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• NHLBI TOPMed - NHGRI CCDG: Intermountain INSPIRE Registry

  The INtermountain Healthcare Biological Samples Collection Project and Investigational REgistry for the On-going Study of Disease Origin, Progression and Treatment (Intermountain INSPIRE Registry) purpose is to collect biological samples, clinical information and laboratory data from Intermountain Healthcare patients. The registry originally collected samples in patients undergoing a coronary angiography as part of the Intermountain Heart Collaborative Study. It has been expanded to collect samples in patients diagnosed with all types of medical conditions, and patients from the general population including those who have not been diagnosed with health related issues. Just over 25,000 individuals have provided samples as part of this registry. The registry enables researchers to develop a comprehensive collection of information that may help in disease management, including determining best medical practices for predicting, preventing and treating medical conditions.

  Study phs001545

• RNA sequencing data from glioblastoma primary cell lines treated with indisulam

  This study aimed to develop NovumRNA, a bioinformatics pipeline designed to predict non-canonical tumor-specific antigens (ncTSAs) from human tumor RNA-sequencing data, potentially broadening the target pool for cancer neo-epitope-based immunotherapies. The splicing-modulating drug indisulam was investigated for its potential to induce aberrant transcriptomes, potentially increasing ncTSAs, subsequently predicted by NovumRNA. Four glioblastoma primary cell lines were derived from patient Cavitron Ultrasonic Aspirator (CUSA) material, cultured as neurospheres, and treated with indisulam or vehicle control. RNA was extracted at 6 and 16 hours post-treatment and sequenced using the NovaSeq platform. The resulting RNA-seq data was analyzed with NovumRNA, using healthy brain GTEx samples as controls, to identify and validate ncTSAs induced by indisulam treatment. NovumRNA is available at: https://github.com/ComputationalBiomedicineGroup/NovumRNA.

  Study EGAS50000000680

• Transcriptomic analysis of B-cell acute lymphoblastic leukaemia (B-ALL) patients treated on the ALL09 clinical trial

  This study provides comprehensive transcriptomic analysis of adolescent and young adult (AYA) patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL09 clinical trial (ACTRN12618001734257). The ALL09 clinical trial is a Phase II single arm study to assess whether substitution of blinatumomab for conventional multi-agent chemotherapy in phase 2 induction leads to improved minimal residual disease negativity rates when compared to the historical AYA ALL trial cohort. Patients treated on this trial were aged 15-40 years, demonstrated morphological diagnosis of CD19 positive B-lineage acute lymphoblastic leukaemia (B-ALL), and were negative for Philadelphia chromosome-positive disease. Transcriptomic sequencing was performed as a correlative study to determine assess patients’ genomic subtypes and enable comparison of clinical outcome in blinatumomab treated patients.

  Study EGAS50000001109

• ECM-free patient-derived organoids preserve diverse prostate cancer lineages and uncover in vitro-enriched cell types

  Patient-derived organoids (PDOs) hold promise for modeling various cancers, yet their application in prostate cancer (PCa) has been limited due to low culture success and the predominance of non-tumor-like cells. Using 164 PCa samples and optimizing culture conditions, we demonstrate that an extracellular matrix (ECM)-free culture method improves PDO take-rates, fostering cell populations with luminal and PCa-specific characteristics. Single-cell RNA sequencing (scRNA-seq) reveals that these ECM-free PDOs closely mirror their original tumors at the transcriptomic level and maintain a diverse array of tumor cell types, unlike traditional Matrigel-based cultures which predominantly yield benign-like cells. This study introduces a PCa PDO single-cell atlas, providing a valuable resource for advancing prostate cancer research.

  Study EGAS50000000807

• Cross-species genomics identifies TAF12, NFYC and RAD54L as novel choroid plexus carcinoma oncogenes

  Choroid plexus carcinomas (CPC) are poorly understood and frequently lethal brain tumors with minimal treatment options. Using a new mouse model of the disease and a large cohort of human CPCs, we performed a cross-species, genome-wide search for novel oncogenes within syntenic regions of chromosome gain. TAF12, NFYC and RAD54L, co-located on human chromosome 1p32-35.3 and mouse chromosome 4qD1-D3, were identified as oncogenes that are gained in tumors in both species and required to initiate and progress the disease in mice. TAF12 and NFYC are transcription factors that regulate the epigenome, while RAD54L plays a central role in DNA repair. Our data identify a group of concurrently gained, novel oncogenes that cooperate in the formation of CPC and unmask potential new avenues for therapy.

