gaps

Gap Analysis Report

Generated: 2026-03-31

Summary Statistics

Note Type	Count
Concepts (total)	346
Order 1	214
Order 2	120
Order 3	12
Summaries	22

Hierarchy Coverage

66 of 120 order-2 claims (55.0%) belong to at least one order-3+ cluster.

Stub Alerts (1)

Concepts with fewer than 30 characters of prose body.

• confounding (order 1) — prose is 20 chars

Hub Alerts (30)

Order-2 claims with degree > 10 (may need splitting).

• Stat1 inactivation mechanism is conserved between mouse and human aneuploid cancers — degree 38
• Mps1 truncation-induced CIN generates convergent recurrent chromosome gains — degree 32
• Chromosomal instability promotes immune cell infiltration into tumors — degree 25
• Merotely causes chromosome missegregation in unstable cells — degree 13
• Subclonal driver events determine therapy response and tumor evolution — degree 17
• Hypoxia-related transcriptional programs are variably expressed in glioblastoma cells — degree 23
• Multipolar divisions are rare and typically produce inviable progeny — degree 28
• Aneuploid cancers inactivate Stat1 to circumvent immune surveillance — degree 29
• Different aneuploid cells share common fitness-related traits — degree 21
• Aneuploidy impairs cell cycle progression in haploid yeast — degree 15
• Extra chromosome genes drive aneuploid phenotypes through imbalanced protein composition — degree 17
• Aneuploidy impairs cell proliferation in trisomic lines — degree 11
• Aneuploidy increases spontaneous tumor formation in aged animals — degree 26
• Increased aneuploidy inhibits chemically and genetically induced tumorigenesis — degree 26
• Aneuploid tumors inactivate Stat1 signaling with increased Myc activity — degree 42
• Extra centrosomes correlate with chromosomal instability in tumors — degree 32
• Stat1 loss combined with Myc activation alleviates CIN-induced immune infiltration — degree 38
• CIN exists independently of classic mitotic defects in most cells — degree 35
• Single-cell sequencing reveals karyotype heterogeneity in lymphomas — degree 32
• Aneuploidy exhibits dual roles as oncogenic and tumor-suppressive — degree 32
• CIN causality toward aneuploidy was previously unanswered — degree 30
• Aneuploidy decreases both organismal and cellular fitness — degree 19
• Aneuploidy causes proliferative disadvantage independent of extra chromosome identity — degree 13
• Elevated merotely generates CIN in stable near-diploid cells — degree 15
• p53 loss is common but not enriched in chromosomally unstable tumors — degree 21
• CENP-E reduction generates aneuploidy and chromosomal instability — degree 34
• Missegregation alone insufficient for aneuploid cell propagation — degree 41
• Proliferation and immune response programs vary across individual glioblastoma cells — degree 15
• Tumors contain multiple subclones with spatial and temporal heterogeneity — degree 15
• ABC bypasses likelihood evaluation through data simulation — degree 11

Orphan Alerts (38)

Order-2 claims with no inbound links.

• BAF generation from RNA-seq reads does not require prior variant calls
• CaSpER algorithm uses expression and BAF values to estimate CNV events
• PCR duplicate filtering and mapping quality threshold improve sequence read quality
• Mitotic spindle architecture and chromosome segregation
• Weak expression signal events require BAF shifts for CNV confirmation
• Simultaneous correction of GC content and mappability improves read count accuracy
• Fixed-size genomic binning enables copy number estimation with limited sequencing depth
• Tumor heterogeneity and stemness dynamics
• Aneuploidy’s dual role in tumorigenesis
• G1-arrested cells after mis-segregation harbor complex karyotypes
• Evolutionary dynamics of asexual populations
• Five-state HMM assigns copy number states and segments genomic regions
• SAC inactivation accelerates mitosis despite incorrect chromosome attachment
• Phylogenetic tree shape as macroevolutionary signal
• G1-arrested aneuploid cells exhibit elevated p53 and CDK inhibitors
• Shallow whole-genome sequencing detects copy number alterations in tumor samples
• Chromosome mis-segregation rarely activates p53 independently
• Array CGH enables aneuploidy screening in preimplantation blastomeres
• Proliferation confounding in gene signatures
• Array CGH detects segmental deletions smaller than 34 Mb
• Array CGH replaces metaphase spreads with genomic clones on slide
• Aneuploidy and cellular fitness
• Minimal Residual Disease and Metastatic Recurrence
• CENP-E motor protein function
• Multiscale BAF smoothing improves CNV call assignment accuracy
• Strong expression signal events require no BAF corroboration for CNV calls
• Single cells show unique chromosome copy numbers beyond clonal karyotype
• Recursive median filtering and multiscale decomposition smooth expression signal noise
• AneuFinder enables automated quantification of copy number heterogeneity
• Human genetic variation architecture
• Tree topology characterization and metrics
• GC content and mappability independently affect sequence read counts
• Aneuploidy, fitness costs, and immune evasion
• Subclonal Dynamics in Cancer Evolution
• Approximate Bayesian Computation Framework
• Intratumoral Transcriptional Heterogeneity in Glioblastoma
• Proteome consequences of aneuploidy
• Array CGH enables single-cell aneuploidy detection within one day

One-Sided Contradictions (0)

Concepts that assert contradictions but cite no sources.

None found.

Hub Candidates (15)

Concepts close to their next hub synthesis threshold (within 1-2 inbound links).

• Most random gene signatures associate with breast cancer outcome (order 2) — 3/5 inbound links
• Phylogenetic metrics distinguish trees from different generative processes (order 2) — 3/5 inbound links
• Subclonal driver events determine therapy response and tumor evolution (order 2) — 9/10 inbound links
• Aneuploidy impairs cell cycle progression in haploid yeast (order 2) — 8/10 inbound links
• Persistent fitness variation exists among circulating influenza viruses (order 2) — 3/5 inbound links
• Whole genome amplification enables single-cell array CGH analysis (order 2) — 3/5 inbound links
• SNP and CNV signals show minimal overlap in gene expression associations (order 2) — 4/5 inbound links
• Extra chromosome genes drive aneuploid phenotypes through imbalanced protein composition (order 2) — 9/10 inbound links
• Nonlinear heteroscedastic regression improves ABC parameter estimation accuracy (order 2) — 3/5 inbound links
• Elevated merotely generates CIN in stable near-diploid cells (order 2) — 8/10 inbound links
• Gene expression levels can computationally infer large-scale copy number variations in chromosomally unstable cells (order 2) — 4/5 inbound links
• Gene expression scales proportionally to whole chromosome copy number in chromosomally unstable CSCs (order 2) — 4/5 inbound links
• Proliferation and immune response programs vary across individual glioblastoma cells (order 2) — 8/10 inbound links
• Copy number alterations account for most differential gene expression between NSCs and glioblastoma CSCs (order 2) — 3/5 inbound links
• Tumors contain multiple subclones with spatial and temporal heterogeneity (order 2) — 8/10 inbound links

Stale Syntheses (0)

Hub concepts with draft synthesis where inbound count has grown by 3+ since last synthesis.

None found.