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 23

System / cell line: hapmap ✕ Assay: correlation ✕ Clear

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
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
Genomics and biology come together to fight HIV.

PMID 18366259 · PMC2270331 · PLoS biology · 2008 · 8 claims · 6 setups

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Genome-wide association studies have identified ~100 genetic polymorphisms robustly (genome-wide significant) linked to common human traits/diseases, but the biological mechanisms behind most remain unknown.

ceph hiv-positive elledge heritability linkage modified
A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

PMID 18710563 · PMC2556685 · BMC genomics · 2008 · 7 claims · 5 setups

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A genome-wide library of nearly 16 million local maximum parsimony phylogenies was constructed from HapMap CEU and YRI SNP data across all human autosomes

hapmap 5-snp genome-wide first maximum mutual pearson
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

independent ceph same unrelated snp individual simulated
An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

PMID 18302794 · PMC2292209 · BMC genetics · 2008 · 7 claims · 5 setups

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Among the four HapMap populations, CHB shows the best correlation with the Shanghai population on allele frequencies, LD, and haplotype frequencies

unrelated shanghai tsnps snp allele linkage
An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

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CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

individuals hapmap egp snp tag median-joining
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
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
A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

PMID 18194558 · PMC2248205 · BMC genetics · 2008 · 8 claims · 5 setups

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A hierarchical/modular approach integrating quality control, LD, physical distance, and gene ontology identifies authentic associations among those found by statistical tests in pooled DNA GWAS

pooled sickle centenarian snp pooled gene
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
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
A pharmacogene database enhanced by the 1000 Genomes Project.

PMID 19745786 · PMC2935084 · Pharmacogenetics and genomics · 2009 · 7 claims · 4 setups

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The database provides a convenient portal for immediate utilization of newly released 1000 Genomes Project (KGP) data in pharmacogenetic studies

ceu hapmap lymphoblastoid genotype-phenotype whole-genome low-coverage
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

representative illumina six snp serial concentration
Identification of genomic regions contributing to etoposide-induced cytotoxicity.

PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

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Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

ceph subset hapmap simulated growth heritability non-parametric
Calibrating the performance of SNP arrays for whole-genome association studies.

PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

american liver simulated hapmap snp gene simulation-based
SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

randomly heirs seattlesnps african resequencing genome-wide tag
What can genome-wide association studies tell us about the genetics of common disease?

PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

case gwa simulated literature cochran-armitage computer
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

Experiments

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

Genomics and biology come together to fight HIV.

A human genome-wide library of local phylogeny predictions for whole-genome inference problems.

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

An evaluation of the performance of HapMap SNP data in a Shanghai Chinese population: analyses of allele frequency, linkage disequilibrium pattern and tagging SNPs transferability on chromosome 1q21-q25.

An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

Identification of common genetic variation that modulates alternative splicing.

Population genomics of human gene expression.

Allelotyping of pooled DNA with 250 K SNP microarrays.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

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

A pharmacogene database enhanced by the 1000 Genomes Project.

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

Identification of genomic regions contributing to etoposide-induced cytotoxicity.

Calibrating the performance of SNP arrays for whole-genome association studies.

SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

What can genome-wide association studies tell us about the genetics of common disease?

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.