  Study EGAS00001000961

• MYC Drives Progression of Small Cell Lung Cancer to a Variant Neuroendocrine Subtype with Vulnerability to Aurora Kinase Inhibition

  Loss of the tumor suppressors RB1 and TP53 and MYC amplification are frequent oncogenic events in small cell lung cancer (SCLC). We show that Myc expression cooperates with Rb1 and Trp53 loss in the mouse lung to promote aggressive, highly metastatic tumors, that are initially sensitive to chemotherapy followed by relapse, similar to human SCLC. Importantly, MYC drives a neuroendocrine-low “variant” subset of SCLC with high NEUROD1 expression corresponding to transcriptional profiles of human SCLC. Targeted drug screening reveals that SCLC with high MYC expression is vulnerable to Aurora kinase inhibition, which combined with chemotherapy strongly suppresses tumor progression and increases survival. These data identify molecular features for patient stratification and uncover a novel targeted treatment approach for MYC-driven SCLC.

  Study EGAS00001002115

• A genetic compendium of human brains from the UK Medical Research Council brain tissue resource

  Common neurodegenerative diseases have a complex genetic architecture. Highly penetrant diseases alleles are found in a significant minority of cases, and common risk alleles are present in a large proportion. Given the central role of genetic factors in the pathogenesis of these disorders, it is critical that mechanistic studies in human subjects and tissue samples are interpreted in an genetically enlightened context. To address this we performed exome sequencing on 1461 human brains accessible through the Medical Research Council (UK) brain banks network. Our findings confirm the complex genetic landscape of neurodegenerative disease. Clinical, pathological and genetic data for the 1461 brains with corresponding exome sequencing data are available within this dataset, enabling the genetic stratification and selection of post-mortem tissue samples for researchers.

  Study EGAS00001001599

• WGS of liver cancer in the Japanese population

  Hepatocellular carcinoma (HCC) is the third leading cancer-related cause of death and the seventh most common form of cancer worldwide, with an estimate of more than 700,000 new cases each year. The most established risk factors of HCC are chronic HBV and HCV infection. HBV infection is responsible for over 50% of the worldwide attributable risk of HCC, especially in East Asia and Africa, while in Japan and several Western countries HCV infection is the most common risk factor for HCC. To gain insights into the molecular alterations of virus-associated HCC, we performed whole genome sequencing (WGS) of 321 HCC tumors from 159 patients. This work was performed as a part of the ICGC (International Cancer Genome Consortium) project.

  Study EGAS00001000678

• Genome-wide association analysis on five isolated populations - Erasmus Rucphen Family (ERF) Study

  ERF is embedded in the Genetic Research in Isolated Population (GRIP) program. Genealogy of GRIP is available from its founding (1600-1650). For ERF, we selected 22 related (first and second degree, non-consanguineous) couples living in GRIP between 1850-1900, and having at least six children baptized in the community church. All living descendants of those couples were invited to participate in ERF1. About 4,000 relatives included in the study form a very complex pedigree, which consists of more than 23,000 members. The participants aged between 18-20 years constitute a unique single family spanning over 23 generations. Around 3,000 individuals have been extensively phenotyped for several psychiatric and somatic traits. All phenotyped individuals are genotyped on genome-wide genotyping arrays.

  Study EGAS00001001134

• Genome_Diversity_in_Africa_Project___ancient_samples___standard_libraries

  Given the central importance of Africa to studies of human origins, genetic diversity and disease susceptibility, large-scale and representative characterisation of genetic diversity in Africa is needed. Analyses of ancient DNA from Africa would complement sequencing of modern African populations and provide unique opportunities to transform our understanding of the pre-history of the region. This approach would greatly refine our understanding of population structure and gene flow in Africa and globally, including genetic signatures of ancient admixture. This low coverage sequencing experiment will allow us to test and refine our pipeline for ancient DNA sequencing.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001182

• Multiregional sequencing of IDH-WT glioblastoma reveals high genetic heterogeneity and a dynamic evolutionary history

  Glioblastoma is the most common and aggressive primary brain malignancy in adults. In addi-tion to extensive inter-patient heterogeneity, glioblastoma shows intra-tumor extensive cellular and molecular heterogeneity, both spatially and temporally. This heterogeneity is one of the main reasons for the poor prognosis and overall survival. Moreover, it raises the important question of whether the molecular characterization of a single bioptic sample, as performed in standard di-agnostics, actually represents the entire lesion. In this study, we sequenced the whole-exome of nine spatially different cancer regions of three primary glioblastomas. We characterized their mutational profiles and copy number alterations, with implications for our understanding of tu-mor biology in relation to clonal architecture and evolutionary dynamics, as well as therapeuti-cally relevant alterations.

