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• WGS and RNA-Seq data from a GBM patient PT-DS9789

  WGS and RNA-Seq data from a GBM patient PT-DS9789

  Dataset EGAD00001004233

• Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy_CM38-RNA

  We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

  Dataset EGAD00001006282

• Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy_CM38-DNA

  We analyzed baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). Analysis of whole transcriptome data showed that T cell infiltration and interferon-gamma signaling signatures corresponded most highly with clinical response to therapy, with a reciprocal decrease in cell cycle and WNT signaling pathways in responding biopsies. Clinical outcome differences were likely not due to differential melanoma cell responses to interferon-gamma, as 57 human melanoma cell lines exposed in vitro to this cytokine showed a conserved interferon-gamma transcriptome response unless they had mutations that precluded signaling from the interferon-gamma receptor. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream interferon-gamma signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

  Dataset EGAD00001006284

• WGS and RNA-Seq data from a GBM patient PT-RV2286

  WGS and RNA-Seq data from a GBM patient PT-RV2286

  Dataset EGAD00001008527

• WGS and RNA-Seq data from a GBM patient PT-WR7927

  WGS and RNA-Seq data from a GBM patient PT-WR7927

  Dataset EGAD00001008531

• WGS and RNA-Seq data from a GBM patient PT-WT4796

  WGS and RNA-Seq data from a GBM patient PT-WT4796

  Dataset EGAD00001008532

• WGS and RNA-Seq data from a GBM patient PT-BM8772

  WGS and RNA-Seq data from a GBM patient PT-BM8772

  Dataset EGAD00001008516

• WGS and RNA-Seq data from a GBM patient PT-GE7528

  WGS and RNA-Seq data from a GBM patient PT-GE7528

  Dataset EGAD00001008519

• WGS and RNA-Seq data from a GBM patient PT-GI2070

  WGS and RNA-Seq data from a GBM patient PT-GI2070

  Dataset EGAD00001008520

• WGS and RNA-Seq data from a GBM patient PT-JR9883

  WGS and RNA-Seq data from a GBM patient PT-JR9883

  Dataset EGAD00001008521

• WGS and RNA-Seq data from a GBM patient PT-LC6372

  WGS and RNA-Seq data from a GBM patient PT-LC6372

  Dataset EGAD00001008522

• WGS and RNA-Seq data from a GBM patient PT-ML9537

  WGS and RNA-Seq data from a GBM patient PT-ML9537

  Dataset EGAD00001008523

• Blood neutrophils in COPD derive from activated progenitors in the bone marrow sc Rhapsody

  Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small airway inflammation, emphysema and severe breathing difficulties. Low-grade systemic inflammation is an established hallmark of severe disease, however, the molecular changes in peripheral immune cells remain far from understood. We combined multi-color flow cytometry with single-cell RNA sequencing and showed that blood neutrophil numbers are significantly increased in COPD and they are a heterogeneous population. A transcriptomic state that expressed interferon response genes correlated with alveolar damage and acute exacerbations. Furthermore, bronchoalveolar neutrophils expressed gene signatures corresponding to certain blood neutrophil states. Last, our data in a murine model of cigarette smoke exposure demonstrated that bone marrow neutrophil progenitors are expanded in smoke-treated animals and display signs of immune activation. Our study provides evidence that COPD systemic inflammation may derive from an activated haematopoietic precursor compartment.

  Dataset EGAD00001009704

• Somatic L1 retrotransposition in normal colorectal epthelium

  Throughout an individual’s lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 406 normal colorectal clones, 12 MUTYH-associated adenomatous clones, and 19 matched colorectal cancer tissues. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 (in 139 clones) and read-through RNA expression profiles (in 116 clones) to investigate the epigenetic regulation of L1 activity.

  Dataset EGAD00001010183

• Targeted capture ctDNA Library CRCQV42Run050-23

  Targeted capture ctDNA Library CRCQV42Run050-23 from patient PBC0002622, buffy coat sample

  Dataset EGAD00001010796

• Targeted capture ctDNA Library CRCQV42Run050-24

  Targeted capture ctDNA Library CRCQV42Run050-24 from patient PBC0002494, buffy coat sample

  Dataset EGAD00001010797

• Targeted capture ctDNA Library CRCQV42Run050-4

  Targeted capture ctDNA Library CRCQV42Run050-4 from patient PBC0001776, buffy coat sample

  Dataset EGAD00001010798

• Targeted capture ctDNA Library CRCQV42Run050-5

  Targeted capture ctDNA Library CRCQV42Run050-5 from patient PBC0001242, buffy coat sample

  Dataset EGAD00001010799

• Targeted capture ctDNA Library CRCQV42Run050-6

  Targeted capture ctDNA Library CRCQV42Run050-6 from patient PBC0001666, buffy coat sample

  Dataset EGAD00001010800

• Targeted capture ctDNA Library CRCQV42Run050-7

  Targeted capture ctDNA Library CRCQV42Run050-7 from patient PBC0001528, buffy coat sample

  Dataset EGAD00001010801

• Targeted capture ctDNA Library CRCQV42Run050-8

  Targeted capture ctDNA Library CRCQV42Run050-8 from patient PBC0001134, buffy coat sample

  Dataset EGAD00001010802

• Targeted capture ctDNA Library CRCQV42Run050-9

  Targeted capture ctDNA Library CRCQV42Run050-9 from patient PBC0002769, buffy coat sample

  Dataset EGAD00001010803

• Targeted capture ctDNA Library CRCQV42Run051-10

  Targeted capture ctDNA Library CRCQV42Run051-10 from patient PBC0001665, plasma sample

