Crowdsourced direct-to-consumer genomic analysis of a family quartet.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26547235", "kind": "science-record", "revision": 8, "content_hash": "sha256:9ca3e683285b63885ac40a386a20997d3ea12276d828552ef6a16f06717d6978", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T22:42:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Crowdsourced direct-to-consumer genomic analysis of a family quartet.", "doi": "10.1186/s12864-015-1973-7", "pmid": "26547235", "authors": ["Manuel Corpas", "Willy Valdivia-Granda", "Nazareth Torres", "Bastian Greshake", "Alain Coletta", "Alexej Knaus", "Andrew P Harrison", "Mike Cariaso", "Federico Moran", "Fiona Nielsen", "Daniel Swan", "David Y Weiss Solís", "Peter Krawitz", "Frank Schacherer", "Peter Schols", "Huangming Yang", "Pascal Borry", "Gustavo Glusman", "Peter N Robinson"], "journal": "BMC genomics", "year": 2015, "abstract": "BACKGROUND: We describe the pioneering experience of a Spanish family pursuing the goal of understanding their own personal genetic data to the fullest possible extent using Direct to Consumer (DTC) tests. With full informed consent from the Corpas family, all genotype, exome and metagenome data from members of this family, are publicly available under a public domain Creative Commons 0 (CC0) license waiver. All scientists or companies analysing these data (\"the Corpasome\") were invited to return results to the family.\nMETHODS: We released 5 genotypes, 4 exomes, 1 metagenome from the Corpas family via a blog and figshare under a public domain license, inviting scientists to join the crowdsourcing efforts to analyse the genomes in return for coauthorship or acknowldgement in derived papers. Resulting analysis data were compiled via social media and direct email.\nRESULTS: Here we present the results of our investigations, combining the crowdsourced contributions and our own efforts. Four companies offering annotations for genomic variants were applied to four family exomes: BIOBASE, Ingenuity, Diploid, and GeneTalk. Starting from a common VCF file and after selecting for significant results from company reports, we find no overlap among described annotations. We additionally report on a gut microbiome analysis of a member of the Corpas family.\nCONCLUSIONS: This study presents an analysis of a diverse set of tools and methods offered by four DTC companies. The striking discordance of the results mirrors previous findings with respect to DTC analysis of SNP chip data, and highlights the difficulties of using DTC data for preventive medical care. To our knowledge, the data and analysis results from our crowdsourced study represent the most comprehensive exome and analysis for a family quartet using solely DTC data generation to date.", "claims": [{"id": "claim-method", "statement": "In order to compare two populations and discriminate if they have different hair colour information, a goodness of fit test was conducted. The goodness of fit test reported a contingency table that could be used to study genotypic frequency differences between “family” and “reference” cohorts. The χ2 and Fisher´s exact statistic were calculated. In order to infer statistical significance, only the Fisher exact test was used due to the small size of Corpas family.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26547235", "locator": "sections[14] \"Red hair analysis\" paragraph 2", "quote": "In order to compare two populations and discriminate if they have different hair colour information, a goodness of fit test was conducted. The goodness of fit test reported a contingency table that could be used to study genotypic frequency differences between “family” and “reference” cohorts. The χ2 and Fisher´s exact statistic were calculated. In order to infer statistical significance, only the Fisher exact test was used due to the small size of Corpas family."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Exome data used is deposited in figShare [http://figshare.com/articles/Corpasome/693052] and can be freely downloaded and used under a CC0 license.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26547235", "locator": "sections[17] \"Deposition of data\" paragraph 2", "quote": "Exome data used is deposited in figShare [http://figshare.com/articles/Corpasome/693052] and can be freely downloaded and used under a CC0 license."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Starting from a common VCF file and selecting significant company-report results, the study found no overlap among annotations; separately, exome and 23andMe variants were compared by matching SNPs by ID in the VCF and 23andMe files, with scripts and data available via figShare.", "kind": "quantitative", "target": {"value": 10.0, "unit": "fold change", "tolerance": null, "source": "We found that most ‘non-concordant’ SNPs (23andMe SNPs not present in the exome) have low coverage (under 10 fold)."