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 856

Assay: mutation ✕ Clear

Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

PMID 16969349 · PMC2360724 · British journal of cancer · 2006 · 8 claims · 8 setups

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K-Ras codon 12 mutations are significantly associated with metastatic (M+) CRC

crc 202-patient pcr-rflp sscp immunohistochemistry
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

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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
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
ATM variants and cancer risk in breast cancer patients from Southern Finland.

PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

familial brca1 same genotype genotyping denaturing direct
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

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K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

a549 western proliferation clonogenic
Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

PMID 16778407 · PMC2729969 · Journal of Korean medical science · 2006 · 7 claims · 8 setups

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The patient was diagnosed with cystic fibrosis based on elevated sweat chloride concentration and identification of two CFTR mutations.

korean forearm patient's lungs direct quantitative family
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

formalin-fixed ffpe paired study direct pcr restriction
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

p53 tp53 yeast-based sequence align-gvgd
Two cases of isolated diffuse mesangial sclerosis with WT1 mutations.

PMID 16479084 · PMC2733967 · Journal of Korean medical science · 2006 · 8 claims · 7 setups

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Two female infants with isolated diffuse mesangial sclerosis (IDMS) and early-onset end-stage renal failure carried heterozygous WT1 mutations (exon 8 366Arg>His; exon 9 396Asp>Tyr)

genomic kidney blood kidneys direct parental renal
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

chimpanzee megablast pcr flanking-sequence
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

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Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

genomic pcr additional cat linkage direct heteroduplex
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
Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

PMID 16417627 · PMC1382246 · BMC genetics · 2006 · 8 claims · 7 setups

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Heterozygous truncating BRCA2 mutations occur in 47% (7/15) of gastrointestinal MSI cancer cell lines/xenografts, a higher rate than previously reported

gastrointestinal ls174t pl3 msi gene rt-pcr rad51
Alstrom syndrome (OMIM 203800): a case report and literature review.

PMID 18154657 · PMC2266715 · Orphanet journal of rare diseases · 2007 · 8 claims · 8 setups

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The proband is a compound heterozygote for two novel ALMS1 mutations, V424I (exon 6) and H3882Y (exon 17), causative for Alstrom syndrome

genomic healthy proband pcr pcr-rflp plasma
Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

PMID 18053270 · PMC2222245 · BMC medical genetics · 2007 · 8 claims · 6 setups

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PITX1 polymorphisms and haplotypes are significantly associated with autism

agre pitx1 parental family-based extended haplotype
'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

PMID 18000506 · PMC2360265 · British journal of cancer · 2007 · 8 claims · 4 setups

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'Classical' EGFR mutations (exon 18 G719X, exon 19 DEL19, exon 21 L858R) are associated with better clinical outcome (disease control) with gefitinib

microdissected genomic ffpe advanced direct nested immunohistochemistry
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

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-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
Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours.

PMID 17940511 · PMC2360241 · British journal of cancer · 2007 · 8 claims · 4 setups

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Treatment of neuroblastoma cell lines with the HDAC inhibitor trichostatin A (TSA) increased transcription of ERRFI1, PIK3CD, RBP7 and CASZ1, indicating possible epigenetic downregulation of these genes in NB

lines tumours real-time bisulphite sequencing

Experiments

Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

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

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

ATM variants and cancer risk in breast cancer patients from Southern Finland.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

Two cases of isolated diffuse mesangial sclerosis with WT1 mutations.

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

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

Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: considerations from somatic mutations in microsatellite unstable (MSI) gastrointestinal cancers.

Alstrom syndrome (OMIM 203800): a case report and literature review.

Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

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.

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours.