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• Pediatric Non-Down Syndrome Acute Megakaryoblastic Leukemia is Characterized by Distinct Genomic Subsets with Varying Outcomes

  Acute Megakaryoblastic Leukemia (AMKL) is a subtype of acute myeloid leukemia (AML) in which cells morphologically resemble abnormal megakaryoblasts.  While extremely rare in adults, AMKL accounts for 4-15% of newly diagnosed childhood AML1-3.  A significant proportion of pediatric AMKL cases occur in children with Down syndrome (DS).  These patients have excellent outcomes and are characterized at the genomic level by a founding GATA1 mutation4-6.  In contrast, AMKL in patients without DS (non-DS-AMKL) is frequently associated with poor outcomes.  Previous efforts have identified chimeric oncogenes in a significant number of cases, including RBM15-MKL1, CBFA2T3-GLIS2, KMT2A gene rearrangements and NUP98-KDM5A7-9.  The etiology of 30-40% of cases, however, remains unknown.  To better understand the genomic landscape of non-DS-AMKL, we performed RNA and exome sequencing on specimens from 99 patients (75 pediatric and 24 adult).  We demonstrate that pediatric non-DS-AMKL is a heterogeneous malignancy that can be divided into seven subgroups with varying outcomes.  These subgroups are characterized by chimeric oncogenes with cooperating mutations in epigenetic and kinase signaling genes.  Overall, these data shed light on the etiology of AMKL and provide useful information for treatment tailoring. 

  Study EGAS00001002183

• LifeChange Data Access Committee

  The LifeChange study aimed at tracking the biological consequences of the societal changes undergone by the Yakut people of Far Eastern Siberia, after the colonization of the region by Russians in the 17th century. This study builds upon more than 15 years of archaeological research conducted in Yakutia, Sakha Republic, an autonomous region of the Russian Federation located in northeastern Siberia. The fieldwork was conducted under the MAFSO program (“Mission Archéologique Française en Sibérie Orientale”, or “French Archaeological Mission in Eastern Siberia”), a collaboration between French researchers and local Yakut experts, including scholars from North-Eastern Federal University in Yakutsk. The program was supported by several inter-university collaborative research agreements, notably between Université Paul Sabatier, Krasnoyarsk State Medical University, and North-Eastern Federal University in Yakutsk. It also received endorsement from the Institute of Ecology and Evolution at CNRS through the International Associated Laboratory “Co-evolution Human-Environment in Eastern Siberia”. The LifeChange Data Access Committee, composed of French and Russian archaeogeneticists, geneticists and archaeologists, reviews any access request to LifeChange data, consisting of genomes of ancient and modern Yakut, Eveni and Evenki individuals sampled in Eastern Siberia for the LifeChange study. The DAC grants access to any academic researcher aiming to study the population history of autochthonous peoples from Siberia. When reviewing data access requests, the DAC members ensure that the applicant will not re-use the data to trace present-day descendants of studied ancient individuals. They also ensure that secondary use of the modern genomic data is conducted in full respect of the conditions stipulated in living participants’ informed consent. Specifically, the applicant is not authorised to (i) use the data for diagnostic purposes, (ii) store the data outside of secure servers, (iii) reidentify research participants, and (iv) share the data with a third party.

