Datasets:
id stringlengths 21 21 | kind stringclasses 3
values | options listlengths 2 6 | target listlengths 2 6 | state stringlengths 161 266 | question stringclasses 28
values | domain stringclasses 4
values | family stringclasses 1
value | source stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|
v3_9c509ddc69cddc06_n | noul | [
"false",
"true"
] | [
0.13,
0.87
] | A qc gate passed the cross-sample concordance; additionally failed the sex-check concordance. Context: under the CAP checklist, during normal operations. Reported by the operator. | Is this scenario one where: manual review is required? | bioinformatics_ops | genomics | yuri_v3 |
v3_3ab08146dbefc7da_n | noul | [
"false",
"true"
] | [
0.21,
0.79
] | An ldlr variant creates a premature stop codon; additionally segregates with disease in the family. Context: de novo in the proband, with staffing at reduced levels. Reported by the operator. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_533649ee97f31b11_n | noul | [
"false",
"true"
] | [
0.64,
0.36
] | A batch of 96 samples shows uniform coverage across the target; additionally passed the cross-sample concordance. Context: before the Friday release, shortly after a software update. Reported by the operator. | Is this scenario one where: manual review is required? | bioinformatics_ops | genomics | yuri_v3 |
v3_751375abffebb75f_n | noul | [
"false",
"true"
] | [
0.6,
0.4
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally has a consensus quality of Q20. Context: at 30x mean depth, under an active deadline. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_faaef94ba7d6c1b3_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.05,
0.68,
0.1,
0.17
] | A panel test order matches the oncology guideline indication; additionally screens 280 conditions without indication. Context: per ACMG recommendations, during the quarterly review. Reported by the on-call engineer. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_913e9b561fd91d2e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.23,
0.4,
0.05,
0.17,
0.06,
0.09
] | The variant-calling run completed with 0 failed checks; additionally shows uniform coverage across the target. Context: under the CAP checklist, under an active deadline. Reported by the supervisor. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_9fffb325e1dca1c7_n | noul | [
"false",
"true"
] | [
0.73,
0.27
] | An amplicon sequence maps to two loci with equal coverage; additionally contains the known pseudo-gene region. Context: at 30x mean depth, during an external partner integration. Reported by the supervisor. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_ae6b45329ea76993_n | noul | [
"false",
"true"
] | [
0.08,
0.92
] | A pharmacogenomic test follows the family history of Huntington disease; additionally was ordered without pre-test counseling documented. Context: under the payer policy, following a recent audit. Reported by the automated check. | Is this scenario one where: pre-test counseling is required? | genetic_testing | genomics | yuri_v3 |
v3_2a31a35cf870cff6_n | noul | [
"false",
"true"
] | [
0.71,
0.29
] | An ldlr variant is a missense change in a conserved domain; additionally has a CADD score of 34. Context: in an unaffected 70-year-old relative, with staffing at reduced levels. Reported by the supervisor. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_5d4464d189243d70_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.03,
0.22,
0.31,
0.42,
0.02
] | The annotation pipeline completed with 0 failed checks; additionally failed the sex-check concordance. Context: in the clinical reporting pipeline, during the holiday freeze. Reported by the automated check. | Rate data integrity risk for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_86012332c9f4c6d2_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.05,
0.57,
0.36,
0.01
] | A cftr mutation has a CADD score of 34; additionally has conflicting functional studies. Context: de novo in the proband, during normal operations. Reported by the monitoring system. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_02ed4547cbfa206f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.09,
0.27,
0.6,
0.03,
0
] | A brca1 variant is absent from population databases at 0.0004 frequency; additionally is a missense change in a conserved domain. Context: in an unaffected 70-year-old relative, during peak load. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_5a1a074e2b7a2c5e_n | noul | [
"false",
"true"
] | [
0.79,
0.21
] | An amplicon sequence has a 4bp insertion in the coding sequence; additionally reveals a premature poly-A signal. Context: with the long-read platform, under reduced staffing. Reported by the review queue. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_fbf9b87f7247f2d1_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.17,
