Kids First: Pediatric Research Project on Adolescent Idiopathic Scoliosis
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ABSTRACT: The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in childhood cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. 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. For the current study, families with inherited adolescent idiopathic scoliosis were included. Both affected and unaffected family members were included.
SECONDARY ACCESSION(S): PRJNA394550PRJNA394551
REPOSITORIES: dbGaP
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Project description:<p>The Gabriella Miller Kids First Pediatric Research Program (<a href="https://www.commonfund.nih.gov/KidsFirst" target="_blank">Gabriella Miller Kids First Pediatric Research Program</a>) (Kids First) is a trans-NIH effort initiated in response to the <a href="https://www.govtrack.us/congress/bills/113/hr2019" target="_blank">2014 Gabriella Miller Kids First Research Act</a> 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). Both, childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions.</p> <p>WGS and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.</p> <p>In collaboration with the University of Utah, DNA from four families were selected for high-depth WGS (60X) including diaphragm and skin tissue to identify mosaicism.</p> <p>In collaboration with the Broad Institute, DNA from four families underwent linked long read sequencing using 10X Genomics technology.</p> <p>Probands with congenital diaphragmatic hernia/defects and both biological parents enrolled as part of the DHREAMS study.</p>
| phs001110 | dbGaP
Project description:<p>The <a href="https://commonfund.nih.gov/KidsFirst">Gabriella Miller Kids First Pediatric Research Program</a> (Kids First) is a trans-NIH effort initiated in response to the <a href="https://www.congress.gov/bill/113th-congress/house-bill/2019/text?q=%7b%22search%22%3A%5b%22\%22hr2019\%22%22%5d%7d&resultIndex=2"> 2014 Gabriella Miller Kids First Research Act</a> and supported by the NIH Common Fund. This program focuses on gene discovery in childhood cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. </p> <p>All of the WGS and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org/">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.</p> <p>Although the survival of children with relapsed osteosarcoma is very poor, little is known about the etiology of treatment failure in this disease. The purpose of this project is to perform whole genome sequencing on serial samples from patients with osteosarcoma obtained before treatment, after treatment, and at relapse/metastasis in order to identify the mutations and pathways that are drivers of drug resistance. If successful, our results may help identify patients at high risk for treatment failure and may yield new treatments for children who cannot currently be cured. </p>
| phs001714 | dbGaP
Project description:<p>The Gabriella Miller Kids First Pediatric Research Program (<a href="https://www.commonfund.nih.gov/KidsFirst">Gabriella Miller Kids First Pediatric Research Program</a>) (Kids First) is a trans-NIH effort initiated in response to the <a href="https://www.govtrack.us/congress/bills/113/hr2019">2014 Gabriella Miller Kids First Research Act</a> 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). Both, childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions.</p> <p>Whole Genome Sequence (WGS) and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.</p> <p>Goals of this ongoing study are to identify novel "congenital cranial dysinnervation disorder" (CCDD) genes and define the role of the wildtype and mutant genes in normal and aberrant development. The umbrella term (CCDD) refers to congenital birth defects with malformation of one or more cranial nerves, typically resulting in limitations of eye and/or face movement. Examples of CCDDs include congenital fibrosis of the extraocular muscles (CFEOM), congenital ptosis, Duane retraction syndrome (DRS), horizontal gaze palsy with progressive scoliosis (HGPPS), congenital 3rd, 4th or 6th nerve palsies, Moebius syndrome (MBS), and hereditary congenital facial paresis (HCFP). In some cases, anosmia, and disorders of hearing, sucking, chewing, swallowing, and breathing may also be classified as CCDDs. CCDDs can be accompanied by additional birth defects such as intellectual and social disabilities, developmental delays, limb anomalies, and cardiac, GI, and GU disorders. The genetic basis of multiple CCDDs has been determined, and the gene mutations typically alter cranial motor neuron identity or function, or perturb axon growth and guidance. Despite these successes, the genetic etiologies of many inherited CCDDs remain unidentified. </p>
| phs001247 | dbGaP