  Dac EGAC50000000713

• Exploring the Genetic Variants Associated with Brain Growth in Children

  Understanding the genetic factors that control brain growth during childhood and adolescence is a priority for neuroscience. Its importance lies partly in the finding that disturbances in the course of brain development characterizes many common childhood behavioral problems. Recent advances in neuroimaging such as the use of non-invasive magnetic resonance imaging have provided a chance to define these trajectories in the living child. The intramural programs of the NIMH and NHGRI have conducted repeated neuroanatomic imaging on children along with the banking of DNA, providing a cohort which is studied for defining developmental trajectories of the brain. A central goal of this cohort is to define the disturbances in brain development that are linked with common behavioral problems, such as excessive impulsivity, hyperactivity and inattention. Studies have demonstrated that problems in these domains are distributed across the entire population and that children with Attention Deficit Hyperactivity Disorder (ADHD) lie at the extreme end of these behavioral dimensions. We found a similar dimensionality in the development of brain regions that are associated with these behavioral problems. Specifically, we showed that the rate of change in both the lateral prefrontal cortex and interconnected striatum during childhood and adolescence was linked to the severity of symptoms of hyperactivity and impulsivity. As symptoms increased, the rate of growth of both structures decreased. The lateral prefrontal cortex and striatum are core components of richly interconnected 'loops' that support a host of cognitive processes, including attention, cognitive control and motor planning. Anomalies in these structures and their connections have been implicated in many childhood behavioral problems, including ADHD. In summary, we aim to identify the common and rare genetic variants that are associated with the developmental trajectories of the lateral-prefrontal cortex and striatum. Identifying genetic variants influencing the growth of these structures may reveal the biological mechanisms underlying dysregulated control of attention, impulse and activity level, which in the extreme constitute ADHD. The study thus could inform our understanding of neurobiology underpinning one of the most common neuropsychiatric disorders of childhood.

  Study phs000962

• NEI CIDR Methylation Profiling of Primary Open Angle Glaucoma in GLAUGEN Samples

  This is a case-control study of Primary Open Angle Glaucoma (POAG). POAG is a progressive optic neuropathy that eventually leads to blindness. More than 30 million people worldwide have Primary Open Angle Glaucoma (POAG), of which greater than 3 million are blind. Gene expression changes in the retina have been observed for POAG. Several recent studies, including the GLAUGEN (Glaucoma Gene Environment) initiative have used GWAS to identify correlative regions of the genome. Despite this, the genetic basis of Glaucoma is not well understood. Epigenetic variation may account for low heritability and environmental effects on human disease. Despite the significant advances being made in understanding the role of epigenetics in gene regulation in other fields, little is known about the relationship between DNA methylation patterns, retinal gene expression, and retinal disease. The goal of this study is to identify differentially methylated regions in the peripheral blood of patients with POAG. The case identification is as per the GLAUGEN description: Cases and controls were recruited from ophthalmology clinics and were examined by ophthalmologists. For cases the clinical exam included intraocular pressure measurements, optic nerve assessment and visual field evaluation. Controls had no family history of glaucoma, normal intraocular pressure and normal optic nerves. POAG and control samples come from Massachusetts Eye and Ear Infirmary (MEEI). These samples were collected and genotyped as part of the GLAUGEN study. From the MEEI, 50 patients were selected from POAG pedigrees, to include all the probands genotyped by CIDR and are currently undergoing exome sequencing, and to include additional genotyped probands who belong to pedigrees of sufficient size and structure that parent of origin effects could be evaluated. Additional individual-level phenotype and genotype data may be obtained through the authorized access portal of phs000308 (Geneva - Glaugen GWAS Study).

  Study phs000461

• Assessment of Neurological Deterioration in Subjects with Late Infantile Neuronal Ceroid Lipofuscinosis

  Late infantile ceroid lipofuscinosis (LINCL) is a rare, rapidly progressing lysosomal storage disease resulting from mutations in the CLN2 gene that lead to deficiency in the lysosomal protease tripeptidyl peptidase I (TPP-I). The symptoms are largely neurological with onset at 2-4 years age with progression to death at age 8-12 yrs. The rareness of the disease and the likelihood of non-uniform progression depending on genotype together limit the data available regarding the natural history of disease progression. Current neurological rating scales are used to give an overall quantitative description of the disease but the categories are generally broad and imprecise. With that background, the primary focus of this study is to use clinical rating scales and magnetic resonance imaging methods to define the natural history of LINCL and to provide objective and sensitive surrogates for neurological status and the impact of experimental treatments in children with LINCL. Together these parameters will be applicable to future clinical studies of novel therapies for LINCL and should be transferrable to other neurological lysosomal storage diseases. Subjects will be assessed at 2 visits separated by ≥1 yr. Brain morphometry, water self-diffusion coefficients and spectroscopic data will be obtained via magnetic resonance. Resulting MRI biomarkers will be compared with neurological assessment of disease severity using the Weill-Cornell LINCL rating scale.