0.28,
0.53,
0.02
] | An amplicon sequence shows strand bias at 4:1; additionally shows even coverage at 500x. Context: at 30x mean depth, immediately after go-live. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_2f17e9434958d6cd_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.43,
0.26,
0.27,
0.04
] | A panel test order is ordered before prescribing clopidogrel; additionally has insurance prior-authorization attached. Context: under the payer policy, while on-call rotation changed. Reported by the on-call engineer. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_7844dfbd4ab3ba52_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.02,
0.38,
0.49,
0.11
] | A pharmacogenomic test includes an incidental-finding opt-out discussion; additionally was ordered without pre-test counseling documented. Context: with the genetic counselor involved, during peak load. Reported by the monitoring system. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_4cf14ba343f7b287_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.31,
0.5,
0.18,
0
] | A qc gate shows a sudden coverage drop in one batch; additionally passed the cross-sample concordance. Context: under the CAP checklist, mid-incident. Reported by the monitoring system. | Rate data integrity risk for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_62dc10ea7331352d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.08,
0.27,
0.53,
0.1,
0.01
] | A rna-seq read set contains the known pseudo-gene region; additionally has a consensus quality of Q20. Context: against the latest reference, mid-incident. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_151e6db9210086a7_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.1,
0.26,
0.61,
0.03
] | A rna-seq read set shows strand bias at 4:1; additionally contains the known pseudo-gene region. Context: at 30x mean depth, during normal operations. Reported by the review queue. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_ce25ce7f999a8b40_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.21,
0.64,
0.14,
0
] | A cftr mutation appears in ClinVar as pathogenic with 2-star review; additionally creates a premature stop codon. Context: in a screening-only context, during the morning shift. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_4a7db0698cb9e9eb_n | noul | [
"false",
"true"
] | [
0.8,
0.2
] | An ldlr variant has conflicting functional studies; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, with a new vendor onboarded. Reported by the monitoring system. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_a9c481f466fc826c_n | noul | [
"false",
"true"
] | [
0.39,
0.61
] | An ldlr variant has conflicting functional studies; additionally segregates with disease in the family. Context: in an unaffected 70-year-old relative, during peak load. Reported by the on-call engineer. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_bc9f6a871c54f37f_c | choice | [
"pre_analytical",
"library",
"sequencing",
"analysis"
] | [
0.27,
0.09,
0.45,
0.19
] | The annotation pipeline passed the cross-sample concordance; additionally shows a sudden coverage drop in one batch. Context: under the CAP checklist, with a new vendor onboarded. Reported by the monitoring system. | Failure class for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_e6bcc1bf37f2da28_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0,
0.9,
0,
0.1
] | A rna-seq read set maps to two loci with equal coverage; additionally has a 4bp insertion in the coding sequence. Context: against the latest reference, during a scheduled maintenance window. Reported by the operator. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_8b11e678d65f6861_n | noul | [
"false",
"true"
] | [
0.51,
0.49
] | A panel test order includes an incidental-finding opt-out discussion; additionally was ordered without pre-test counseling documented. Context: under the payer policy, as part of a compliance sweep. Reported by the on-call engineer. | Is this scenario one where: the panel scope is appropriate? | genetic_testing | genomics | yuri_v3 |
v3_63336403263550ea_n | noul | [
"false",
"true"
] | [
0.16,
0.84
] | A pharmacogenomic test tests a single variant with strong indication; additionally was ordered without pre-test counseling documented. Context: with the genetic counselor involved, following a recent audit. Reported by the monitoring system. | Is this scenario one where: the indication supports the test? | genetic_testing | genomics | yuri_v3 |
v3_7b57313d4eeab974_c | choice | [
"pre_analytical",
"library",
"sequencing",
"analysis"
] | [
