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 21

System / cell line: normal ✕ Assay: snp-array ✕ Clear

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

sidcon real mixtures snp re-analysis
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.

hapmap bladder prostate simulated affymetrix simulation
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
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original
Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

cervical tumors pap tumor snp fluorescence fish
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
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
Functional copy-number alterations in cancer.

PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups

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RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.

pleomorphic hapmap large snp computational
Current and future directions in genomics of amyotrophic lateral sclerosis.

PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

american sals dutch irish genome laser expression
Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

PMID 19681120 · PMC3430375 · Genes, chromosomes & cancer · 2009 · 8 claims · 5 setups

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PCDH10 promoter hypermethylation is a frequent event in invasive cervical cancer

invasive lines normal cervical snp methylation-specific bisulphite
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
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

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

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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
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

PMID 19903341 · PMC2810663 · Genome biology · 2009 · 7 claims · 3 setups

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GAP is a method for automatic detection of absolute segmental copy number and genotype status from SNP-array cancer genome profiles

breast snp flow karyotyping
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 49

B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

dlbcl normal same lymphoma help errbs massarray
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
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
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
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
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

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

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

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

Functional copy-number alterations in cancer.

Current and future directions in genomics of amyotrophic lateral sclerosis.

Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

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

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

Interpretation of genomic data: questions and answers.

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

An integrated genomic analysis of human glioblastoma multiforme.

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.