional bridge amplification. We took advantage of the diverse but highly cell-unique expression of immune cell receptors to quantify index switching on single cell RNA-seq data that were sequenced on HiSeq 3500 and HiSeq 4000. By utilizing the unique T-cell receptor (TCR) expression, we could quantify the spread-of-signal from many different wells (n=51 from total three batches) due to index switching. We used TraCer to reconstruct full-length TCR from all samples, and then used Kallisto to quantify TCR gene expression. We found index switching in all three batches of experiments investigated. The median percentage of incorrectly detected markers was estimated to be 4.2% (interquartile range (IQR): 2.0%-8.7%). We did not detect any consistent pattern of certain indices to be more prone for switching than others, suggesting that index switching is a stochastic process. We confirm that index switching is a problem that affects all samples run in multiplexed libraries on Illumina HiSeq 3500 and HiSeq 4000 platforms.

  Study EGAS00001002911

• scRNA-seq of total bone marrow and T cells from multiple myeloma long-term survivors

  scRNA This dataset contains 50 scRNA-seq samples from bone marrow aspirates of 11 multiple myeloma patients experiencing long-term survival and 3 healthy donors. For each donor, total bone marrow and CD3+ T cells were sequenced. For multiple myeloma patients, paired samples were collected at initial diagnosis and between 7-17 years after first-line therapy. Bone marrow mononuclear cells were isolated by Ficoll density gradient centrifugation. For sorting of total bone marrow cells singlet, live cells were gated and sorted, for sorting of T cells CD45+, CD3+ cells were gated and sorted on either FACSAria Fusion or FACSAria II. Single-cell RNA sequencing were generated using 10x Genomics single-cell RNAseq technology (Chromium Single Cell 3’ Solution v2) according to the manufacturer’s protocol and sequenced on an Illumina HiSeq4000 (paired end, 26 and 74 bp). Bulk RNA Singlet, live CD3+CD4- CXCR3+CD8+ and CD3+CD4- CXCR3-CD8+ cells were sorted from 7 bone marrow and 3 peripheral blood samples of 7 multiple myeloma patients using a FACSAria Fusion machine. Bulk-RNA sequencing libraries were generated using the SMART Seq Stranded Total RNA-Seq kit (Takara) and sequenced using the Illumina NovaSeq 6000 platform (2 x 100 bp).

  Dataset EGAD00001010025

• Reconstruction of complex rearrangement patterns causing the initiation of clear cell renal cell carcinoma.

  The genomic hallmark of clear cell renal cell carcinoma is the loss of the short arm of chromosome three. This appears to be the earliest genomic event in the formation of these cancers. Often chromosome 3 is lost at the same time as part of chromosome 5 is duplicated via an unbalanced translocation, often with features consistent with focal chromothripsis. In this study, we sought to reconstruct the chromothriptic event that underlies the initiation of kidney cancer. We used long read sequencing (promethION, Oxford Nanopore Technologies) of patient tumour-derived DNA to elucidate how a single cell division error can generate cancer genome complexity.

  Dataset EGAD00001005495

• The Prostate, Lung, Colon, Ovary Screening Trial (PLCO)

  The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a large population-based randomized trial designed and sponsored by the National Cancer Institute (NCI) to determine the effects of screening on cancer-related mortality and secondary endpoints in over 150,000 men and women aged 55 to 74. The screening component of the trial was completed in 2006. However, participants have been under follow-up for cancer incidence and mortality since that time. In addition, PLCO included a large biological sample biorepository which has served as a unique resource for cancer research, particularly for etiologic and early-marker studies. As part of these efforts, PLCO has been used for a large number of genome-wide association and exome sequencing studies for different types of cancer. Recently, a blood DNA methylation analysis was conducted in annexes case-controls study of breast cancer.

  Study phs001286

• From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle

  This project aims at revisiting the "matrilineal puzzle" from a population genetics' point of view. The dataset consists of 719 individuals from 12 populations sampled in continental Southeast Asia and genotyped at 598764 loci. This dataset can only be accessed and used for non-commercial research purposes with a finality complying with the informed consent provided by donors. For accessing the data, please provide: 1. An explicit title for the project you wish to use the data for. 2. A detailed institutional affiliation of all recipients and users of the data. 3. A summary (500 words) of the research project, with emphasis on its scientific and societal finality, and predicted outputs. If access is granted by the DAC, data cannot be shared with a third party not initially involved in the project, without the third party officially applying for accessing the data.