0.21,
0.06,
0.5,
0.23
] | A batch of 96 samples shows uniform coverage across the target; additionally completed with 0 failed checks. Context: under the CAP checklist, while legacy systems are still active. Reported by the supervisor. | Failure class for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_ff7a1503cb2f0a7c_n | noul | [
"false",
"true"
] | [
0.54,
0.46
] | A batch of 96 samples has a duplicated sample ID in the manifest; additionally shows uniform coverage across the target. Context: for the research cohort, with a new vendor onboarded. Reported by the on-call engineer. | Is this scenario one where: a sample swap is suspected? | bioinformatics_ops | genomics | yuri_v3 |
v3_9207703ac918f00c_n | noul | [
"false",
"true"
] | [
0.62,
0.38
] | A contig assembly matches the expected amplicon size; additionally has a 4bp insertion in the coding sequence. Context: with the long-read platform, during normal operations. Reported by the review queue. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_c8a41f8398a79ff2_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.01,
0.54,
0.07,
0.38
] | A cftr mutation matches the reference sequence exactly; additionally causes a frameshift at codon 1200. Context: in an unaffected 70-year-old relative, with staffing at reduced levels. Reported by the on-call engineer. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_ce36c3c9621c747d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.04,
0.76,
0.2,
0
] | An ldlr variant has conflicting functional studies; additionally has a CADD score of 34. Context: de novo in the proband, during the quarterly review. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_6372f9339e842d35_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.03,
0.18,
0.64,
0.15
] | A pharmacogenomic test follows the family history of Huntington disease; additionally is requested for an adopted adult with no family history. Context: per ACMG recommendations, with staffing at reduced levels. Reported by the automated check. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_17d52d3fe5fc0985_n | noul | [
"false",
"true"
] | [
0.53,
0.47
] | A panel test order was ordered without pre-test counseling documented; additionally has insurance prior-authorization attached. Context: with the genetic counselor involved, during the holiday freeze. Reported by the supervisor. | Is this scenario one where: the indication supports the test? | genetic_testing | genomics | yuri_v3 |
v3_e36af2ae959a202e_n | noul | [
"false",
"true"
] | [
0.57,
0.43
] | A contig assembly matches the expected amplicon size; additionally reveals a premature poly-A signal. Context: in the variant-calling pipeline, shortly after a software update. Reported by the on-call engineer. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_6b4b3c1098c9603d_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.04,
0.62,
0.28,
0.06,
0
] | A batch of 96 samples completed with 0 failed checks; additionally produced a VCF with 3.2M variants against an expected 4.5M. Context: under the CAP checklist, during the morning shift. Reported by the automated check. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_e2179abc58a4ed0a_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.09,
0.52,
0.01,
0.38
] | A tp53 variant matches the reference sequence exactly; additionally creates a premature stop codon. Context: de novo in the proband, following a recent audit. Reported by the supervisor. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_aa15e4c66cef29ec_n | noul | [
"false",
"true"
] | [
0.3,
0.7
] | A cftr mutation is absent from population databases at 0.0004 frequency; additionally is a missense change in a conserved domain. Context: de novo in the proband, with staffing at reduced levels. Reported by the monitoring system. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_c82fd82731308c4e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.27,
0.58,
0.14,
0
] | A batch of 96 samples produced a VCF with 3.2M variants against an expected 4.5M; additionally passed the cross-sample concordance. Context: under the CAP checklist, during the system migration. Reported by the supervisor. | Rate data integrity risk for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_eb8e7b852efe2d28_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.03,
0.05,
0.15,
0.37,
0.38,
0.02
] | A tp53 variant causes a frameshift at codon 1200; additionally matches the reference sequence exactly. Context: in a patient with the phenotype, while on-call rotation changed. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_34e0cda1469550e3_n | noul | [
"false",
"true"
] | [
0.76,
0.24
