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).

• HapMap-based study of the 17q21 ERBB2 amplicon in susceptibility to breast cancer.

  PMID 17117180 · PMC2360759 · British journal of cancer · 2006 · 6 claims · 5 setups

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  Common genetic variation (tSNPs and haplotypes) across the 400-kb 17q21 ERBB2 amplicon is not associated with breast cancer risk in British women.

  white same hapmap snp haplotype tagging

• 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

• 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

• Design and analysis issues in genome-wide somatic mutation studies of cancer.

  PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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  Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

  hypothetical panel colorectal germline simulation targeted genome-wide

• Targeted capture and massively parallel sequencing of 12 human exomes.

  PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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  Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

  hapmap unrelated na18507 randomly targeted array-based molecular

• 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

• 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

• 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

• 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

• 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

• Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

  PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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  Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

  estonian hapmap ceu snp tagsnp marker

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• The promise and reality of personal genomics.

  PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

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  Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

  ak1 six whole-genome copy-number genotyping-based

• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

  PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups

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  CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.

  missense same synthetic tp53 random support principal

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• SNPdetector: a software tool for sensitive and accurate SNP detection.

  PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

  inbred unrelated zebra same pcr manual comparative

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative

• Accurate whole human genome sequencing using reversible terminator chemistry.

  PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

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  A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

  bac flow-sorted same yoruba reversible snp targeted

• Reconstructing Indian population history.

  PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

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  Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

  indian pairs gujarati genome-wide principal fst-based

• The diploid genome sequence of an individual human.

  PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups

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  Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing

  donor huref whole-genome assembly-to-assembly snp