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).

• Allelotype of squamous cell carcinoma of the head and neck: fractional allele loss correlates with survival.

  PMID 7577465 · PMC2033926 · British journal of cancer · 1995 · 7 claims · 4 setups

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  Allelic imbalance/LOH occurs most frequently on chromosome arms 3p, 9p, 17p and 18q (>45% LOH) in SCCHN

  scchn subset microsatellite fractional survival

• High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

  PMID 11207044 · PMC2363776 · British journal of cancer · 2001 · 8 claims · 4 setups

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  The SAFB locus region on chromosome 19p13.2-3 shows a very high rate of loss of heterozygosity (LOH) in primary breast cancer, indicating presence of a breast tumour-suppressor gene locus

  breast microdissected loh rt-pcr pcr

• p16INK4 gene mutations are relatively frequent in ampullary carcinomas.

  PMID 9414654 · PMC5921281 · Japanese journal of cancer research : Gann · 1997 · 8 claims · 2 setups

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  P16INK4 gene mutations are relatively frequent in sporadic ampullary carcinomas

  sporadic loss mutational

• p53 mutations in urinary bladder cancer.

  PMID 11384101 · PMC2363660 · British journal of cancer · 2001 · 6 claims · 5 setups

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  p53 mutations are strongly associated with high-grade/high-stage bladder tumors and are nearly absent in lowly malignant tumors (Ta, G1-G2a)

  urinary tumor patients single multiplex-pcr dyedeoxy loss

• Long-term survival and transmission of INI1-mutation via nonpenetrant males in a family with rhabdoid tumour predisposition syndrome.

  PMID 18087273 · PMC2361463 · British journal of cancer · 2008 · 8 claims · 5 setups

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  The malignant brain tumours in patients III-1, III-3, and III-4, originally classified as anaplastic ependymomas, are in fact atypical teratoid/rhabdoid tumours (AT/RT)

  constitutional formalin-fixed tumour blood sanger denaturing immunohistochemistry

• The homeobox gene CDX2 in colorectal carcinoma: a genetic analysis.

  PMID 11161380 · PMC2363702 · British journal of cancer · 2001 · 7 claims · 7 setups

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  No CDX2 mutations predisposing to sporadic colorectal cancer were identified

  genomic pcr cdna informative sscp pcr automated

• High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

  PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

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  High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

  tumour serum nsclc comparative snp methylation

• OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci.

  PMID 17098932 · PMC1669730 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  OncoDB.HCC integrates human HCC LOH, CGH, microarray/proteomic expression, PubMed-reported gene data, and rodent HCC QTLs into a single physical-map-based database

  paired hcc rodent semi-quantitative microarray comparative

• Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

  PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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  Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

  normalized individuals subset same affymetrix fluorescent snp

• Absence of somatic alterations of the EB1 gene adenomatous polyposis coli-associated protein in human sporadic colorectal cancers.

  PMID 9823979 · PMC2063196 · British journal of cancer · 1998 · 6 claims · 4 setups

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  No somatic point mutations were found in the entire EB1 coding sequence in sporadic colorectal cancers or adenomas

  sporadic pcr colorectal rt-pcr direct microsatellite

• 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

• Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

  PMID 16420694 · PMC1382255 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  SNPscan is a web-accessible tool that displays SNP copy number, genotype call, and LOH p-value data together in a single plot per sample

  lymphoblastoid skin ceph genomic snp array pcr

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

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  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative

• Rapid detection of allele loss in colorectal tumours using microsatellites and fluorescent DNA technology.

  PMID 8512811 · PMC1968523 · British journal of cancer · 1993 · 6 claims · 3 setups

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  Fluorescently labelled microsatellite PCR products analysed on an automated DNA sequencer allow rapid, automated quantitation (peak size, height, area) of allele loss, avoiding drawbacks of radioactive RFLP analysis.

  fresh-frozen paired pcr genomic fluorescent automated

• A comprehensive catalogue of somatic mutations from a human cancer genome.

  PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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  Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

  colo-829 additional whole-genome conventional pcr

• Re-evaluating early breast neoplasia.

  PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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  The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

  dcis breast patient-matched premalignant comparative combined cdna

• WAF1/CIP1 structural abnormalities do not contribute to cell cycle deregulation in ovarian cancer.

  PMID 8645586 · PMC2074480 · British journal of cancer · 1996 · 7 claims · 5 setups

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  No WAF1/CIP1 coding mutations were found in any of 36 ovarian carcinomas sequenced, including tumors with LOH on 6p and those lacking p53 mutations

  ovarian blood tumor pcr sequencing loss

• Somatic and germline mutation in GRIM-19, a dual function gene involved in mitochondrial metabolism and cell death, is linked to mitochondrion-rich (Hurthle cell) tumours of the thyroid.

  PMID 15841082 · PMC2361763 · British journal of cancer · 2005 · 8 claims · 5 setups

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  Somatic missense GRIM-19 mutations occur in a subset of sporadic Hürthle cell carcinomas but not in non-Hürthle cell thyroid carcinomas or blood donors

  sporadic hürthle pcr loss semi-quantitative

• Accuracy of predicting the genetic risk of disease using a genome-wide approach.

  PMID 18852893 · PMC2561058 · PloS one · 2008 · 8 claims · 4 setups

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  Deterministic equations can predict the accuracy (r_gĝ) of genome-wide genetic risk/value prediction for continuous, dichotomous, and case-control study designs.

  simulated stochastic

• A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

  PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups

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  A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.

  genomic laser-capture cell-free hela sscp loss transcription