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).

Publications 1.3k Datasets 392.5k Experiments 39

System / cell line: tumor ✕ Assay: allele ✕ Clear

Multiple genetic alterations cause frequent and heterogeneous human histocompatibility leukocyte antigen class I loss in cervical cancer.

PMID 10727458 · PMC2193119 · The Journal of experimental medicine · 2000 · 8 claims · 8 setups

Full-text index only

Tumor-associated HLA class I alterations were present in 90% of cervical cancer lesions tested

cervical frozen genomic peripheral multiparameter flow immunohistochemistry
Detection of mutations in EGFR in circulating lung-cancer cells.

PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

Full-text index only

The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

blood archived nsclc plasma microfluidic allele-specific standard
Anterior diffuse retinoblastoma: mutational analysis and immunofluorescence staining.

PMID 19653712 · PMC2810483 · Archives of pathology & laboratory medicine · 2009 · 6 claims · 7 setups

Full-text index only

Anterior diffuse retinoblastoma, traditionally considered sporadic/nonheritable, can arise from a germline RB1 mutation and thus may be heritable

enucleated tumor anterior immunofluorescence rb1 fine-needle
Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups

Has reproduction · 75

scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data

aida merkel-cell 20k myeloma scrna-seq
Development of a fluorescent multiplex assay for detection of MSI-High tumors.

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

Full-text index only

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
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups

Full-text index only

A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.

urothelial hapmap snp plot baf
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

Full-text index only

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

sporadic wilms fetal 293t loh multiplex genome-wide
Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

PMID 16224153 · PMC2779276 · Journal of Korean medical science · 2005 · 7 claims · 4 setups

Full-text index only

High-level-loss (LOH-H) tumors show a tendency toward unmethylation in Maspin, CAGE, MAGE-A2, and RABGEF1 genes

microdissected same bisulfite-modified pcr microsatellite methylation-specific bisulfite
Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 30

Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

tumor each rna-seq whole-genome targeted pcr-based
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

Full-text index only

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
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

Full-text index only

Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

Full-text index only

Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

Full-text index only

Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

breast hek293 erβ1 allelic luciferase stability
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

Full-text index only

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
p53 mutations in urinary bladder cancer.

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

Full-text index only

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
Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR.

PMID 16961930 · PMC1570477 · Molecular cancer · 2006 · 8 claims · 6 setups

Full-text index only

Somatic deletion of the maternal NF1 allele occurred in the melanoma of an NF1 patient, demonstrating biallelic NF1 inactivation.

peripheral microdissected formalin-fixed microsatellite conventional digital
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

Full-text index only

Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

Full-text index only

-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

Full-text index only

Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

Full-text index only

TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

snap-frozen tumor u-2-os patients pcr bisulphite loss

Experiments

Multiple genetic alterations cause frequent and heterogeneous human histocompatibility leukocyte antigen class I loss in cervical cancer.

Detection of mutations in EGFR in circulating lung-cancer cells.

Anterior diffuse retinoblastoma: mutational analysis and immunofluorescence staining.

Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

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

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

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

Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

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

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

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

p53 mutations in urinary bladder cancer.

Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.