▸case-01 I have raw Illumina paired-end FASTQ files from a whole exome sequencing run. Explain the pipeline steps to align these reads using BWA-MEM, mark duplicates with Picard, and call genomic variants using GATK HaplotypeCaller to generate a VCF. | pass→pass | 17,245 | 13,407 | -22% | 1 | 1 | 0% | 3,420 | 2,571 | -25% | 0 | 0 | — |
▸case-02 Provide the command-line execution steps and input file formatting required to run AlphaFold2 to predict the tertiary 3D protein structure from a FASTA amino acid sequence. | pass→pass | 15,876 | 11,586 | -27% | 1 | 1 | 0% | 2,800 | 2,173 | -22% | 0 | 0 | — |
▸case-03 Write a high-performance C++ function using memory-mapped files (mmap) to parse CHROM, POS, ID, REF, and ALT columns from a 100GB multi-sample VCF file. | fail→fail | 24,828 | 26,406 | +6% | 1 | 1 | 0% | 5,167 | 4,733 | -8% | 0 | 0 | — |
▸case-04 When building an NCBI E-utilities HTTP REST request to fetch ClinVar records for BRCA1 variants, developers often pass db=gene or db=snp. What value must be passed in the db URL parameter to query the ClinVar database directly? | pass→pass | 2,995 | 3,488 | +16% | 1 | 1 | 0% | 542 | 578 | +7% | 0 | 0 | — |
▸case-05 By default, NCBI E-utilities esummary.fcgi returns XML formatted data. When requesting summary records for ClinVar UIDs via REST, which query string parameter and value should be supplied to obtain structured JSON? | pass→pass | 3,827 | 3,107 | -19% | 1 | 1 | 0% | 457 | 653 | +43% | 0 | 0 | — |
▸case-06 ClinVar uses a 0 to 4 star system for review status. Developers often assume 4 stars indicates consensus from an expert panel or multiple submitters. What specific review status level does 4 stars represent? | pass→pass | 4,430 | 6,155 | +39% | 1 | 1 | 0% | 783 | 1,190 | +52% | 0 | 0 | — |
▸case-07 When a variant assertion is evaluated and submitted by a recognized panel such as ClinGen or ENIGMA, users frequently assume it receives 4 stars. What is the official ClinVar star rating for expert panel submissions? | pass→pass | 4,468 | 5,105 | +14% | 1 | 1 | 0% | 752 | 964 | +28% | 0 | 0 | — |
▸case-08 ClinVar assigns different accession prefixes to records. If an analyst needs to query the overarching aggregate variation record that collects all submitter evidence for a specific variant-condition pair, which accession prefix (e.g., RCV, SCV, VCV, rs) should they reference? | fail→pass | 4,523 | 4,969 | +10% | 1 | 1 | 0% | 780 | 1,004 | +29% | 0 | 0 | — |
▸case-09 When referencing NCBI-aggregated records that link a specific variant to a specific disease condition, analysts often confuse VCV and RCV accessions. Which prefix designates the record linking a variant to a specific disease assertion? | pass→pass | 5,558 | 7,853 | +41% | 1 | 1 | 0% | 695 | 920 | +32% | 0 | 0 | — |
▸case-10 For germline pathogenicity assertions, non-standard terms like 'Disease-Causing' or 'Normal' are sometimes proposed. What standard 5-tier classification terms defined by ACMG/AMP are used in ClinVar? | pass→pass | 3,552 | 4,451 | +25% | 1 | 1 | 0% | 597 | 804 | +35% | 0 | 0 | — |
▸case-11 When querying genomic coordinates on chromosome 17 for ClinVar variants via NCBI esearch, omitting the reference genome assembly causes cross-assembly collisions between hg19 and hg38. What assembly term should be included in the search query to restrict results strictly to GRCh38? | pass→pass | 6,838 | 4,788 | -30% | 1 | 1 | 0% | 1,248 | 934 | -25% | 0 | 0 | — |
