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 27

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

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
Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

genomic pools training siddt individual pooled k-correction
Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups

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Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA

pooled pool snps snp snapshot individual
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
Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

PMID 19096718 · PMC2603445 · Molecular vision · 2008 · 7 claims · 5 setups

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CYP1B1 mutations are implicated in POAG among Iranians, notably in the juvenile-onset form

genomic cyp1b1 poag microarray-based dideoxy sanger
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
Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

irish iccss postmortem genomic snp haplotype logistic
Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

amish unrelated same overall microsatellite combinatorial permutation
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
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
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
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
Modeling the amplification dynamics of human Alu retrotransposons.

PMID 16201008 · PMC1239904 · PLoS computational biology · 2005 · 8 claims · 4 setups

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Combining sequence diversity (π) and insertion polymorphism level (IPL) statistics can statistically exclude implausible Alu amplification scenarios and narrow the range of plausible ones for individual subfamilies.

simulated genome population computer comparative population
The brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism and depression in Mexican-Americans.

PMID 17632285 · PMC2686836 · Neuroreport · 2007 · 7 claims · 4 setups

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BDNF SNP rs6265 (Val66Met) is significantly associated with diagnosis of major depression in Mexican-Americans

genomic same participants genotyped snp hardy-weinberg clinical
Selecting additional tag SNPs for tolerating missing data in genotyping.

PMID 16259642 · PMC1316880 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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There exists a subset of SNPs (robust tag SNPs) that can distinguish all distinct haplotypes even when up to m SNPs are missing

simulated hudson's chromosome robust
Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

PMID 16848906 · PMC1543620 · Molecular pain · 2006 · 8 claims · 5 setups

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COMT SNP5 (rs740603, intron 1) shows significant association with maximum post-operative pain rating

surgical candidate haplotype allele
Genomic screen for loci associated with tobacco usage in Mission Indians.

PMID 16472381 · PMC1386651 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Regular tobacco use (h2=0.37±0.11) and persistent tobacco use (h2=0.34±0.12) are moderately heritable in this Mission Indian sample

mission pedigrees same participants genotyping multipoint heritability
Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

PMID 17634103 · PMC1947971 · BMC genomics · 2007 · 8 claims · 4 setups

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A closed-form approximation to the F-test non-centrality parameter (NCP) incorporating genetic model parameters (disease allele frequency, marker allele frequency, prevalence, genotype relative risk, sample size, genetic model, number of pools/replicates, machine variability) can be used to compute power for DNA pooling association studies

modeled analytic factorial power
PDA: Pooled DNA analyzer.

PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

heterozygous pools ordered peak pooled single-point
Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

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A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

asian random subjects unrelated arms-pcr msei sanger

Experiments

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

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

Allelotyping of pooled DNA with 250 K SNP microarrays.

Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

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

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

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

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

Identification of common genetic variation that modulates alternative splicing.

Modeling the amplification dynamics of human Alu retrotransposons.

The brain-derived neurotrophic factor rs6265 (Val66Met) polymorphism and depression in Mexican-Americans.

Selecting additional tag SNPs for tolerating missing data in genotyping.

Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans.

Genomic screen for loci associated with tobacco usage in Mission Indians.

Incorporation of genetic model parameters for cost-effective designs of genetic association studies using DNA pooling.

PDA: Pooled DNA analyzer.

Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.