Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:20164091", "kind": "science-record", "revision": 5, "content_hash": "sha256:922b1eae3486a3dd3260df6207f08b01d13bda3ed45271c27d0f44d02bbca151", "created_at": "2026-11-01T15:14:33Z", "updated_at": "2026-11-01T21:19:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries.", "doi": "10.1093/nar/gkq072", "pmid": "20164091", "authors": ["Michal Mokry", "Harma Feitsma", "Isaac J Nijman", "Ewart de Bruijn", "Pieter J van der Zaag", "Victor Guryev", "Edwin Cuppen"], "journal": "Nucleic acids research", "year": 2010, "abstract": "Microarray-based enrichment of selected genomic loci is a powerful method for genome complexity reduction for next-generation sequencing. Since the vast majority of exons in vertebrate genomes are smaller than 150 nt, we explored the use of short fragment libraries (85-110 bp) to achieve higher enrichment specificity by reducing carryover and adverse effects of flanking intronic sequences. High enrichment specificity (60-75%) was obtained with a relative even base coverage. Up to 98% of the target-sequence was covered more than 20x at an average coverage depth of about 200x. To verify the accuracy of SNP/mutation detection, we evaluated 384 known non-reference SNPs in the targeted regions. At approximately 200x average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% false negative calls, mostly due to low coverage. Using the same settings, a total of 1197 novel candidate variants were detected. Verification experiments revealed only eight false positive calls, indicating an overall false positive rate of less than 1 per approximately 200,000 bp. Taken together, short fragment libraries provide highly efficient and flexible enrichment of exonic targets and yield relatively even base coverage, which facilitates accurate SNP and mutation detection. Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542.", "claims": [{"id": "claim-method", "statement": "Here, we introduce a dedicated parameter to represent the evenness of coverage score, E. Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:20164091", "locator": "sections[8] \"Calculation of evenness score\" paragraph 2", "quote": "Here, we introduce a dedicated parameter to represent the evenness of coverage score, E."}, {"asset": "source:pmid:20164091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:20164091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the evenness score (E) to assess uniformity of enrichment coverage and found that short-fragment libraries produced efficient, relatively even exonic coverage with accurate SNP/mutation detection; the raw sequencing data, alignment files, and called SNPs are available from GEO under accession GSE18542.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:20164091", "locator": "sections[1] \"INTRODUCTION\" paragraph 2", "quote": "These results indicate that the use of short fragment libraries results firstly in highly efficient enrichment with relatively even base coverage over the targeted region and that secondly the sensitivity and specificity of SNP/mutation calling is very high."}, {"asset": "source:pmid:20164091", "locator": "sections[15] \"Identification of polymorphic positions\" paragraph 2", "quote": "Taken together, at ∼200× average sequence coverage, we were able to survey 96.4% of 1.69 Mb of genomic sequence with only 4.2% of false negative calls, while 3.6% of targeted regions had to be marked as unsurveyed."}, {"asset": "source:pmid:20164091", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the evenness score (E) to assess uniformity of enrichment coverage and found that short-fragment libraries produced efficient, relatively even exonic coverage with accurate SNP/mutation detection; the raw sequencing data, alignment files, and called SNPs are available from GEO under accession GSE18542.", "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:20164091"], "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": "complete", "blocked_on": null, "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": ["data:geo:GSE18542"], "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": ["data:geo:GSE18542"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:20164091", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/nar/gkq072", "sha256": "sha256:174e4b283d52e4fe45a01ad5b023caf6366e8d85b5a723a2f7a8ae4d537de209", "bytes": 39448, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/nar/gkq072", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC2879533", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE18542", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18542", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18542", "version": null, "note": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM461681", "GSM461682", "GSM461683", "GSM461684"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "9138;9442", "taxon": "Homo sapiens", "title": "Highly efficient genomic enrichment of human exonic sequences through short-fragment libraries", "resolution_checked_at": "2026-11-01T15:14:33Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:20164091:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b1052c34ee3c6dd6a019f0bec9be17a7c9aedcaf7996609a84abfd6ca06e7b88", "bytes": 