Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity.

  PMID 35418127 · PMC9008010 · Scientific data · 2022 · 6 claims · 5 setups

  Has reproduction · 87

  This dataset is the most comprehensive public-facing dataset of ultra-deep ctDNA sequencing data generated to date

  contrived enzymatically extracted targeted

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

  Has reproduction · 50

  TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

  t-cell hcc1395 targeted whole-exome

• Profiling critical cancer gene mutations in clinical tumor samples.

  PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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  OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

  clinical fresh same pediatric mass sanger barcoded

• Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

  PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

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  MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

  proband's peripheral hmsh2 microsatellite direct targeted

• Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

  PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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  2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

  sporadic wilms fetal 293t loh multiplex genome-wide

• Development of a fluorescent multiplex assay for detection of MSI-High tumors.

  PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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  Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

  colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry

• Molecular tumor profiling: translating genomic insights into clinical advances.

  PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

  Full-text index only

  Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

  breast ovarian panel tumor gene-expression candidate-gene large-scale

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups

  Has reproduction

  Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.

  tcga metastatic tumor-only whole-exome wes copy-number

• Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

  PMID 35680918 · PMC9184574 · Scientific data · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Four reference samples (Sample A, Sample B, Sample C, Sample Spike-in/AC5) were developed with large numbers of high-confidence positive and negative small variant positions to serve as known content for oncopanel performance assessment.

  agilent burning integrated igenetech targeted

• Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas.

  PMID 18790768 · PMC2651569 · Molecular cancer therapeutics · 2008 · 8 claims · 6 setups

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  CDK4 mutations (K22Q, R24C, R24L) alone do not confer resistance to the BRAF inhibitor SB590885

  melanoma metastatic wm39 451lu mtt pcr array

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• Utilization of genomic signatures to identify phenotype-specific drugs.

  PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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  A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

  nci-60 breast mda-mb-231 signature-drug gene signature

• Identification of HNPCC by molecular analysis of colorectal and endometrial tumors.

  PMID 15528786 · PMC3839268 · Disease markers · 2004 · 8 claims · 5 setups

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  The Bethesda criteria, with a few modifications, are appropriate to identify families eligible for MMR mutation genetic testing

  colorectal endometrial microsatellite immunohistochemistry germline

• Genomics: applications in mechanism elucidation.

  PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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  Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

  extract panel saccharomyces inbred affinity cytotoxicity genome-wide

• Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

  PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

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  PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

  pancreatic same tumor pet sscp methylation-specific microsatellite

• Evolutionarily conserved human targets of adenosine to inosine RNA editing.

  PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

  panel brain chicken flna comparative rt-pcr homology

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide

• Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

  PMID 19737971 · PMC2994259 · Molecular cancer research : MCR · 2009 · 8 claims · 8 setups

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  CLSPN is a mediator protein essential for the ATR- and CHK1-dependent checkpoint response to replicative stress or single-stranded DNA

  ebv-immortalized sporadic same caucasian genomic denaturing genotyping

• Can we find the genes involved in complex traits?

  PMID 15461809 · PMC545590 · Genome biology · 2004 · 8 claims · 8 setups

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  Large regions of the mouse genome exist in linkage disequilibrium (LD), including a 40 Mb region on the X chromosome, reflecting selection against recombination to preserve allelic combinations.

  inbred strains 000-strain recombinant snp expression eqtl

• A case report of familial benign hypocalciuric hypercalcemia: a mutation in the calcium-sensing receptor gene.

  PMID 16642557 · PMC2687637 · Yonsei medical journal · 2006 · 8 claims · 6 setups

  Full-text index only

  A heterozygous E297K mutation (GAG→AAG, exon 4) of the CaSR gene was identified in a Korean family with FBHH.

  genomic proband pcr pcr-rflp bone