  Dataset EGAD00001010804

• Targeted capture ctDNA Library CRCQV42Run051-11

  Targeted capture ctDNA Library CRCQV42Run051-11 from patient PBC0002989, plasma sample

  Dataset EGAD00001010805

• Targeted capture ctDNA Library CRCQV42Run051-12

  Targeted capture ctDNA Library CRCQV42Run051-12 from patient PBC0001516, plasma sample

  Dataset EGAD00001010806

• Targeted capture ctDNA Library CRCQV42Run051-13

  Targeted capture ctDNA Library CRCQV42Run051-13 from patient PBC0001319, plasma sample

  Dataset EGAD00001010807

• Targeted capture ctDNA Library CRCQV42Run051-14

  Targeted capture ctDNA Library CRCQV42Run051-14 from patient PBC0002989, plasma sample

  Dataset EGAD00001010808

• Targeted capture ctDNA Library CRCQV42Run051-15

  Targeted capture ctDNA Library CRCQV42Run051-15 from patient PBC0001224, buffy coat sample

  Dataset EGAD00001010809

• Targeted capture ctDNA Library CRCQV42Run051-16

  Targeted capture ctDNA Library CRCQV42Run051-16 from patient PBC0002533, buffy coat sample

  Dataset EGAD00001010810

• Targeted capture ctDNA Library CRCQV42Run051-17

  Targeted capture ctDNA Library CRCQV42Run051-17 from patient PBC0002995, buffy coat sample

  Dataset EGAD00001010811

• Targeted capture ctDNA Library CRCQV42Run051-19

  Targeted capture ctDNA Library CRCQV42Run051-19 from patient PBC0002294, buffy coat sample

  Dataset EGAD00001010812

• Targeted capture ctDNA Library CRCQV42Run051-20

  Targeted capture ctDNA Library CRCQV42Run051-20 from patient PBC0003587, buffy coat sample

  Dataset EGAD00001010813

• Targeted capture ctDNA Library CRCQV42Run051-21

  Targeted capture ctDNA Library CRCQV42Run051-21 from patient PBC0001665, buffy coat sample

  Dataset EGAD00001010814

• Targeted capture ctDNA Library CRCQV42Run051-22

  Targeted capture ctDNA Library CRCQV42Run051-22 from patient PBC0002989, buffy coat sample

  Dataset EGAD00001010815

• Targeted capture ctDNA Library CRCQV42Run051-23

  Targeted capture ctDNA Library CRCQV42Run051-23 from patient PBC0001516, buffy coat sample

  Dataset EGAD00001010816

• Targeted capture ctDNA Library CRCQV42Run051-24

  Targeted capture ctDNA Library CRCQV42Run051-24 from patient PBC0001319, buffy coat sample

  Dataset EGAD00001010817

• Targeted capture ctDNA Library CRCQV42Run051-4

  Targeted capture ctDNA Library CRCQV42Run051-4 from patient PBC0001224, plasma sample

  Dataset EGAD00001010818

• Targeted capture ctDNA Library CRCQV42Run051-5

  Targeted capture ctDNA Library CRCQV42Run051-5 from patient PBC0002533, plasma sample

  Dataset EGAD00001010819

• Targeted capture ctDNA Library CRCQV42Run051-6

  Targeted capture ctDNA Library CRCQV42Run051-6 from patient PBC0002995, plasma sample

  Dataset EGAD00001010820

• Targeted capture ctDNA Library CRCQV42Run051-8

  Targeted capture ctDNA Library CRCQV42Run051-8 from patient PBC0002294, plasma sample

  Dataset EGAD00001010821

• Targeted capture ctDNA Library CRCQV42Run051-9

  Targeted capture ctDNA Library CRCQV42Run051-9 from patient PBC0003587, plasma sample

  Dataset EGAD00001010822

• Targeted capture ctDNA Library CRCQV42Run42-10

  Targeted capture ctDNA Library CRCQV42Run42-10 from patient PBC0003643, saliva sample

  Dataset EGAD00001010823

• Targeted capture ctDNA Library CRCQV42Run42-12

  Targeted capture ctDNA Library CRCQV42Run42-12 from patient PBC0001375, plasma baseline sample

  Dataset EGAD00001010824

• Targeted capture ctDNA Library CRCQV42Run42-13

  Targeted capture ctDNA Library CRCQV42Run42-13 from patient PBC0001467, TNBC FFPE sample

  Dataset EGAD00001010825

• Targeted capture ctDNA Library CRCQV42Run42-14

  Targeted capture ctDNA Library CRCQV42Run42-14 from patient PBC0001375, TNBC FFPE sample

  Dataset EGAD00001010826

• Targeted capture ctDNA Library CRCQV42Run42-16

  Targeted capture ctDNA Library CRCQV42Run42-16 from patient PBC0001413, TNBC FFPE sample

  Dataset EGAD00001010827

• Targeted capture ctDNA Library CRCQV42Run42-17

  Targeted capture ctDNA Library CRCQV42Run42-17 from patient PBC0001375, saliva sample

  Dataset EGAD00001010828

• Targeted capture ctDNA Library CRCQV42Run42-4

  Targeted capture ctDNA Library CRCQV42Run42-4 from patient PBC0001375, plasma baseline sample

  Dataset EGAD00001010829

• Targeted capture ctDNA Library CRCQV42Run42-6

  Targeted capture ctDNA Library CRCQV42Run42-6 from patient PBC0001224, plasma 9 month sample

  Dataset EGAD00001010830

• Targeted capture ctDNA Library CRCQV42Run42-7

  Targeted capture ctDNA Library CRCQV42Run42-7 from patient PBC0001299, plasma 15 month sample

  Dataset EGAD00001010831