1113, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#T1", "version": null, "note": "Enrichment statistics", "structure": {"pmcid": "PMC2879533", "section_index": 5, "section_title": "Enrichment hybridization and elution", "row_count": 16, "column_count": 5}, "table": {"label": "Table 1.", "caption": "Enrichment statistics", "rows": [["", "Library1", "Library2", "Library3", "cLibrary1"], ["Length of sequenced tags", "35", "35", "35", "50"], ["Microarray slide", "new", "new", "reused", "new"], ["Amount of hybridized DNA (µg)", "3", "3", "6.5", "3"], ["Washing temperature", "RT", "42°C", "RT", "RT"], ["Mappable tags (millions)", "6.64", "18.88", "17.05", "14.10"], ["Uniquely mappable tags (millions)", "4.97", "12.70", "13.98", "10.78"], ["Mappable sequence on target (%)", "56", "40", "61", "53"], ["Uniquely mappable sequence on target (%)", "67", "60", "75", "69"], ["Bases covered 1× (%)", "99.59", "99.38", "99.88", "99.97"], ["Bases covered 10× (%)", "92.49", "93.18", "98.08", "99.37"], ["Bases covered 20× (%)", "83.17", "86.77", "95.46", "98.13"], ["Bases covered with 10% of average coveragea (%)", "95", "90", "95", "98"], ["Bases covered with 25% of average coveragea (%)", "86", "77", "86", "92"], ["Bases covered with 50% of average coveragea (%)", "69", "60", "69", "76"], ["Evenness score E (%)b", "70.2", "62.4", "70.1", "74.8"]], "row_count": 16, "column_count": 5, "numeric_cells": 59, "header_rows": 1, "locator": "section[5]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:20164091:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6e4d3041002f5c2fe1b8db226f7a39a3079f2cb86a1e44a923080c6dc4a6e7c2", "bytes": 717, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T2", "version": null, "note": "SNP calling statistics", "structure": {"pmcid": "PMC2879533", "section_index": 7, "section_title": "Mapping of sequencing data and SNP calling", "row_count": 8, "column_count": 5}, "table": {"label": "Table 2.", "caption": "SNP calling statistics", "rows": [["", "Library 1", "Library 2", "Library 3", "Library 1"], ["Length of sequenced tags", "35", "35", "35", "50"], ["Average coverage", "67×", "148×", "204×", "213×"], ["SNP positions validated", "384", "384", "384", "384"], ["SNP positions filtered due to low coverage (<20×) (%)", "18.8", "25.8", "3.4", "1.8"], ["SNPs with enough coverage filtered out for other reasons (%)a", "26.5", "21.1", "27.9", "6.0"], ["SNPs identified after filtering (with at least 20× coverage) (%)", "54.7", "53.1", "68.7", "92.2"], ["False-negative discovery rate (%)", "45.3", "46.9", "31.3", "7.8"]], "row_count": 8, "column_count": 5, "numeric_cells": 34, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE18542 not downloaded", "asset:data:geo:GSE18542 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Evenness score (E)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "Here, we introduce a dedicated parameter to represent the evenness of coverage score, E. Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Evenness score (E)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE18542"], "resolved_accessions": ["GSE18542"], "statements": ["Raw sequencing data, alignment files and called SNPs have been submitted into GEO database http://www.ncbi.nlm.nih.gov/geo/ with accession number GSE18542."], "basis": "The paper names GSE18542 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:20164091", "data:geo:GSE18542", "asset:table:pmid:20164091:1", "asset:table:pmid:20164091:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE18542"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:43Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 76736, "completion_tokens": 3366, "cached_tokens": 47776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:20164091", "type": "paper", "label": "pmid:20164091"}, {"id": "source:pmid:20164091", "type": "manuscript", "label": "PMID 20164091 full text"}, {"id": "data:geo:GSE18542", "type": "dataset", "label": "GEO GSE18542"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:20164091", "type": "paper", "label": "pmid:20164091"}, {"id": "source:pmid:20164091", "type": "manuscript", "label": "PMID 20164091 full text"}, {"id": "data:geo:GSE18542", "type": "dataset", "label": "GEO GSE18542"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-20164091", "type": "extraction", "used": ["source:pmid:20164091"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE18542", "type": "accession_resolution", "used": ["data:geo:GSE18542"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:20164091", "parent_hash": "sha256:ded2a2f474eaf06c33fdea787fe8b81bcad59eb9bfa013b5054a245a13aa34df", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE18542 licence not read", "asset:data:geo:GSE18542 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["NP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment s", "Microarray-based enrichment of selected genomic loci is"], "order_basis": "paper_text_order:10", "id": "assay:1"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["l method for genome complexity reduction for next-generation sequencing. Since the vast majority of exons in vertebr"], "order_basis": "paper_text_order:196", "id": "assay:2"}]}