] | An ldlr variant is absent from population databases at 0.0004 frequency; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, during the morning shift. Reported by the review queue. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
v3_3fe1c0e4613f9a06_n | noul | [
"false",
"true"
] | [
0.07,
0.93
] | A prenatal panel tests a single variant with strong indication; additionally has insurance prior-authorization attached. Context: under the payer policy, with staffing at reduced levels. Reported by the review queue. | Is this scenario one where: the indication supports the test? | genetic_testing | genomics | yuri_v3 |
v3_4f986136cae20c3e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.04,
0.14,
0.54,
0.27,
0.01
] | A brca1 variant appears in ClinVar as pathogenic with 2-star review; additionally creates a premature stop codon. Context: in an unaffected 70-year-old relative, at the end of the fiscal period. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_e66949268c682da2_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.29,
0.36,
0.28,
0.05,
0
] | An ldlr variant has a CADD score of 34; additionally is a silent change with no splice impact. Context: de novo in the proband, mid-incident. Reported by the operator. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_d354720f02c8da49_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.01,
0.01,
0.09,
0.63,
0.25
] | An ldlr variant is a missense change in a conserved domain; additionally causes a frameshift at codon 1200. Context: in a screening-only context, under an active deadline. Reported by the on-call engineer. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_bfc02b582c93b066_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.85,
0.06,
0.05,
0.04
] | An amplicon sequence contains a stop codon mid-open-reading-frame; additionally shows 99.8% identity across the target region. Context: with the long-read platform, while on-call rotation changed. Reported by the review queue. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_47283396bbddcadb_n | noul | [
"false",
"true"
] | [
0.41,
0.59
] | A rna-seq read set reveals a premature poly-A signal; additionally shows even coverage at 500x. Context: in the variant-calling pipeline, as part of a compliance sweep. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_00e69bf25bc1ee06_n | noul | [
"false",
"true"
] | [
0.97,
0.03
] | A qc gate shows 14 samples below the 20x depth threshold; additionally failed the sex-check concordance. Context: under the CAP checklist, with staffing at reduced levels. Reported by the automated check. | Is this scenario one where: the run meets release criteria? | bioinformatics_ops | genomics | yuri_v3 |
v3_000979895bbfaa41_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0,
0.01,
0.48,
0.51
] | A brca1 variant has conflicting functional studies; additionally is a silent change with no splice impact. Context: in an unaffected 70-year-old relative, mid-incident. Reported by the on-call engineer. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_9f41b3271de23d08_c | choice | [
"valid",
"ambiguous",
"artifact",
"contaminated"
] | [
0.9394,
0.0505,
0.0101,
0
] | An amplicon sequence has a consensus quality of Q20; additionally matches the expected amplicon size. Context: at 30x mean depth, during normal operations. Reported by the monitoring system. | Sequence verdict for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_c0f1e58c7f02e137_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.01,
0.02,
0.14,
0.68,
0.15
] | A brca1 variant causes a frameshift at codon 1200; additionally creates a premature stop codon. Context: in a screening-only context, during an external partner integration. Reported by the review queue. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_64d1d81f8377c588_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.11,
0.07,
0.5,
0.32
] | An ldlr variant matches the reference sequence exactly; additionally causes a frameshift at codon 1200. Context: in a screening-only context, shortly after a software update. Reported by the supervisor. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_b9f28598c3a811f3_n | noul | [
"false",
"true"
] | [
0.06,
0.94
] | The variant-calling run shows swapped indices in two lanes; additionally failed the sex-check concordance. Context: under the CAP checklist, while on-call rotation changed. Reported by the operator. | Is this scenario one where: manual review is required? | bioinformatics_ops | genomics | yuri_v3 |
v3_08e4551e767c4b8c_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.2,
0.37,
0.21,
0.19,
0.03,
0