  Study EGAS00001005128

• Size-tagged preferred ends in maternal plasma DNAshed light on the production mechanism and showutility in noninvasive prenatal testing

  Cell-free DNA molecules in the plasma of pregnant women exhibit nonrandom fragmentation with preferred end sites. We studied if such preferred end sites might bear any re- lationship with fragment lengths of plasma DNA. Short and long plasma DNA molecules were associated with different preferred DNA end sites. Analysis of size-tagged preferred ends could be used for measuring fetal DNA fraction and for facilitating fetal trisomy 21 detection. Fetal preferred end sites were generally located in the nucleosome cores, while the maternal ones were located in the linker regions. This con- ceptual framework provides an explanation of the relative shortness of fetal DNA in maternal plasma and brings us closer to understanding the biological mechanisms that influence plasma DNA fragmentation.

  Study EGAS00001002831

• Adeno-associated virus in the liver: natural history and consequences in tumor development

  Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (40-80%). AAV infection has long been considered as non-pathogenic1, however few years ago we reported for the first time recurrent clonal AAV2 insertion in the pathogenesis of human hepatocellular carcinoma (HCC) developed on normal liver. These clonal viral insertions target cancer driver genes, including CCNA2, CCNE1, TERT, TNFSF10 and MLL4, leading to their overexpression. The viral inserted sequences involved in almost all the cases the 3’ inverse tandem repeat (ITR) of AAV2, which is important for virus integration in host DNA and exhibits a promoter/enhancer activity. Here, we used RNA sequencing (RNA-seq) to investigate their functional impact on the tissue, such as fusion transcript generation events.

  Study EGAS00001003310

• UCSF Pediatric Bithalamic Glioma Genome Project

  Brain tumors are the most common solid tumors of childhood, and the genetic drivers and optimal therapeutic strategies for many of the different subtypes remain unknown. We performed targeted next-generation sequencing of approximately 500 cancer-associated genes on a cohort of 13 pediatric bithalamic diffuse gliomas, a lethal brain tumor of childhood for which the genetic basis is largely unknown. We identified that bithalamic diffuse gliomas harbor frequent mutations in the EGFR oncogene in the absence of accompanying gene amplification and only rare histone H3 mutation. These EGFR mutations were either small in-frame insertions within exon 20 (intracellular tyrosine kinase domain) or missense mutations within exon 7 (extracellular ligand-binding domain). Accompanying alterations included frequent TP53 mutation, CDK6 amplification or CDKN2C mutation, and BCOR and BCORL1 mutation or deletion.

  Study EGAS00001004033

• Most HCCs in Taiwan show the mutational signature of aristolochic acid

  Plants in the genus Aristolochia contain the mutagen aristolochic acid (AA) and have been widely used in traditional medicines and for weight loss. AA binds covalently to genomic DNA and induces a highly distinctive mutational signature. While AA involvement in urinary-tract cancers in Taiwan is known, the possible role of AA in hepatocellular carcinomas (HCCs) in Taiwan has not been examined. Here, we whole-exome sequenced 98 unselected HCCs from Taiwan and analyzed the mutational signatures for evidence of AA mutagenesis. Remarkably, more than 78% of HCCs showed strong evidence of AA mutagenesis, often associated with high mutation burdens. Non-synonymous mutations in genes known to be HCC driver genes were detected. Importantly, we elucidated the potential of immunotherapy in this cohort of liver cancer patients.

  Study EGAS00001002301

• Pediatric Low-Grade Glioma RNA and Targeted Sequencing

  Pediatric low-grade gliomas (pLGG) are frequently driven by genetic alterations in the RAS/MAPK pathway yet show unexplained variability in their clinical outcome. To address this, we characterized a cohort of >1,000 clinically annotated pLGG. 84% of cases harbored a driver alteration, while those without an identified alteration also often exhibited up-regulation of the RAS/MAPK pathway. pLGG could be broadly classified based on their alteration type. Rearrangement-driven tumors were diagnosed at a younger age, enriched for WHO grade I histology, infrequently progressed, and rarely resulted in death as compared to SNV-driven tumors. Further sub-classification of clinical-molecular correlates stratified pLGG into risk categories. These data highlight the biological and clinical differences between pLGG subtypes and opens avenues for future treatment refinement.