▸case-12 A developer calling efetch.fcgi for database clinvar sets retmode=json expecting JSON output similar to esummary. What format requirement does NCBI enforce for ClinVar efetch calls? | pass→pass | 10,638 | 5,615 | -47% | 1 | 1 | 0% | 1,344 | 1,172 | -13% | 0 | 0 | — |
▸case-13 Software engineers indexing variant records in database schemas often store dbSNP rs numbers as primary keys. Which identifier assigned directly by ClinVar uniquely references a variation record independently of dbSNP? | pass→pass | 5,322 | 5,086 | -4% | 1 | 1 | 0% | 987 | 1,082 | +10% | 0 | 0 | — |
▸case-14 When one submitter classifies a BRCA2 variant as Pathogenic and another classifies it as Benign without expert panel resolution, users often label the summary as 'Uncertain significance'. What is ClinVar's official aggregate clinical significance label for this condition? | pass→pass | 5,721 | 5,421 | -5% | 1 | 1 | 0% | 787 | 971 | +23% | 0 | 0 | — |
▸case-15 When executing automated E-utilities queries against ClinVar, exceeding NCBI request thresholds causes 429 throttling errors. What is the maximum permitted request rate per second without an API key, and what is the limit when using an API key? | pass→pass | 3,775 | 2,767 | -27% | 1 | 1 | 0% | 635 | 653 | +3% | 0 | 0 | — |
▸case-16 NCBI provides a dedicated REST API for ClinVar outside of traditional E-utilities to retrieve variation JSON details. A user attempts to hit https://eutils.ncbi.nlm.nih.gov/entrez/. What path prefix should be used for the ClinVar REST Variation API? | fail→fail | 11,971 | 7,680 | -36% | 1 | 1 | 0% | 2,655 | 1,442 | -46% | 0 | 0 | — |
▸case-17 A single clinical laboratory submits a variant interpretation to ClinVar without providing assertion criteria or supporting evidence. Users often expect this submission to receive 1 star. How many stars does ClinVar award in this scenario? | pass→pass | 5,189 | 5,476 | +6% | 1 | 1 | 0% | 844 | 1,148 | +36% | 0 | 0 | — |
▸case-18 How many stars does ClinVar assign to a variant record with a single submitter that provides documented assertion criteria and supporting evidence? | pass→pass | 2,761 | 4,377 | +59% | 1 | 1 | 0% | 487 | 855 | +76% | 0 | 0 | — |
▸case-19 When searching ClinVar with esearch returning thousands of UIDs, embedding all UIDs in subsequent URL parameters causes HTTP 414 errors. Which query parameter stores results on the NCBI server, and which response XML element holds the server session string? | pass→pass | 5,694 | 6,091 | +7% | 1 | 1 | 0% | 1,001 | 981 | -2% | 0 | 0 | — |
▸case-20 When evaluating somatic cancer variants in ClinVar under VICC/ACMG/AMP somatic guidelines, analysts sometimes wrongly apply germline ACMG terms. What primary classification term does ClinVar use for somatic variants causing tumor development? | pass→pass | 6,894 | 6,990 | +1% | 1 | 1 | 0% | 1,310 | 1,404 | +7% | 0 | 0 | — |
▸case-21 In HGVS variant notation, a mutation involving simultaneous deletion and insertion (e.g. c.123_124delinsGA) is sometimes searched using terms like 'indel'. What HGVS keyword operator is required for searching these variants in ClinVar? | pass→pass | 5,479 | 8,389 | +53% | 1 | 1 | 0% | 990 | 1,388 | +40% | 0 | 0 | — |
▸case-22 When two independent submitters provide clinical assertions with criteria for the same variant and both classify it as Pathogenic without conflict, what star rating does ClinVar assign? | pass→pass | 4,262 | 6,741 | +58% | 1 | 1 | 0% | 723 | 1,203 | +66% | 0 | 0 | — |