Project description:<p>Francesca Petralia,Nicole Tignor,Boris Reva, et al., (2020) <a href="https://www.cell.com/cell/fulltext/S0092-8674(20)31451-3" target="_blank">Cell 183, 1962-1985</a></p><p>We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.</p><p>The Children's Brain Tumor Network (CBTN) and the Pacific Pediatric Neuro-Oncology Consortia (PNOC) are collaborative research consortia focused on identifying therapies for children with brain tumors (<a href="https://cbttc.org" target="_blank">https://cbttc.org</a>). The consortia have contributed a <a href="https://kidsfirstdrc.org/support/studies-and-access/#SD_BHJXBDQK" target="_blank">Pediatric Brain Tumor Atlas (PBTA) dataset</a>, a cohort of 991 brain tumor subject clinical data, with associated whole genome sequencing and RNAseq hosted by the Gabriella Miller Kids First Data Resource (<a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>) as part of the Gabriella Miller Kids First Pediatric Research Program (Kids First). Kids First is a Pan NIH Common Fund program dedicated to the development of large-scale data resources to help researchers uncover new insights into the biology of childhood cancer and structural birth defects (<a href="https://commonfund.nih.gov/KidsFirst" target="_blank">https://commonfund.nih.gov/KidsFirst</a>).</p><p>Mass Spectrometry raw data generation along with preliminary analyses were performed at the <a href="https://tcmp.hms.harvard.edu/" target="_blank">Thermo Fisher Scientific Center for Multiplexed Proteomics (TCMP)</a>, Harvard Medical School (HMS) under the direction of <a href="https://cellbio.med.harvard.edu/people/faculty/gygi" target="_blank">Prof. Steven Gygi</a>. Samples were prepared using the streamline (SL)-TMT protocol (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994137/" target="_blank">Navarrete-Perea et al., 2018</a>) and MS analysis was performed using the SPS-MS3 strategy (<a href="https://www.nature.com/articles/nmeth.1714" target="_blank">Ting et al., 2011</a>) developed in the <a href="https://gygi.med.harvard.edu/" target="_blank">Gygi lab</a>. Additional data analyses from the CPTAC Common Data Analysis Pipeline (<a href="https://www.ncbi.nlm.nih.gov/pubmed/26860878" target="_blank">Rudnick et al., 2016</a>) and from the University of Michigan Proteomics and Integrative Bioinformatics Laboratory (<a href="https://github.com/Nesvilab" target="_blank">https://github.com/Nesvilab</a>) are also provided. All raw and processed genomic data, as well as pathology reports, radiology reports, MRIs, histology slide images are accessible via the <a href="https://portal.kidsfirstdrc.org/dashboard" target="_blank">Kids First DRC (Data Resource Center)</a>.</p>
2021-02-04 | MSV000086810 | MassIVE
Project description:<p>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).</p> <p>Multi-center, prospective observational cohort study of individuals with congenital heart defects (CHD). Phenotypic data and source DNA derived from 300 probands and their parents, and family of interest collected to investigate relationships between genetic factors and phenotypic and clinical outcomes in patients with CHD.</p> <p>This Kids First project represents a subset of the PCGC data. Other PCGC data can be accessed through <a href="study.cgi?study_id=phs001194">phs001194</a> and other Kids First data can be accessed through <a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>.</p>
| phs001138 | dbGaP
Project description:<p>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).</p><p>
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</div><div>All of the WGS and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.
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</div><div><br></div><div>Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications.</div><div><br></div><p></p>
| phs002162 | dbGaP
Project description:<p>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).</p><p>
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</div><div>All of the WGS and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org/" target="_blank">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.
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</div><div><br></div><div>Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information.
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| phs002161 | dbGaP
Project description:<p>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).</p> <p>All of the WGS and phenotypic data from this study are accessible through dbGaP and <a href="kidsfirstdrc.org" target="_blank">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.</p> <p>The focus of this study is to identify novel risk variants for OFC in Africa and Asian OFC case-parent triads through analysis of Whole Genome Sequencing data.</p>
| phs001997 | dbGaP
Project description:<p>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).</p> <p>All of the WGS and phenotypic data from this study are accessible through dbGaP and <a href="https://kidsfirstdrc.org/">kidsfirstdrc.org</a>, where other Kids First datasets can also be accessed.</p> <p>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.</p>
| phs001738 | dbGaP