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• CPM table for POPLAR (GO28953)

  This dataset contains counts per million for 192 tumor samples profiled by RNA-seq for the entire transcriptome for samples originating from POPLAR (GO28753).

  Dataset EGAD00001008631

• RNA-Seq data for manuscript titled: A sporadic Alzheimers blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies

  RNA-Seq data for manuscript titled: A sporadic Alzheimers blood-brain barrier model for developing ultrasound-mediated delivery of Aducanumab and anti-Tau antibodies

  Dataset EGAD00001008670

• ALCHEMIST Study

  The ALCHEMIST study will accrue patients that are potentially eligible for the Intergroup adjuvant studies and perform central EGFR and ALK genotyping using a central reference laboratory certified by the Clinical Laboratory Improvement Amendments of 1988 (CLIA). Patients may either present prior to surgery with resectable NSCLC, may present following complete resection (before or after adjuvant chemotherapy). Eligibility is limited to those with NSCLC of a non-squamous histological subtype and those with adequate performance status and organ function for future trial eligibility. All subjects must submit tissue for central EGFR and ALK genotyping, as well as additional tissue for advanced genomics at the CCG. Subjects may have had local genotyping done prior to registration, however if these results shows no targetable EGFR or ALK alterations (or if it shows a KRAS mutation) then the patient will not be eligible for this screening protocol given the primary aim is to facilitate accrual to the adjuvant studies. All subjects will provide peripheral blood for matched normal DNA. All subjects (including those known to have EGFR or ALK alterations with local genotyping) will have formalin-fixed tissue collected for central genotyping. The testing will be performed at Response Genetics (Los Angeles, CA), a commercial CLIA-certified laboratory. ALK FISH will be performed using the Vysis break-apart probe and EGFR sequencing will be performed of exons 18-21. It is preferred that a full tumor block be submitted, but if unavailable, 15 unstained slides can be submitted. Genotyping results are expected to be provided to the treating clinician within 14 business days of submission so they can be used to determine eligibility for the randomized adjuvant studies, or to confirm the local results. Results will also be reported at intervals to the study team for update into the Alliance database. In addition to the commercial genotyping at Response Genetics, tissue will be collected for research genomics by CCG. For those patients with a block available, this will be forwarded to the CCG after clinical testing at Response Genetics. For patients without a block available, 15 unstained slides should be submitted to the CCG BCR for exploratory analysis. A peripheral blood specimen will also be collected and sent to the CCG BCR to use as matched normal. Specimens will be coded. Over the course of the study, the CCG will perform advanced genomic analysis of the resected lung cancer specimens in a research, non-CLIA environment. Following completion of the genomic analysis, the results can be matched with the clinical follow-up results using a link between the samples codes and the patient identifiers for correlative analyses. Subjects participating in the follow-up portion of the ALCHEMIST study, as well as those participating in the adjuvant therapeutic studies, are expected to undergo a standard-of-care diagnostic biopsy to confirm recurrence. At least two core biopsies, minimum, should be obtained as part of this recurrence biopsy. Paraffin embedded tissue from this biopsy will be used for confirmation of recurrence, for CLIA genomics to plan subsequent clinical trials, and for additional research genomics by the CCG. Plasma will additionally be collected at recurrence and sent to CCG for study of circulating free DNA (cfDNA). Data for the ALCHEMIST study is not yet available to be accessed by the public at this time; when ready it will be made available at the GDC Data Portal.

  Study phs001140

• DAC Recurrent resistance mutations to lirafugratinib delineate treatment sequences for FGFR2-driven tumors

  DAC for Recurrent resistance mutations to lirafugratinib delineate treatment sequences for FGFR2-driven tumors

  Dac EGAC50000000699

• Exome data for an Australian Aboriginal population

  Genotype and exome data for an Australian Aboriginal population: a reference panel for health-based research.

  Dataset EGAD00001001661

• SV-based ctDNA detection in soft tissue sarcoma

  33 patients with localized soft tissue sarcoma consented for ctDNA tracking in the peri-operative and surveillance periods. WGS at a target of 15x coverage was performed from DNA extracted from FFPE of localized soft tissue sarcoma. Structural variants were identified from WGS and ddPCR assays were designed for tumor informed tracking of SV for ctDNA.

  Study EGAS50000001811

• Fastq data for ChIP-Seq (H3K9me3) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (H3K9me3) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001408

• Fastq data for ChIP-Seq (Input) assays for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  Fastq data for ChIP-Seq (Input) assays assay for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001409

• WGS for fibroblasts colonies

  This dataset contains WGS for fibroblasts colonies obtained from carriers and non-carriers of germline POLD1 L474P. Data for single-cell colonies obtained from immortalized fibroblasts are present for eight out of 16 family members (six carriers and two non-carriers). Sequences obtained for colonies after approximately 40 passages also present for six out of these eight colonies (four carriers and 2 non-carriers). Samples marked with "_F2" and "_F3" represent sequences of single cell-derived colonies and colonies after ~40 passages correspondingly.

  Dataset EGAD00001009283

• cfMethyl-seq data (cfSort study) from serial plasma samples of NSCLC patients

  The cfMethyl-Seq libraries of the serial plasma cfDNA samples from the four NSCLC patients were constructed following the standard protocol. 10 ng of cfDNA in the volume of 25 µl was used as input material. 5’-end dephosphorylation was done with 3 µl 10xCutSmart buffer and 2 µl quick CIP from NEB (Ipswich, MA) at 37 oC for 30 min then heat-inactivated at 80 oC for 5 min. The 3’-end blocking was done with 0.5 µl 10xCutSmart buffer, 3 µl 2.5 mM CoCl2, 1 µl terminal transferase (all from NEB), and 0.5 µl 1 mM ddGTP at 37 oC for 2 h followed by 75 oC for 20 min. The mixture was then purified with 2x AmpureXP beads (Beckman Coulter, Indianapolis, IN) and eluted in 21.5 µl RT-PCR grade water (Thermo-Fisher, Waltham, MA). Restriction digestion was done with 2.5 µl 10xCutSmart buffer and 1 µl MspI (NEB) for 18 h at 37  oC and 20 min at 65 oC . 0.5 µl 10xCutSmart buffer, 0.3 µl dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 µl Klenow (exo-, 5U/µl, NEB) and 2.6 µl RT-PCR water, 0.6 µl 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30  oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 µl 10xThermoFisher HC T4 ligase buffer, 0.4 µl 100 mM ATP (ThermoFisher), 0.2 µl 50 mM DTT, 1 µl ThermoFisher HC T4 DNA ligase (30 Weiss Unit/µl), 5 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 µl RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 µl of universal and index primer each) and 25 µl KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98  oC for 45 s, 15 cycles of 98  oC for 15 s, 60  oC for 30 s and 72  oC for 30 s, followed by a final extension at 72  oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 µl EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.

  Dataset EGAD00001010881