] | A panel test order is ordered before prescribing clopidogrel; additionally tests a single variant with strong indication. Context: with the genetic counselor involved, at the end of the fiscal period. Reported by the supervisor. | Rate consent-process completeness for this scenario on a 0-5 scale. | genetic_testing | genomics | yuri_v3 |
v3_761f68d2e9ef6c06_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.58,
0.3,
0.11,
0.01
] | A cftr mutation segregates with disease in the family; additionally creates a premature stop codon. Context: in a screening-only context, shortly after a software update. Reported by the monitoring system. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_858bbe728cbf59f1_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.22,
0.35,
0.35,
0.08
] | A panel test order includes an incidental-finding opt-out discussion; additionally follows the family history of Huntington disease. Context: under the payer policy, at the end of the fiscal period. Reported by the automated check. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_94fd1cbdb1b4411f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.03,
0.29,
0.61,
0.07,
0
] | An alignment result shows 99.8% identity across the target region; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, while legacy systems are still active. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_371e6c63e44e5b86_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0,
0.3,
0.69,
0.01
] | A qc gate shows 14 samples below the 20x depth threshold; additionally produced a VCF with 3.2M variants against an expected 4.5M. Context: in the clinical reporting pipeline, while on-call rotation changed. Reported by the on-call engineer. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_af88a9000fef93bf_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.05,
0.05,
0.09,
0.41,
0.39,
0.01
] | A pharmacogenomic test has insurance prior-authorization attached; additionally follows the family history of Huntington disease. Context: in the minors-assent context, with a new vendor onboarded. Reported by the monitoring system. | Rate consent-process completeness for this scenario on a 0-5 scale. | genetic_testing | genomics | yuri_v3 |
v3_8724948b482a3637_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.04,
0.44,
0.5,
0.02
] | A brca1 variant appears in ClinVar as pathogenic with 2-star review; additionally causes a frameshift at codon 1200. Context: in a patient with the phenotype, immediately after go-live. Reported by the review queue. | Rate evidence strength for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_b26e75b079c85242_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.12,
0.42,
0.37,
0.06,
0.01
] | An amplicon sequence shows even coverage at 500x; additionally has a 4bp insertion in the coding sequence. Context: with the long-read platform, during the morning shift. Reported by the supervisor. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_1b13ae4be6102bb7_c | choice | [
"release",
"release_partial",
"hold_all",
"reprocess"
] | [
0.31,
0.2,
0.35,
0.14
] | A batch of 96 samples passed the cross-sample concordance; additionally has a contamination estimate of 8%. Context: for the research cohort, immediately after go-live. Reported by the automated check. | Batch disposition for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_6be377e727bfacd9_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.07,
0.35,
0.23,
0.28,
0.05,
0.02
] | A contig assembly shows even coverage at 500x; additionally contains the known pseudo-gene region. Context: with the long-read platform, while legacy systems are still active. Reported by the on-call engineer. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_bbf28e4a2b91225b_n | noul | [
"false",
"true"
] | [
0.15,
0.85
] | A contig assembly has a 4bp insertion in the coding sequence; additionally matches the expected amplicon size. Context: with the long-read platform, during the holiday freeze. Reported by the automated check. | Is this scenario one where: the sequence supports the expected amplicon? | sequence_analysis | genomics | yuri_v3 |
v3_aca082edb71776bf_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.21,
0.28,
0.5,
0.01
] | An ldlr variant is absent from population databases at 0.0004 frequency; additionally has conflicting functional studies. Context: de novo in the proband, mid-incident. Reported by the operator. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_aeb3f7e97173b00b_n | noul | [
"false",
"true"
] | [
0.59,
0.41
] | An amplicon sequence shows 99.8% identity across the target region; additionally contains a stop codon mid-open-reading-frame. Context: in the variant-calling pipeline, as part of a compliance sweep. Reported by the on-call engineer. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_99c6d0818a5c89bd_c | choice | [