}, "evidence": [{"asset": "source:pmid:26547235", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Starting from a common VCF file and after selecting for significant results from company reports, we find no overlap among described annotations."}, {"asset": "source:pmid:26547235", "locator": "sections[3] \"Comparison of exome and 23andMe data\" paragraph 2", "quote": "SNPs were matched by ID (not by coordinates) in both the VCF exome and the 23andMe files. The scripts and data used are available via figShare."}, {"asset": "source:pmid:26547235", "locator": "sections[3] \"Comparison of exome and 23andMe data\" paragraph 2", "quote": "We found that most ‘non-concordant’ SNPs (23andMe SNPs not present in the exome) have low coverage (under 10 fold)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Starting from a common VCF file and selecting significant company-report results, the study found no overlap among annotations; separately, exome and 23andMe variants were compared by matching SNPs by ID in the VCF and 23andMe files, with scripts and data available via figShare.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26547235"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26547235", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12864-015-1973-7", "sha256": "sha256:0a92c8c03298d88db50bf3a7c8882a3d8d11ac40891a8d1d0869f136a8f2d894", "bytes": 56839, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12864-015-1973-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4636840", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:26547235:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:46934e77d2d799844ca8c4a209dcfab84c26300df6eb1efe53a3346509a5236c", "bytes": 2252, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab1", "version": null, "note": "Summary of the crowdsourced data with its metadata. The dataset includes a total of 27 files and 18,463 MB of data", "structure": {"pmcid": "PMC4636840", "section_index": 12, "section_title": "Crowdsourced data", "row_count": 22, "column_count": 9}, "table": {"label": "Table 1", "caption": "Summary of the crowdsourced data with its metadata. The dataset includes a total of 27 files and 18,463 MB of data", "rows": [["Type", "Provider", "Source", "Platform", "Format", "Year obtained", "# files", "Individuals(s)", "Approx. size (MB)"], ["Genotype", "23andMe", "Saliva", "SNP chip v2", "bed.zip", "2009", "1", "Son", "5"], ["Genotype", "23andMe", "Saliva", "SNP chip v3", "bed.zip", "2011", "1", "Mother", "8"], ["Genotype", "23andMe", "Saliva", "SNP chip v3", "bed.zip", "2011", "1", "Father", "8"], ["Genotype", "23andMe", "Saliva", "SNP chip v3", "bed.zip", "2011", "1", "Daughter", "8"], ["Genotype", "23andMe", "Saliva", "SNP chip v3", "bed.zip", "2011", "1", "Aunt", "8"], ["Annotation", "SNPedia", "SNP chip v2", "Phenotypes", "txt", "2012", "1", "Son", "0.3"], ["Annotation", "SNPedia", "SNP chip v3", "Phenotypes", "txt", "2012", "1", "Mother", "0.4"], ["Annotation", "SNPedia", "SNP chip v3", "Phenotypes", "txt", "2012", "1", "Father", "0.4"], ["Annotation", "SNPedia", "SNP chip v3", "Phenotypes", "txt", "2012", "1", "Daughter", "0.4"], ["Annotation", "SNPedia", "SNP chip v3", "Phenotypes", "txt", "2012", "1", "Aunt", "0.4"], ["Whole Exome Sequencing", "BGI", "Saliva", "SE Illumina HiSeq 2000", "fastq.gz", "2011", "4", "Son", "2400"], ["Whole Exome Sequencing", "BGI", "Saliva", "PE Illumina HiSeq 2000", "fastq.gz", "2013", "2", "Mother", "2000"], ["Whole Exome Sequencing", "BGI", "Saliva", "PE Illumina HiSeq 2000", "fastq.gz", "2013", "2", "Father", "2000"], ["Whole Exome Sequencing", "BGI", "Saliva", "PE Illumina HiSeq 2000", "fastq.gz", "2013", "2", "Sister", "2400"], ["Alignment", "InSilicoDB", "SE Illumina HiSeq 2000", "BWA", "bam", "2013", "1", "Son", "2900"], ["Alignment", "InSilicoDB", "PE Illumina HiSeq 2000", "BWA", "bam", "2013", "1", "Mother", "1800"], ["Alignment", "InSilicoDB", "PE Illumina HiSeq 2000", "BWA", "bam", "2013", "1", "Father", "1600"], ["Alignment", "InSilicoDB", "PE Illumina HiSeq 2000", "BWA", "bam", "2013", "1", "Daughter", "2200"], ["Annotation", "InSilicoDB", "Bam from Son, Mother, Father, Daughter", "GATK", "VCF", "2013", "1", "Son, Mother, Father, Daughter", "124.6"], ["Metagenomics", "BGI", "Fecal frozen sample", "PE Illumina HiSeq 2000", "fastq.gz", "2013", "2", "Son", "1000"], ["Total", "", "", "", "", "", "27", "", "18463.5"]], "row_count": 22, "column_count": 9, "numeric_cells": 76, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab1"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "fisher_exact", "label": "Categorical (contingency table) analysis", "dsl_operations": ["contingency_table", "chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In order to compare two populations and discriminate if they have different hair colour information, a goodness of fit test was conducted. 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