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• Transcriptional Profiling of Macrophages In Situ in Metastatic Melanoma Reveals Localization-Dependent Phenotypes and Function

  Therapeutic interventions modulating immune function at the tumor site could improve outcomes in cancer. Here we analyzed metastatic melanoma, a tumor type highly responsive to T-cell based therapies, and found that the tumor-infiltrating T cells are localized closely to CD14+ monocytes/macrophages rather than to melanoma cells. Using novel immunofluorescence-guided laser capture micro-dissection, we analyzed transcriptomes of CD3+ T cells, CD14+ monocytes/macrophages and melanoma cells in non-dissociated tissue. CD14+ cells localized in tumors beds displayed specific transcriptional signatures distinct from CD14+ cells that were localized in tumor stroma.The 8 distinct metastatic melanoma samples are from the Cooperative Human Tissue Network (CHTN). 64 RNA-seq files are available from 16 intraCD14+, 16 stromaCD14+, 16 cancer cells, 8 intraCD3+ and 8 stromaCD3+ cells. 2 LCM harvests were completed for the CD14+ and cancer cells on two sections of the samples. One harvest was done for the CD3+ samples.The processed data (TPM/raw counts tables) are available on GEO under GSE180124. 

  Study phs002564

• The Influence of Gut Microbiota on the Speciation and Toxicity of Mercury During Pregnancy

  There are few studies that have characterized maternal gut microbiota and fetal methylmercury exposure, yet microbes likely modulate this relationship. The primary objective of our pilot study was to determine associations between gut microbial taxa and mercury concentrations in multiple biomarkers (stool, hair, and cord blood). Our secondary objective was to determine the contribution of gut microbial mercury methylation to stool methylmercury.

  Study phs000970

• Whole-genome sequencing of two probands with hereditary spastic paraplegia reveals novel splice-donor region mutation and known pathogenic mutation in SPG11

  Hereditary spastic paraplegias (SPG) are a group of heterogeneous neurodegenerative disorders, which are often presented with overlapping phenotypes such as progressive paraparesis and spasticity. To assist the diagnosis of SPG subtypes, next-generation sequencing is often used to provide supporting evidence. In this study, we report the case of two probands from the same family with SPG symptoms, including bilateral lower limbs weakness, unsteady gait, cognitive decline, dysarthria and slurring of speech since age of 14. Subsequent whole-genome sequencing revealed that the patients are compound heterozygous for mutations in SPG11 gene, including the paternally inherited c.6856C>T (p.Arg2286*) mutation and the novel maternally inherited c.2316+5G>A splice donor region mutation. Mutations in SPG11 are the common cause of autosomal recessive Spastic Paraplegia type 11. According to the ClinVar database, there are already 101 reported pathogenic mutations in SPG11 that are associated with SPG. To our knowledge, this is the first report of SPG11 mutations in our local population. Novel splice mutation identified in this study would enrich the catalog of SPG11 mutations, potentially leading to better genetic diagnosis of SPG.

  Study EGAS00001001849

• Saliva_Fulani_Database

  In total, 90 DNA samples were genotyped on the Illumina Infinium H3Africa Consortium array (designed for 2,271,503 SNPs; using BeadChip type: H3Africa_2019_20037295_B1). Genotyping was performed at the SNP&SEQ Technology Platform (NGI/SciLifeLab Genomics, Sweden). Saliva Fulani dataset includes individuals from the following populations: 30 individuals from Senegal_FulaniLinguere, 30 individuals from Mauritania_FulaniAssaba, and 30 individuals from Mali_FulaniInnerDelta.

  Dataset EGAD50000000653

• Malagasy Genomics University of Antananarivo Dataset

  Mid-pass whole genome sequencing was performed for 264 Malagasy individuals across three geographic regions across the island of Madagascar (west coast, central highlands, and southern highlands). This dataset includes the VCF from joint variant calling with reference populations as specified in the associated publication.

  Dataset EGAD50000000708

• Colon Cancer Organoid Cultures and Tumors RNASeq Data

  Four micrograms of total RNA was used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), following manufacturer's protocol. The adaptor-ligated libraries were enriched by 6 cycles of polymerase chain reaction (PCR). Libraries were sequenced using the Novaseq 6000 with paired end 151bp reads.

  Dataset EGAD00001005753

• Peripheral blood DNA methylation of Crohn's disease patients starting treatment with adalimumab, vedolizumab or ustekinumab

  In the current study we performed a longitudinal case-control study comparing the peripheral blood DNA methylome of Crohn's disease (CD) patients that were classified as responders and non-responders to adalimumab, vedolizumab, and ustekinumab. Patients with active CD were prospectively recruited and followed up for around 27 weeks into treatment during which response assessment took place. Response was defined as a strict combination of endoscopic- (≥50% reduction in SES-CD score) combined with either corticosteroid-free clinical- (≥3 point drop87 in HBI or HBI ≤4 and no systemic steroids) and/or biochemical response (C-reactive protein (CRP) and fecal calprotectin reduction ≥50% or ≤5 g/mL and fecal calprotectin ≤250 µg/g).

  Study EGAS00001007532

• PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

  The dataset includes RNA sequencing data on PRE- treatment biopsies of lymph node metastasis (n=80) The technology used for sequencing is llumina HiSeq 2500

  Dataset EGAD00001012116

• NIDDK⁄CIDR Inflammatory Bowel Disease Genetics Consortium (IBDGC) Genome Wide Association Study in Familial Crohn's Disease

  The National Institute of Diabetes and Digestive and Kidney Diseases Inflammatory Bowel Disease Genetics Consortium (NIDDK - IBDGC) conducted a genome wide association study (GWAS) using the Human Omni2.5-Quad beadchip from Illumina to identify disease variants associated with familial Crohn's disease. This study includes a subset of individuals from an original cohort of affected subjects and affected/unaffected relatives from a previous linkage scan which showed increased linkage evidence at three novel risk loci. A total of 708 samples were selected based on various criteria for inclusion from the 6 Genetic Research Centers (GRC) in North America that participate in the IBDGC. This project was supported by an ancillary R01 grant from the NIDDK with resources made available through the IBDGC.

  Study phs000367

• Colorectal cancer organoid-stroma biobank cohort

  In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect the cell type heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Whole exome sequencing and transcriptome analysis in various in vitro and in vivo contexts was performed to study the influence of the TME on the CRC phenotype.

  Dataset EGAD00001011173