"single_variant",
"targeted_panel",
"whole_exome",
"whole_genome"
] | [
0,
0.93,
0.06,
0.01
] | A panel test order screens 280 conditions without indication; additionally is ordered before prescribing clopidogrel. Context: per ACMG recommendations, while on-call rotation changed. Reported by the supervisor. | Test type for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_677dbd70afa387e3_c | choice | [
"pre_analytical",
"library",
"sequencing",
"analysis"
] | [
0.06,
0.02,
0.4,
0.52
] | The variant-calling run shows uniform coverage across the target; additionally shows swapped indices in two lanes. Context: in the clinical reporting pipeline, immediately after go-live. Reported by the monitoring system. | Failure class for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_4cdc2616e6469714_n | noul | [
"false",
"true"
] | [
0.09,
0.91
] | The annotation pipeline failed the sex-check concordance; additionally shows 14 samples below the 20x depth threshold. Context: under the CAP checklist, during a scheduled maintenance window. Reported by the automated check. | Is this scenario one where: manual review is required? | bioinformatics_ops | genomics | yuri_v3 |
v3_5e7a22be5a522b11_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.1,
0.36,
0.54,
0
] | A brca1 variant has a CADD score of 34; additionally has conflicting functional studies. Context: de novo in the proband, during peak load. Reported by the automated check. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_18b66fc5d0156706_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.02,
0.06,
0.37,
0.5,
0.05,
0
] | An alignment result shows 99.8% identity across the target region; additionally maps to two loci with equal coverage. Context: in the variant-calling pipeline, during the morning shift. Reported by the monitoring system. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_c770ab769b0bc307_n | noul | [
"false",
"true"
] | [
0.75,
0.25
] | A brca1 variant segregates with disease in the family; additionally is a silent change with no splice impact. Context: in a patient with the phenotype, with a new vendor onboarded. Reported by the monitoring system. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_a8c806037bb6f95e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0,
0.07,
0.88,
0.05
] | The variant-calling run produced a VCF with 3.2M variants against an expected 4.5M; additionally failed the sex-check concordance. Context: under the CAP checklist, during the holiday freeze. Reported by the automated check. | Rate data integrity risk for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_d4ef2525db111527_c | choice | [
"pre_analytical",
"library",
"sequencing",
"analysis"
] | [
0.73,
0.07,
0.03,
0.17
] | The variant-calling run completed with 0 failed checks; additionally has a contamination estimate of 8%. Context: for the research cohort, with a new vendor onboarded. Reported by the on-call engineer. | Failure class for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_f38f5df51d45ad2f_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.11,
0.18,
0.18,
0.29,
0.21,
0.03
] | An ldlr variant matches the reference sequence exactly; additionally has a CADD score of 34. Context: de novo in the proband, with staffing at reduced levels. Reported by the supervisor. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_2165c17211c6529e_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.07,
0.16,
0.39,
0.35,
0.02
] | A prenatal panel includes an incidental-finding opt-out discussion; additionally screens 280 conditions without indication. Context: under the payer policy, during the holiday freeze. Reported by the monitoring system. | Rate consent-process completeness for this scenario on a 0-5 scale. | genetic_testing | genomics | yuri_v3 |
v3_ac41df5f6aad3c24_n | noul | [
"false",
"true"
] | [
0.84,
0.16
] | A panel test order screens 280 conditions without indication; additionally follows the family history of Huntington disease. Context: under the payer policy, while on-call rotation changed. Reported by the review queue. | Is this scenario one where: the indication supports the test? | genetic_testing | genomics | yuri_v3 |
v3_ea869e4ee6c8cd06_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0.07,
0.42,
0.42,
0.07,
0.01
] | An amplicon sequence has a 4bp insertion in the coding sequence; additionally matches the expected amplicon size. Context: with the long-read platform, mid-incident. Reported by the on-call engineer. | Rate call confidence for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_280f4a3e51dbf4f7_n | noul | [
"false",
"true"
] | [
0.61,
0.39