  Study EGAS00001004242

• Molecular sub-classification of hormone receptor-positive breast cancer

  Patients with estrogen and/or progesterone receptor-positive breast cancer benefit from hormonal treatment, yet high global death burdens due to high prevalence and long-term recurrence risk call for biomarkers to guide additional treatment approaches. From a prospective, observational study of postmenopausal early breast cancer patients treated with tamoxifen or aromatase inhibitors gene expression analyses of 612 tumors was performed using the NanoString® Breast Cancer 360 panel. We identified novel gene expression signatures, i.e. BRCAness and Tumor Inflammation Signature (associated with high tumor lymphocyte infiltration), that may aid to select high-risk patients in order to improve adjuvant treatment by targeting DNA repair deficiency or immune-checkpoints in addition to standard chemo-endocrine treatment. The overall goal is to foster novel concepts for a stratified early breast cancer management.

  Study EGAS00001004594

• Single-cell RNA sequencing of 22 Hodgkin lymphoma tumors and 5 reactive lymph nodes

  Hodgkin lymphoma (HL) is characterized by an extensively dominant tumor microenvironment (TME) composed of different types of non-cancerous immune cells with rare malignant cells. Characterization of the cellular components and their spatial relationship is crucial to understanding crosstalk and therapeutic targeting in the TME. We performed single-cell RNA sequencing of more than 127,000 cells from 22 HL tissue specimens and 5 reactive lymph nodes, profiling for the first time the phenotype of the HL-specific immune microenvironment at single-cell resolution. Library preparation was performed using the 10x Genomics Chromium system, and Illumina sequencing was used to generate 3' gene expression data for every cell. Downstream analysis was performed in R to identify HL-specific microenvironment patterns and identify novel cell populations.

  Study EGAS00001004085

• Patient-derived organoids as a novel tool to study cervical cancer

  Cervical cancer is the most prevalent gynecological malignancy worldwide, often caused by infection with a high-risk human papillomavirus. Currently, there are only limited number of human-derived culture systems available that enable to study the viral infection for short-term. Here, we report on establishment of long-term human-derived organoid cultures from both healthy ecto- and endocervical epithelia that closely recapitulate the tissues of origin by maintaining the authentic histological and tissue-specific gene expression profiles. Additionally, using material from patients’ Pap-brush material, a successful panel of long-term patient-derived cancer organoids was established that maintain the causative viral infection in vitro and show differential response to common chemotherapy regimens. This study provides a promising platform for cervical cancer research and studying direct virus-host interactions.

  Study EGAS00001004439

• RP-1843 Arcagen - Gastrointestinal rare cancers (GI)

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 1 (32 patients): Mesothelioma of the peritoneum (n=21) and Pseudomyxoma peritonei/mucinous adenocarcinoma of the appendix (n=11) - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

  Study EGAS00001006299

• Single cell whole genome sequencing of high hyperdiploid acute lymphoblastic leukemia

  This dataset was collected from viable bone marrow cells obtained at diagnosis from nine patients with high hyperdiploid ALL and one normal bone marrow sample. All samples were subjected to low pass single cell whole genome sequencing with the median sequencing coverage of 0.02x. Single nuclei in G0/G1 phase were isolated using a fluorescence-activated cell sorting (FACS) cytometer. DNA libraries were constructed and associated next-generation sequencing was carried out by European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. Further details regarding the DNA libraries construction are available by Bos et. al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8931-7_15). The dataset has been used for copy number aberrations analysis.

  Study EGAS00001006347

• ATAC-Seq of inflamed and non-inflamed biopsies

  Inflamed and non-inflamed biopsies were digested for 45 minutes at 37ºC with collagenase from Clostridium histolyticum (Sigma). Suspension cells were then stained with an antibody cocktail to sort live CD8-CD4+ T cells. After isolating crude nuclei of two thousand live CD4+ T cells, they were treated with Tagment DNA buffer and Tagment DNA Enzyme (Nextera DNA Library Prep Kit, Illumina), and then the DNA was purified by MinElute PCR Purification Kit (Qiagen). Transposed DNA fragments were amplified using specific adapters followed by purification with MinElute PCR Purification Kit (Qiagen). Fragments from 240-360pb were selected in the PippinHT system (Sage Science). The quality of the library and its DNA concentration were assessed by Bioanalyzer instruments (Agilent Technologies) and ultimately submitted for sequencing using Illumina HiSeq 2500 sequencer, V4 chemistry.

