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 26

System / cell line: chromosomes ✕ Assay: haplotype ✕ Clear

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

population blood genomic hapmap snp survival allele
Analysis of concordance of different haplotype block partitioning algorithms.

PMID 16356172 · PMC1343594 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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Each block partitioning algorithm infers blocks differing in number, size, and coverage under different SNP density and allele frequency conditions.

simulated subsamples coalescent diversity-based ld-based
Efficacy assessment of SNP sets for genome-wide disease association studies.

PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

hapmap affymetrix illumina genome-wide swept comparative
Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

PMID 17653048 · PMC2776539 · Molecular vision · 2007 · 8 claims · 4 setups

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No RP patient among 68 Japanese subjects carried a RHO mutation causing an amino acid substitution

blood-derived genomic chromosomes rho whole-locus pcr haplotype
Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease.

PMID 18977788 · PMC2743849 · The British journal of ophthalmology · 2009 · 7 claims · 5 setups

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ABCA4 carrier-frequency-based prevalence estimates of arSTGD (1:1000 and 1:870) are substantially higher than the previously reported phenotypic prevalence of 1:10,000

healthy spanish arstgd denaturing-hplc abcr400 direct
Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

PMID 19716302 · PMC2748900 · Current biology : CB · 2009 · 7 claims · 4 setups

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Direct sequencing of a 13-generation pedigree yields a Y-chromosome mutation rate of 3.0 × 10^-8 mutations/nucleotide/generation

flow-sorted cell-line family lymphoblastoid y-chromosome capillary y-str
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
The vertebrate genome annotation (Vega) database.

PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

genome zebrafish pig nod manual comparative transcript
Sequence variation in the human transcription factor gene POU5F1.

PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

genomic multi-species inferred international resequencing comparative haplotype
Genome sequence, comparative analysis, and population genetics of the domestic horse.

PMID 19892987 · PMC3785132 · Science (New York, N.Y.) · 2009 · 8 claims · 7 setups

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Produced a high-quality draft genome assembly of the domestic horse (EquCab2.0)

single horse eight twelve genome fish chip-on-chip
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

PMID 16202172 · PMC1260020 · BMC medical genetics · 2005 · 8 claims · 3 setups

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HA-1 allele and genotype frequencies were determined in 131 unrelated Italian subjects (HA-1H=0.43, HA-1R=0.57), consistent with Hardy-Weinberg equilibrium and prior North American Caucasian data.

genomic sequence-specific direct melting
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence
Are p.I148T, p.R74W and p.D1270N cystic fibrosis causing mutations?

PMID 15287992 · PMC509248 · BMC medical genetics · 2004 · 8 claims · 7 setups

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A CF-causing second mutation (c.3199del6 or the novel c.3395insA) was found in cis with p.I148T in all CF patients in this cohort who carried p.I148T

genomic family chromosomes hela dgge oligonucleotide restriction
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
Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

PMID 17764569 · PMC2072945 · BMC medical genetics · 2007 · 7 claims · 4 setups

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A nonsense mutation in CDK5RAP2 exon 4, correctly designated 246T>A (Y82X), was identified in all four affected individuals of a Pakistani family linked to MCPH3

pakistani affected unrelated one microsatellite sanger mutation
Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

PMID 18697827 · PMC3711528 · Journal of medical genetics · 2008 · 8 claims · 8 setups

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Four novel JARID1C mutations (p.A77T, p.V504M, p.E468GfsX2, p.R1481GfsX9) were identified in males with mental retardation across three screened cohorts.

genomic family carrier jarid1c dhplc allele-specific restriction
Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

PMID 19929093 · PMC2945731 · The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2009 · 8 claims · 4 setups

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The translocation breakpoints disrupt SLC31A1 (intron 1) on chromosome 9 and a predicted gene containing CCL2 (5'UTR/exons) on chromosome 17

family genomic case-control case fluorescence long-range mutation
Genetic polyploid phasing from low-depth progeny samples.

PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

Has reproduction · 73

WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

solanum illumina pacbio wh-ppg
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race

Experiments

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

Analysis of concordance of different haplotype block partitioning algorithms.

Efficacy assessment of SNP sets for genome-wide disease association studies.

Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease.

Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

The vertebrate genome annotation (Vega) database.

Sequence variation in the human transcription factor gene POU5F1.

Genome sequence, comparative analysis, and population genetics of the domestic horse.

Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

Are p.I148T, p.R74W and p.D1270N cystic fibrosis causing mutations?

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

Previously described sequence variant in CDK5RAP2 gene in a Pakistani family with autosomal recessive primary microcephaly.

Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia.

Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

Genetic polyploid phasing from low-depth progeny samples.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.