] | A rna-seq read set contains a stop codon mid-open-reading-frame; additionally shows strand bias at 4:1. Context: at 30x mean depth, following a recent audit. Reported by the automated check. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_4163c50bec7bf221_c | choice | [
"single_variant",
"targeted_panel",
"whole_exome",
"whole_genome"
] | [
0.22,
0.63,
0.08,
0.07
] | A pharmacogenomic test was ordered without pre-test counseling documented; additionally follows the family history of Huntington disease. Context: per ACMG recommendations, under an active deadline. Reported by the supervisor. | Test type for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_4737ed2545b5b089_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.07,
0.6,
0.14,
0.19
] | A panel test order targets 47 genes for a nonspecific fatigue complaint; additionally tests a single variant with strong indication. Context: under the payer policy, while legacy systems are still active. Reported by the operator. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_3b9d285cff738a39_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.01,
0,
0.02,
0.49,
0.46,
0.02
] | An alignment result has a 4bp insertion in the coding sequence; additionally reveals a premature poly-A signal. Context: with the long-read platform, while legacy systems are still active. Reported by the supervisor. | Rate alignment quality for this scenario on a 0-5 scale. | sequence_analysis | genomics | yuri_v3 |
v3_8ca3f295594f09eb_c | choice | [
"approve",
"approve_modified",
"defer_counseling",
"deny"
] | [
0.18,
0.53,
0.26,
0.03
] | A panel test order tests a single variant with strong indication; additionally includes an incidental-finding opt-out discussion. Context: in the minors-assent context, under an active deadline. Reported by the monitoring system. | Order review for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_4f32745f16ac09f1_n | noul | [
"false",
"true"
] | [
0.51,
0.49
] | A brca1 variant segregates with disease in the family; additionally is a silent change with no splice impact. Context: in a patient with the phenotype, during normal operations. Reported by the on-call engineer. | Is this scenario one where: this warrants reporting back? | variant_interpretation | genomics | yuri_v3 |
v3_a53a06bf0aa2ab3c_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.36,
0.61,
0.02
] | A batch of 96 samples has a contamination estimate of 8%; additionally shows swapped indices in two lanes. Context: before the Friday release, under an active deadline. Reported by the automated check. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_f034d1dd08320936_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.12,
0.79,
0.08
] | A brca1 variant causes a frameshift at codon 1200; additionally has a CADD score of 34. Context: in a patient with the phenotype, while on-call rotation changed. Reported by the operator. | Rate pathogenicity score for this scenario on a 0-5 scale. | variant_interpretation | genomics | yuri_v3 |
v3_7db6b470320d73db_c | choice | [
"single_variant",
"targeted_panel",
"whole_exome",
"whole_genome"
] | [
0.81,
0.19,
0,
0
] | A pharmacogenomic test is ordered before prescribing clopidogrel; additionally was ordered without pre-test counseling documented. Context: under the payer policy, under reduced staffing. Reported by the supervisor. | Test type for this scenario. | genetic_testing | genomics | yuri_v3 |
v3_5425ee00b6756b15_c | choice | [
"pathogenic",
"likely_pathogenic",
"VUS",
"likely_benign"
] | [
0.2,
0.25,
0.5,
0.05
] | A tp53 variant is a missense change in a conserved domain; additionally causes a frameshift at codon 1200. Context: in a screening-only context, shortly after a software update. Reported by the review queue. | Acmg class for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_93a250ef6b68401b_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.07,
0.02,
0.06,
0.25,
0.56,
0.04
] | A prenatal panel screens 280 conditions without indication; additionally has insurance prior-authorization attached. Context: per ACMG recommendations, under an active deadline. Reported by the monitoring system. | Rate clinical appropriateness for this scenario on a 0-5 scale. | genetic_testing | genomics | yuri_v3 |
v3_76bc1d5a70812323_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.42,
0.08,
0.15,
0.35
] | A contig assembly reveals a premature poly-A signal; additionally shows 99.8% identity across the target region. Context: in the variant-calling pipeline, during the system migration. Reported by the operator. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_5173634fe1e6c528_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0.15,
0.55,
0.29,
0.01,
0