  Study EGAS00001007344

• EGA synthetic data

  Synthetic Data One of the limitations in genomics research is that human genomics data is not openly available; access must be controlled according to participant consent agreements and data protection regulations such as GDPR. Obtaining authorization to access such data can sometimes take a long time, resulting in delays to important research work. In this context, synthetic genomic and phenotype data can be useful resources for researchers to avoid these delays. Synthetic data are artificially generated datasets, often created with algorithms, which can be used without the need for authorization to test new products and tools, build technical demonstrators, validate data models, and train AI models. The EGA provides access to synthetic cohort datasets augmented with rich synthetic metadata that overcomes these real data usage restrictions. Whilst synthetic datasets are not included in the general EGA mandate and services, we can consider such submissions and evaluate their acceptance on the basis of their unique use cases not already covered by existing synthetic datasets. Access to synthetic data studies is managed by the EGA Helpdesk Data Access Committee. Study ID Title Located in EGAS00001002472 CINECA synthetic cohort EUROPE UK1 referencing fake samples Central EGA EGAS00001005591 Synthetic data - Genome in a Bottle Central EGA EGAS00001005042 Test Study for EGA using data from 1000 Genomes Project - Phase 3 Central EGA EGAS00001005702 Human genomic and phenotypic synthetic data for the study of rare diseases Central EGA EGAS50000000190 EOSC4Cancer Synthetic Colorectal Cancer Genomic data Central EGA EGAS50000000086 Synthetic - FEGA Sweden Heilsa synthetic dataset December 2023 Federated EGA Sweden EGAS50000000678 Synthetic - GDI synthetic data Federated EGA Spain

  Documentation synthetic-data

• EGAD00010000538

  28 unlinked autosomal microsatellite loci for 20 African and 4 philippine populations

  Dataset EGAD00010000538

• SAIF Alignment File

  This is the bam file generated after alignment using BWA program for the SAIF genome

  Dataset EGAD00001000249

• RNA Editing Exome

  Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project.

  Dataset EGAD00001000626

• TP53_KO_RPE1_SNPs

  Allelic imbalance data for cell lines derived from RPE1 with TP53 knockout

  Dataset EGAD00010001566

• SOGEN_MATRILINEAL_PUZZLE

  598764 SNPs genotyped for 719 indivuals, merge from Illumina Omni1 and Illumina Omni2.5

  Dataset EGAD00010001724

• README-for-EGAS00001004349-linking-HIPO-K09R-WGS-files

  Dataset EGAD00001006739

• Genotypes_Agta

  Genotype data for Agta hunter-gatherers Philippines

  Dataset EGAD00010002140

• Access to dataset, "Feasibility of Functional Precision Medicine for Guiding Treatment of Relapsed/Refractory Pediatric Cancers"

  Access to sequencing data from project.

  Dac EGAC50000000124

• PGx validation GSAv3

  Samples genotyped using Illumina Infinium Global Screening Array v3 for assessing pharmacogenomic genes

  Dataset EGAD00010002645

• Internal Medicine II Technical University Munich DAC

  Data sharing agreement Klinikum rechts der Isar der Technischen Universität München for MEMORI NGS files

  Dac EGAC50000000165

• PDX WES for #87, #95, #32, #217, #86

  Exome sequencing of tumour PDX and matched patient blood

  Dataset EGAD50000000215

• SMPaeds cfDNA lcWGS

  Low coverage whole genome sequencing (0.5-4X) for cfDNA collected from blood plasma.

