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• The_Causes_of_Clonal_Blood_Cell_Disorders_Study___SCOR_Custom

  We took a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We grew these up into colonies, then whole genome sequenced each colony. Somatic mutations act as a unique barcode for each clone. We have designed a panel for targeted resequencing of the mutations that we find. We are now looking for these mutations in the peripheral blood, to see the dynamics of how HSCs contribute to the peripheral blood in health.

  Study EGAS00001002257

• Osteosarcoma mate-pair and RNA-sequencing

  DNA mate pair and RNA sequencing data of conventional osteosarcomas. Mate pair libraries, with average insert sizes of 2-4 kb, were prepared for sequencing using the Nextera Mate Pair Library Preparation Kit. Paired-end 76 base pair reads were generated using an Illumina NextSeq 500 sequencing instrument. Total RNA was enriched for polyadenylated RNA using magnetic oligo(dT) beads. Enriched RNA was prepared for sequencing using the TruSeq RNA Sample Preparation Kit v2 and paired-end 151 base pair reads were generated from the cDNA libraries using an Illumina NextSeq 500 instrument.

  Study EGAS00001003842

• KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population

  The killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 encodes cell surface glycoproteins that bind class I human leukocyte antigen (HLA) molecules as well as some other ligands. KIR gene gene copy number variation associates with the outcome of transplantations and susceptibility to immune-mediated diseases. Here we describe a stand-alone and freely available gene content imputation for 12 KIR genes. The models were trained using 818 Finnish biobank samples genotyped for 5774 KIR-region SNPs and analysed for KIR gene content with targeted sequencing.

  Study EGAS00001005457

• Identifying autosomal recessive mutations causing neurological disorders

  The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations.

  Study EGAS00001000023

• Genome-Wide Association Study of Amyotrophic Lateral Sclerosis in Finland

  The genetic etiology of amyotrophic lateral sclerosis (ALS) is not well understood. Finland has one of the highest incidence of ALS in the world, making it an ideal population for study. To identify genetic risk factors for this fatal neurodegenerative disease, we undertook a genome-wide association study of 405 Finnish patients diagnosed with ALS and 497 Finnish controls. Two loci that exceeded the Bonferroni threshold for genome-wide significance were identified. One was located on chromosome 21q22, corresponding to the known autosomal recessive D90A allele of the SOD1 gene. The other was detected on the short arm of chromosome 9, which had been previously identified in linkage studies of families with ALS. Together, these two loci account for most of the increased incidence of ALS observed in this population.

  Study phs000344

• Evolutionary Origins of Recurrent Pancreatic Cancer

  Surgery is the only curative option for patients with Stage I/II pancreatic cancer, nonetheless most patients will recur after surgery and die of their disease. To identify novel opportunities for management of recurrent pancreatic cancer we performed whole exome or targeted sequencing of 10 resected primary cancers and their matched intrapancreatic recurrences or distant metastases. We identified that recurrent disease develops from a monophyletic or polyphyletic origin, and this distinction has potential clinical relevance. In all patients, treatment induced genetic bottlenecks led to a modified genetic landscape and subclonal heterogeneity for driver gene alterations in part due to intermetastatic seeding. In one patient what was believed to be recurrent disease was an independent (second) primary tumor. These findings strongly advocate for routine post-treatment sampling in the management of recurrent pancreatic cancer.

  Study EGAS00001004097

• Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

  In this study we generated single-cell whole transcriptome and surface marker expression data for 24 samples of 19 AML patients as well as one healthy donor. We followed the CITEseq protocol with the 3' 10x Genomics scRNAseq kit version 3.1 To increase the coverage of the mitochondrial genome we generated mitochondrial libraries following a protocol termed Optimized 10x. Based on TAPseq, we generated libraries to increase the coverage of selected nuclear SNVs. Exome sequencing was generated for 15 patients to identify nuclear variants. Bulk ATAC was obtained for 9 samples to facilitate the discovery of mitochondrial SNVs. MutaSeq (modified version of SmartsSeq2) was performed on cells from 3 patients. Targeted DNAseq from single-cell derived colonies was generated for 1 patient.

