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).

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

  PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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  MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

  genomic domestic pooled colorectal snp pooling microsatellite

• Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

  PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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  The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

  genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage

• Completing the map of human genetic variation.

  PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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  A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

  genomic fosmid full hapmap paired targeted genotyping

• Microdroplet-based PCR enrichment for large-scale targeted sequencing.

  PMID 19881494 · PMC2779736 · Nature biotechnology · 2009 · 7 claims · 5 setups

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  Microdroplet PCR enables massively parallel singleplex amplification (up to ~1.5 million reactions, up to 4,000 targets) for targeted sequencing enrichment

  genomic single targeted scale-up variant

• Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer.

  PMID 19644707 · PMC2778717 · Human genetics · 2009 · 7 claims · 5 setups

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  Resequencing of the 97-kb 10q11.2 region identified 241 novel polymorphisms not previously reported in dbSNP

  genomic plco hapmap computational targeted long-range genotype

• Challenges and standards in integrating surveys of structural variation.

  PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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  There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

  genomic hapmap reference independent comparative snp fosmid

• Global variation in copy number in the human genome.

  PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

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  A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

  hapmap subset blood snp array karyotyping

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• 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

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• 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

• 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

• 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

• 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

• QuickSNP: an automated web server for selection of tagSNPs.

  PMID 17517769 · PMC1933212 · Nucleic acids research · 2007 · 7 claims · 3 setups

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  QuickSNP is a freely available automated web server for selecting tagSNPs from a chromosomal region, genes within a region, or a specified gene list, with a gene-centric selection option

  genes selected chromosome automated gene-centric tagsnp

• Gene-centric characteristics of genome-wide association studies.

  PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups

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  High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.

  phase omim snps snp disease genomic

• Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

  PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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  Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

  genomic sequenced korean common sanger sequence population

• Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

  PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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  ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

  hapmap combined coriell ceu allele-specific linear one-sample

• Genomic medicine and developing countries: creating a room of their own.

  PMID 18487990 · PMC7096950 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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  Developing countries can harness human genetic variation to benefit their populations and economies rather than only importing technology from developed nations.

  key polio asthma patients in-depth viral genetic