  Study phs001575

• A PROSTATE TUMORGRAFT PANEL TO ACCELERATE PRECISION MEDICINE

  The management of advanced prostate cancer (PCa) has strongly evolved in the last decade with the introduction of the next generation of androgen receptor pathway inhibitors which have considerably improved patient outcomes. Most recently, the investigation of genomic landscape has provided targetable molecular alterations such as homologous gene DNA repair defects correlated with response to PARP inhibitors. Despite these significant advances, while localized PCa is generally associated with favorable outcome, metastatic PCa is currently considered incurable. For further investigations in precision treatment, the development of preclinical models representing the complex prostate tumor heterogeneity are mandatory. Accordingly, we aimed to establish a resource of patient-derived xenograft (PDX) models that exemplify each phase of this multistage disease for accurate and rapid evaluation of candidate therapies.

  Study EGAS00001007033

• Whole-genome sequencing in 14 cases and whole-exome sequencing in 90 cases of Chinese ESCC

  Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide1. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC)2-3. Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 14 ESCC cases and whole-exome sequencing in 90 cases.

  Study EGAS00001001487

• RNA-seq data from the EUROBATS Project in four tissues: Fat, LCL, Skin and whole Blood.

  EUROBATS consists of RNA-seq data for female twins in lisphoblastoide cell lines (LCL), abdominal adipose tissue (Fat), abdominal skin tissue (Skin) and whole blood (Blood). The samples are a combination of MZ twins, DZ twins and singletons. The goal of the project is to find biomarkers related with the ageing process and cellular senescence.

  Study EGAS00001000805

• Transcriptomic Profile of Whole Blood Cells from Elderly Subjects fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label Study

  Open label study to evaluate the safety of Lactobacillus rhamnosus GG ATCC 53103 (LGG) in elderly subjects. Fifteen healthy elderly volunteers, ages 65-80 were enrolled in a study in which they received LGG capsules containing 1 x 1010 CFU, twice daily for 28 days and were followed through day 56. The study subjects completed a daily diary, a telephone call on study days 3, 7 and 14 and study visits at the Massachusetts General Hospital Clinical Research Center at baseline, day 28 and day 56. During each visit, the subject diary, interim history, potential adverse effects and concomitant medications were reviewed and vital signs and a physical examination were performed. Routine blood tests were obtained to monitor for safety during visits and nasopharyngeal and stool samples were collected for microbiome analysis. Volunteers interested in participating in the effect of LGG probiotic on the Human whole Blood Transcriptome substudy also had blood drawn for DNA and RNA extraction, after signing the substudy consent form. The main objective of the study was to assess the safety and tolerability of 2 x 1010 CFU LGG administered orally to elderly subjects for 28 days. Secondary objectives were to evaluate the richness and microbial diversity in nasopharyngeal and stool specimens using pyrosequencing, and to compare cytokine production in response to bacterial stimulation by following the kinetics of mRNA expression of pro and anti-inflammatory genes and different signaling pathways, in relation to changes in stool Bifidobacterium and Lactobacillus spp. The study was reviewed and approved by the Partners Human Research Committee (IRB # 2010P001695) and was registered at ClinicalTrials.gov (NCT01274598). The main results regarding the clinical signs and safety of intervention is published in PLoS One. 2014 Dec 1;9(12):e113456. doi: 10.1371/journal.pone.0113456. eCollection 2014. PMID: 25438151. RNA sequencing for transcriptome analysis was only done in 11 of the 15 subjects as RNA integrity and quantity had to be optimal for the three times where blood was collected in order for a subject to be included in the study. The information regarding the microbiome data associated with this study is presented in a separate paper, which can be found at dbGaP study accession, phs000896, and PMID: 25873374.

  Study phs000928

• cfDNAme allows early prediction of PE

  Preeclampsia (PE) is a leading cause for peripartal morbidity, especially if developing early in gestation. To enable prophylaxis to prevent PE, it is essential that pregnancies at risk of PE are identified early, in the first trimester. To identify patients at risk, we profiled methylomes of plasma-derived cell-free DNA (cfDNA) from pregnant women. We detected DNA methylation differences between control and PE pregnancies that enable risk stratification of patients, at PE diagnosis but also presymptomatically, around 12 weeks of gestation.

  Study EGAS00001007071