  Dataset EGAD50000000782

• Indonesian Genome Diversity Project 3

  Term and condition for Indonesian Diversity Project v3. 254 Low Coverage genome from Wallacean and West Papuan, Indonesia

  Dac EGAC50000000312

• DAC for Hematological toxicity following CAR-T cells injection

  Data access committee to have access to Hematological toxicity following CAR-T cells injection

  Dac EGAC50000000490

• Cardiac fibroblast DAC

  DAC for reviewing requests to access data on cardiac fibroblasts as described by Aguado-Alvaro et al (Nature Communications, 2025)

  Dac EGAC50000000479

• BCR-HGBCL-DH-BCL2 project DAC

  Data Access Committee for high-grade B cell lymphomas MYC-BCL2 datasets

  Dac EGAC50000000500

• Therapy and RNA group Ghent DAC

  This is a Data Access Committee for datasets of the Therapy and RNA group Ghent (TaRGeT, Belgium).

  Dac EGAC50000000491

• Small Intestine Adenocarcinoma Subtyping Data Access Committee

  DAC created for the Molecular classification of small intestinal adenocarcinomas Study in Amsterdam UMC.

  Dac EGAC50000000663

• Brain mets discovery cohort variant calls

  These are the variant calls for the 50 brain tumour samples in the discovery cohort.

  Dataset EGAD00001005982

• RNAseq data

  RNAseq data for 10 patients: 10 tumors and 10 cell lines

  Dataset EGAD00001002691

• Exome sequencing VCF files for glioma progression

  Exome sequencing VCF files describing mutations during glioma progression.

  Dataset EGAD00001001887

• Whole genome sequencing data of ccRCCs

  Whole genome sequencing data of ccRCCs were utilized for somatic variations calling.

  Dataset EGAD00001004588

• Genome-wide DNA Methylation Analysis Reveals a Unique Methylation Pattern for Pleural Mesothelioma Compared to Healthy Pleura and Other Lung Diseases

  Study EGAS00001007783

• Biomarker Data Subset

  This dataset contains data for CBC counts and absolute protein abundance measurements from ELISA experiments.

  Dataset EGAD00001011163

• Phylogenetic reconstruction of breast cancer

  This dataset contains the fastq files used for this study

  Dataset EGAD00001006121

• Establishing Reliability for Quantitative EEG, Transcranial Doppler, Behavioral Outcomes and Optical Coherence Tomography in SWS: The Next Step toward Biomarker Development

  Sturge-Weber syndrome (SWS) is a rare, congenital syndrome with vascular malformations of the brain, skin and eye. The underlying cause of SWS is unknown and the extent of involvement varies greatly from patient to patient. Those with brain involvement present with seizures, stroke-like episodes and neurologic deficits, usually in infancy. Those with eye involvement frequently develop vision threatening glaucoma and retinal injury. Treatment has been largely symptomatic and hampered by delayed diagnosis and the rarity of the condition. The purpose of this study is to determine the reliability of non-invasive measures to be developed as biomarkers for SWS and to determine inter-rater reliability where appropriate. This includes measuring reliability for: Power asymmetry on Quantitative Electroencephalogram Asymmetry of Transcranial Doppler velocity and pulsatility Behavioral outcome measures (PEDI, Erhardt, Modified Rankin Scale) Optical Coherence Tomography Approximately 40 subjects will participate in this observational, cross-sectional study. The first version study release included data of the first n=25 subjects.

  Study phs001281

• CPTAC: Microscaled Proteogenomic Methods for Precision Oncology

  Cancer proteogenomics combines genomics, transcriptomics and mass spectrometry-based proteomics to gain insights into cancer biology and treatment outcomes. To promote clinical investigation, we developed a "microscaled" proteogenomics approach for tumor-rich frozen core needle biopsies. Tissue-sparing specimen processing ("Biopsy Trifecta EXTraction", BioTExt) and microscaled proteomics (MiProt) generated deep-scale proteogenomics datasets. As a proofof- concept, biopsies were accrued from ERBB2 positive (ERBB2+) breast cancers before and 48 to 72 hours after the first dose of neoadjuvant trastuzumab-based chemotherapy. Multi-omics comparisons were conducted between samples associated with residual disease versus complete pathological response (pCR). Integrated analyses diagnosed diverse molecular causes of treatmentresistance including: 1) absence of ERBB2 amplification (false-ERBB2&#43); 2) insufficient ERBB2 activity for therapeutic sensitivity despite ERBB2 amplification (pseudo-ERBB2&#43); 3) resistance features in true-ERBB2+ cases including androgen receptor signaling, mucin expression and an inactive immune microenvironment; 4) lack of acute phospho-ERBB2 down-regulation in nonpCR cases. We conclude microscaled cancer proteogenomics could improve diagnostic precision.

  Study phs001907