  Study EGAS00001007078

• Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer

  No consensus strategies exist for prognosticating metastatic castration-resistant prostate cancer (mCRPC). Circulating tumor DNA fraction (ctDNA%) is increasingly reported by commercial and laboratory tests but its utility for risk stratification is unclear. Here, we intersect ctDNA%, treatment outcomes, and clinical characteristics across 738 plasma samples from 491 male mCRPC patients from two randomized multicentre phase II trials and a prospective province-wide blood biobanking program. ctDNA% correlates with serum and radiographic metrics of disease burden and is highest in patients with liver metastases. ctDNA% strongly predicts overall survival, progression-free survival, and treatment response independent of therapeutic context and outperformed established prognostic clinical factors. Recognizing that ctDNA-based biomarker genotyping is limited by low ctDNA% in some patients, we leverage the relationship between clinical prognostic factors and ctDNA% to develop a clinically-interpretable machine learning tool that predicts whether a patient has sufficient ctDNA% for informative ctDNA genotyping (available online: https://www.ctDNA.org). Our results affirm ctDNA% as an actionable tool for patient risk stratification and provide a practical framework for optimized biomarker testing.

  Study EGAS50000000211

• Longitudinal genome-wide analysis of progressive chronic lymphocytic leukemia under uniform front-line therapy of pentostatin, cyclophosphamide, and rituximab

  Samples from two-center prospective phase 2 clinical trail conducted at Ohio State University (Columbus, OH) and Mayo Clinic (Rochester, MN) were analyzed in 12 cases. All patients had progressive CLL as defined by National Cancer Institute (NCI) Working Group criteria. Patients provided written informed consent for correlative studies according to the Declaration of Helsinki on an institutional review board approved protocol for the collection and use of samples for research purposes from both participating institutions. Eligible patients received a regimen consisting of pentostatin (2 mg/m2), cyclophosphamide (600 mg/m2), and rituximab (375 mg/m2) provided intravenously on day 1 of a 21-day cycle for a maximum of 6 cycles. Responses were assessed by NCI Working Group criteria and included a bone marrow evaluation and two-color flow cytometry 2 months after completion of therapy. Peripheral blood samples from these patients collected longitudinally before (Pre-Baseline), at (Baseline) and after therapy (Relapse) were analyzed for genomic heterogeneity and clonal complexity by high throughput Exome sequencing.

  Study phs000794

• POISED (Peanut Oral Immunotherapy: Safety, Efficacy, and Discovery)

  Phase 2 POISED (Peanut Oral Immunotherapy: Safety, Efficacy, Discovery) Study In this randomized, double-blind, placebo-controlled (DBPC) clinical trial, blinded placebo group received oat flour, whereas in active participants, dosage was built-up for over ~ 52 weeks and subsequently maintained on 4000 mg peanut protein, daily for next 52 weeks. 80 (98.77%) per-protocol active participants passed the food challenge at week 104. Subsequently, for 12 weeks, peanut ingestion was avoided in a randomized group of 51 blinded active participants (i.e., peanut avoidance group). 21 (41.2%) participants in the peanut avoidance group passed the 4000 mg double-blind, placebo-controlled food challenge (DBPCFC) without any allergic reaction at week 117, thus demonstrating sustained unresponsiveness. These 21 participants continued oral immunotherapy (OIT) for every three months and afterwards were allowed to continue peanut OIT discontinuation if they passed. 8 participants passed the DBPCFCs, 12 months after peanut discontinuation (week 156), i.e. they achieved long-term sustained unresponsiveness with no allergic reaction in response to food challenge. For detailed description, please refer to Chinthrajah et al., PMID: 31522849.

  Study phs003071