  Study EGAS00001003727

• Patient-derived conditionally reprogrammed cells (CRCs) were established and characterized to assess their biological properties and to apply these to test the efficacies of drugs.

  RNA seq data was used for the characterization and profiling of the created patient-derived cells and in vivo tissue.

  Study EGAS00001001702

• CITE-seq for peripheral blood samples of 5 breast cancer patients

  We have 5 breast cancer patients who received VEN therapy. We collected their peripheral blood samples before and after long-term Venetoclax treatment. We apply CITE-seq protocol to these samples. This collection contains the all CITE-seq data for patients.

  Dataset EGAD00001008751

• CBD-KEY-CITESEQ-LINKER: Linker file for CITEseq sequencing data

  Linker file for COMBAT CITEseq sequencing data. Links COMBAT sample IDs with sequencing pools and their associated raw sequence data. Sequence data can be found in the following datasets: ADT data: EGAD00001007962 GEX data: EGAD00001008007 VDJ (B-cell): EGAD00001007964 VDJ (T-cell): EGAD00001007965

  Dataset EGAD00001008008

• The Genetics of Type 2 Diabetes Consortium (GoT2D): Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 Diabetes

  The Genetics of Type 2 Diabetes Consortium (GoT2D) is a collaboration between the University of Michigan, the Broad Institute and the Wellcome Trust Centre for Human Genetics. The overall aim is to extend upon recent efforts, such as genome-wide association studies (GWAS) and large scale meta-analyses. While they have proved successful at mapping genomic loci that influence human diseases, like type 2 diabetes, much of the heritability remains unexplained. In this study, we use next generation sequencing and genotyping technologies to query for lower frequency variants in the human genome. Thereby, allowing a deeper characterization of the spectrum of alleles associated with type 2 diabetes risk, and a better assessment of the genes that play a role in the etiology of type 2 diabetes development. We studied 1,326 T2D cases and 1,331 normoglycemic controls from Northern and Central Europe (Sweden, Finland, UK, and Germany). To efficiently characterize the entire genome sequence of each individual, we performed low-coverage (~5x) whole-genome sequencing, augmented by deep coverage (~100x) sequencing of the exome (Fuchsberger et al, 2016), and dense (2.5M) single nucleotide polymorphism (SNP) genotyping using the HumanOmni2.5 array. The data deposited in dbGaP will include all the Swedish, Finnish, and UK samples, but the German data will be deposited in the European Genome-phenome Archive (EGA), by virtue of the project specific funding requirements.

  Study phs000840

• H3.3G34R/V-transformed interneuron progenitors co-opt PDGFRA for gliomagenesis

  Histone H3.3 glycine 34 to arginine/valine (H3.3G34R/V) mutations occur in deadly hemispheric high-grade gliomas. These tumors show exquisite regional and temporal specificity, suggesting a developmental context permissive to the effects of G34R/V mutations. Here we present the molecular landscape of G34R/V gliomas (n=85) and show that 50% bear activating mutations in PDGFRA, with strong selection pressure for PDGFRAMUT clones at recurrence. We show that G34R/V tumors arise in interneuron progenitors of the foetal ventral forebrain expressing GSX2 and the DLX family of homeobox transcription factors, where terminal neuronal differentiation is impaired through aberrant G34R/V-mediated H3K27me3. Frequent co-occurrence of G34R/V & PDGFRAMUT is facilitated in this interneuron lineage-of-origin as PDGFRA forms an aberrant chromatin loop with the adjacent GSX2, hijacking its active chromatin conformation. At the single-cell level, G34R/V tumours entirely lack oligodendroglial transcriptional programs prominent in other glioma entities, and instead harbour dual neuronal and astroglial compartments. CRISPR-removal of H3.3G34R/V does not impact tumorigenicity suggesting this mutation becomes dispensable, while PDGFRAMUT are potently oncogenic regardless of G34 mutation. Collectively, our results suggest that G34R/V gliomas arise in foetal interneuron progenitors unable to undergo terminal differentiation, enabling co-option of PDGFRA through inappropriate expression and activating mutations to promote gliogenesis and oncogenicity. Reliance on PDGFRA for oncogenesis may be of therapeutic opportunity in G34R/V glioma.

