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• UK10K COHORT ALSPAC

  The UK10K project proposes a series of complementary genetic approaches to find new low-frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome-wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein-coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will directly analyse quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a two-generation prospective study. Pregnant women living in one of three health districts in the former county of Avon with an expected delivery date between April 1991 and December 1992 were eligible to be enrolled in the study, and this formed the initial point of contact for the development of a large, family based resource. Information has been collected on the children and the mothers through retrieval of biological materials (e.g. antenatal blood samples, placentas), biological sampling (e.g. collection of cord blood, umbilical cord, milk teeth, hair, toenails, blood and urine), self-administered questionnaires, data extraction from medical notes, linkage to routine information systems and at repeat research clinics.

  Study EGAS00001000090

• UK10K_NEURO_ASD_FI

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches.These samples are a subset of a nationwide collection of Finnish autism spectrum disorder (ASD) samples. The samples have been collected from Central Hospitals across Finland in collaboration with the University of Helsinki. The samples consist of 93 individuals with a diagnosis of autistic disorder or Asperger syndrome from 36 families with at least two affected individuals. Of these individuals, 16 can be genealogically connected to form two large pedigrees originating from Central Finland, suggesting possible genetic risk factors shared identical by descent within the pedigrees. All diagnoses are based on ICD-10 and DSM-IV diagnostic criteria for ASDs. Additional phenotypic data is available for a subset of the individuals.For further information with regard to this cohort please contact Aarno Palotie (Aarno.palotie@helsinki.fi).

  Study EGAS00001000110

• Sample Multiplexing Oligo Comparison

  In this study, we compared various multiplexing reagents, including MULTI-Seq, Hashtag antibody, and CellPlex, in patient-derived xenografts (PDXs). We found that all multiplexing reagents worked well in cell types robust to ex vivo manipulation but suffered from signal-to-noise issues in more delicate sample types. We also compared the performance of fixed scRNA-Seq kits and CRISPR-based destruction of non-informative genes.

  Study EGAS50000000153

• Utlizing the RA signature to predict response to TNFi

  This study involves bulk RNA-seq analyses of blood cells from patients with rheumatoid arthritis who have had an inadequate response to methotrexate, collected before and 12 weeks after effective treatment with either etanercept or adalimumab. Peripheral blood mononuclear cells were stimulated with anti-CD3 for 24 hours and sorted into CD4+, CD19+, and CD4-CD19- (DN) populations for bulk RNA-seq.

  Study phs002562

• Inherited T Cell Defects: Diagnosis, Mechanisms and Treatments

  Infants with abnormal newborn screen results for severe combined immunodeficiency (SCID) and their parents were enrolled in UCSF IRB approved protocols with informed consent to have molecular and immunologic investigation to determine the cause of the infant's low T lymphocytes. Studies included exome sequencing of DNA from the infant and both parents. Candidate variants were investigated in mouse and zebrafish model organisms.

  Study phs002968

• Ciliopathies Exome Sequencing Initiative

  The study is aimed at identifying new genes involved in pediatric brain disorders from inbred families originating predominantly in the Middle East. Each patient analyzed to date has a specific and highly unique neurodevelopmental disorder that is likely to be recessive in nature. Many patients have one of the diseases along the "ciliopathy" spectrum of diseases, with evidence of kidney failure, retinal blindness and cerebellar ataxia.

  Study phs000288

• Million Veteran Program (MVP) Summary Results from Non-Sensitive Omics Studies

  MVP is an ongoing prospective cohort study and mega‐biobank in the Department of Veterans Affairs Healthcare System designed to study genetic influences on health and disease among veterans. This is the accession to hold publicly available results. Results from sensitive phenotypes or MVP population subsets can be found at accession phs001672 and will require an application for access.

  Study phs002453

• A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy

  In this prospective study, custom genome-wide exome and whole transcriptome sequencing (NGS) was used to identify genomic events and associated expression changes in advanced Small Cell Lung Cancer (SCLC) and attempt to prescribe systemic therapy based on the results. Tumor/normal pairs were sequenced from 12 patients with advanced SCLC for this study.

  Study phs001366

• Developmental Dynamics of Translation in the Human Brain

  We performed ribosome profiling and RNA sequencing from a total of 43 adult brain and 30 prenatal brain samples. The age of adult brain donors ranged from 18 to 82 years (average 39.5 years), with an average post-mortem interval of 9.9 hours. The gestational age of prenatal cortex samples ranged from 12 to 23 weeks, with a mean of 19.9 weeks. 

  Study phs002489

• Investigating Human Placentation and Pregnancy Using First Trimester Chorionic Villi

  Chorionic villus sampling (CVS) is routinely used for prenatal diagnosis of cytogenetic disorders, but also possesses great potential for studying placentation. To better understand villi biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10-14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes.

  Study phs001320