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 79

System / cell line: reference ✕ Assay: genotyping ✕ Clear

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

PMID 20003400 · PMC2806376 · BMC genetics · 2009 · 7 claims · 4 setups

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Pooled genotyping on the Affymetrix 500k platform using PPC yields highly accurate allele frequency estimates (correlation 0.988) comparable to or better than the 10k/100k platforms.

case hapmap snp individual allele
"Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

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An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission
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
HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

PMID 15629059 · PMC5172246 · Genomics, proteomics & bioinformatics · 2003 · 7 claims · 5 setups

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HLA-A gene shows high polymorphism in the Northern Chinese Han population, with 74 gene types and 36 alleles detected in 161 individuals

genomic ihwg peripheral allele sequence-based pcr sbt
Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

individually reference equimolar independently snp reference pooled
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

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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
Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

pools individual same parental pooled individual test-retest
Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups

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SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping

pooled single same caucasian snp individual quantification
Allelotyping of pooled DNA with 250 K SNP microarrays.

PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

pool nspi individual snp individual call
Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

Has reproduction · 45

Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

original sire-son whole-genome multi-sample graph-based
Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

peripheral ceph individuals cases strp genotyping fluorescent
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood
Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups

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Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm

unrelated same haplotype caucasian snp haplotype group
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

normal genomic sk-br-3 cancer snp quantitative allele-specific
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

PMID 19083245 · PMC2662477 · Blood cells, molecules & diseases · 2009 · 7 claims · 4 setups

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A new CYP2C9 coding polymorphism, G1078A (D360N) in exon 7, was identified in an African American patient who experienced major gastrointestinal hemorrhage on warfarin therapy

african index cyp2c9 study pyrosequencing pcr custom
Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.

PMID 18842150 · PMC2577186 · BMC microbiology · 2008 · 7 claims · 8 setups

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MDA-amplified DNA from minute gastric biopsy specimens enables concurrent PCR-based genotyping of bacterial (H. pylori) and human host genes from a single DNA source

mda-amplified pylori-positive multiplex pyrosequencing pcr
The past and future of tuberculosis research.

PMID 19855821 · PMC2745564 · PLoS pathogens · 2009 · 8 claims · 6 setups

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Integrating systems biology with epidemiology ('systems epidemiology') will be required to better predict TB's trajectory and eliminate the disease

clinical mycobacterium mtbc patients fingerprinting whole-genome microarray

Experiments

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

Functional copy-number alterations in cancer.

HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

Allele quantification using molecular inversion probes (MIP).

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

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

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

Allelotyping of pooled DNA with 250 K SNP microarrays.

Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

A potentially deleterious new CYP2C9 polymorphism identified in an African American patient with major hemorrhage on warfarin therapy.

Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.

The past and future of tuberculosis research.