] | A qc gate shows uniform coverage across the target; additionally has a duplicated sample ID in the manifest. Context: for the research cohort, during a scheduled maintenance window. Reported by the automated check. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_5423c75ee770e4a1_c | choice | [
"pre_analytical",
"library",
"sequencing",
"analysis"
] | [
0.41,
0.11,
0.24,
0.24
] | A qc gate passed the cross-sample concordance; additionally shows swapped indices in two lanes. Context: for the research cohort, as part of a compliance sweep. Reported by the monitoring system. | Failure class for this scenario. | bioinformatics_ops | genomics | yuri_v3 |
v3_135c491edd05a8cb_c | choice | [
"SNV",
"insertion",
"deletion",
"structural"
] | [
0.13,
0,
0,
0.87
] | An alignment result maps to two loci with equal coverage; additionally shows 99.8% identity across the target region. Context: at 30x mean depth, during the holiday freeze. Reported by the on-call engineer. | Variant type for this scenario. | sequence_analysis | genomics | yuri_v3 |
v3_2be5d094838afec6_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0,
0,
0.01,
0.26,
0.7,
0.03
] | A batch of 96 samples shows 14 samples below the 20x depth threshold; additionally failed the sex-check concordance. Context: for the research cohort, under an active deadline. Reported by the operator. | Rate run quality for this scenario on a 0-5 scale. | bioinformatics_ops | genomics | yuri_v3 |
v3_8f97805b7efb2ad3_n | noul | [
"false",
"true"
] | [
0.74,
0.26
] | A tp53 variant has a CADD score of 34; additionally matches the reference sequence exactly. Context: in a screening-only context, at the end of the fiscal period. Reported by the monitoring system. | Is this scenario one where: this variant is clinically significant? | variant_interpretation | genomics | yuri_v3 |
v3_cf0f4f9904f391f7_n | noul | [
"false",
"true"
] | [
0.77,
0.23
] | A contig assembly matches the expected amplicon size; additionally has a consensus quality of Q20. Context: at 30x mean depth, during an external partner integration. Reported by the operator. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_bc6ee2952b5ff2d9_n | noul | [
"false",
"true"
] | [
0.66,
0.34
] | An amplicon sequence shows 99.8% identity across the target region; additionally shows strand bias at 4:1. Context: against the latest reference, with staffing at reduced levels. Reported by the monitoring system. | Is this scenario one where: a real variant is present? | sequence_analysis | genomics | yuri_v3 |
v3_9d94f3023f9fa3b6_n | noul | [
"false",
"true"
] | [
0.21,
0.79
] | A batch of 96 samples passed the cross-sample concordance; additionally shows swapped indices in two lanes. Context: in the clinical reporting pipeline, during normal operations. Reported by the monitoring system. | Is this scenario one where: manual review is required? | bioinformatics_ops | genomics | yuri_v3 |
v3_989e01cddd0ae3ed_s | score | [
"0",
"1",
"2",
"3",
"4",
"5"
] | [
0.05,
0.03,
0.08,
0.3,
0.5,
0.04
] | A pharmacogenomic test follows the family history of Huntington disease; additionally has insurance prior-authorization attached. Context: in the minors-assent context, during peak load. Reported by the monitoring system. | Rate clinical appropriateness for this scenario on a 0-5 scale. | genetic_testing | genomics | yuri_v3 |
v3_090b9e8b643c6bfd_c | choice | [
"functional",
"segregation",
"population",
"computational"
] | [
0.1,
0.23,
0.07,
0.6
] | A tp53 variant has a CADD score of 34; additionally has conflicting functional studies. Context: in an unaffected 70-year-old relative, during the quarterly review. Reported by the review queue. | Evidence category for this scenario. | variant_interpretation | genomics | yuri_v3 |
v3_2d7de8e421a5431c_n | noul | [
"false",
"true"
] | [
0.24,
0.76
] | A tp53 variant segregates with disease in the family; additionally appears in ClinVar as pathogenic with 2-star review. Context: de novo in the proband, during the quarterly review. Reported by the review queue. | Is this scenario one where: the evidence supports pathogenicity? | variant_interpretation | genomics | yuri_v3 |
End of preview. Expand in Data Studio
JEV corpus - genomics family
31,350 typed calibrated decision rows from the jev-distill-corpus-v3 corpus, grouped by family.
Each row is one typed decision: kind (noul / choice / score), a state, a question, options, and a target probability distribution over the options.
Domains in this family
bioinformatics_ops- 7,958 rowsvariant_interpretation- 7,903 rowssequence_analysis- 7,870 rowsgenetic_testing- 7,619 rows
Other views of the same data
- per-domain:
SargeDev/jev-corpus-<domain> - the whole corpus in one repo: SargeDev/jev-distill-corpus-v3
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