  Study EGAS00001004301

• Combining transcription factor binding affinities with open chromatin data for accurate gene expression prediction

  The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid cost and labour intensive TF ChIP-seq assays.It is important to develop reliable and fast computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices.TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq, using either peaks or footprints as input.In addition to open-chromatin data, also Histone-Marks (HMs) can be used in TEPIC to identify candidate TF binding sites.TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength.Using machine learning techniques, we show that incorporating low affinity binding sites improves our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites.Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance.In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq datasets.Finally, we show that these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

  Study EGAS00001002073

• Center for Common Disease Genomics (CCDG) - Cardiovascular: BioImage Cohort

  The genetic basis of cardiovascular disease in individuals of non-European ancestry remains largely unknown. Availability of ethnically diverse study populations is essential to fully investigate the underlying causes of disease. The BioImage Study enrolled adults aged 55-80 in a prospective observational study. Subjects had no prior history of cardiovascular disease, but were identified to be at intermediate to high risk for atherosclerotic cardiovascular events (PMID: 25790876). The recruiting target was a cohort with similar demographics to the US population in terms of race and ethnicity. Produced as part of the NHGRI Centers for Common Disease Genomics, this study contains whole genome sequence data and variant calls from 922 African American participants of the BioImage Study.

  Study phs002325

• Development of Novel Chondrosarcoma Organoid Models for Drug Discovery

  Chondrosarcoma is a rare and aggressive malignant bone tumor characterized by resistance to conventional chemotherapy and radiotherapy. Its pathogenesis remains poorly understood, although recurrent mutations such as IDH1 have been implicated in tumor development. We treated patients with chondrosarcoma at the Osaka International Cancer Institute and established two organoid cultures from resected tumor specimens using a modified air-liquid interface method. After serial passaging, the organoids were successfully xenografted into NOD-scid IL2Rgnull (NSG) mice. The established organoids retained key histological features and genetic characteristics of the original tumors. These organoid models provide a novel and reliable platform for studying the biology of chondrosarcoma and may facilitate the development of effective therapeutic strategies for this treatment-resistant tumor.

  Study JGAS000834

• NHLBI TOPMed: Study of African Americans, Asthma, Genes and Environment (SAGE)

  This is a parallel case-control pharmacogenetic study of bronchodilator drug response among African American children with and without asthma. Each participant had spirometry measured using the KoKo PFT System. Asthmatic participants were administered with 4 puffs of HFA Albuterol. Healthy participants were given a baseline spirometry test. The overall goal is to identify genetic factors which are predictive of drug response in children with asthma. The principal tools include a questionnaire and biological specimen collection. Participants were 8-21 years old at time of recruitment. Children with asthma have physician-diagnosed asthma, symptoms and medications.

  Study phs000921

• Biology and Molecular Analysis of Human Hematopoiesis Genetics

  In this study we have performed exome sequencing using the hybrid capture method that has previously been described (Gnirke et al., Nature Biotechnology, 2009) on genomic DNA samples from patients with the congenital bone marrow failure syndrome that affects the erythroid lineage, specifically, Diamond-Blackfan anemia. This disease is characterized by a hypoplastic anemia and approximately 50% of cases are attributable to mutations in ribosomal protein gene subunits. The other 50% of cases do not have a known genetic etiology and the purpose of this study is to attempt to delineate such causes.

  Study phs000474

• Single Cell Colony Whole Genome Sequencing Data From Individuals With Telomere Syndromes

  This is an observational study which examined the phylogenetic evolution of somatic clonal mutations in POT1 mutation carriers. Two individuals with telomere syndromes who carry a heterozygous germline POT1 p.R273Q variant and one related control who did not carry this variant were studied. Single cell hematopoietic colonies were derived from peripheral blood mononuclear isolates. These colonies were analyzed by whole genome sequencing (WGS) and phylogenetic trees were reconstructed accordingly. Phylogenetic reconstruction of somatic mutations show clonality is increased among POT1 p.R273Q mutation carriers and co-occurs with known clonal hematopoiesis driver mutations, including DNMT3A and/or JAK2.

  Study phs003207

• Multi-Omic Investigation of Beckwith-Wiedemann Syndrome Wilms Tumor

  Wilms’ Tumor (WT), also known as nephroblastoma, is one of the most common malignant kidney tumors diagnosed in children. One of the most common WT predisposition syndromes is Beckwith-Wiedemann Syndrome (BWS, OMIM: 130650), which affects approximately 1/10,000 live births. In this study, we perform Whole Exome Sequencing (WES), DNA methylation array, and messenger RNA-Sequencing (mRNA-Seq), to examine the genomic, methylomic, and transcriptomic signature of BWS WT. We analyzed six tumor-normal paired samples, three BWS tumor only samples, and four non-BWS control samples to identify BWS WT drivers.

  Study phs002769