Index

Research Wiki Index

Sources (27)

• nowell1976-clonal-evolution-tumor-progression — Nowell (1976): The clonal evolution model of tumor progression. Science.
• greaves2012-clonal-evolution-cancer — Greaves & Maley (2012): Clonal evolution in cancer. Nature.
• nik-zainal2012-21-breast-cancers — Nik-Zainal et al. (2012): Mutational processes in 21 breast cancers. Cell.
• mcgranahan2017-clonal-heterogeneity-tumor-evolution — McGranahan & Swanton (2017): Clonal heterogeneity and tumor evolution. Cell.
• turajlic2019-genetic-heterogeneity-cancer — Turajlic et al. (2019): Resolving genetic heterogeneity in cancer. Nature Reviews Genetics.
• gerstung2020-evolutionary-history-cancer — Gerstung et al. (2020): The evolutionary history of 2,658 cancers. Nature.
• tarabichi2021-subclonal-reconstruction — Tarabichi et al. (2021): A practical guide to cancer subclonal reconstruction. Nature Methods.
• castorina2009-tumor-growth-instability — Castorina et al. (2009): Tumor growth instability and its implications for chemotherapy. Cancer Research.
• traina2010-norton-simon-modeling — Traina et al. (2010): Optimizing chemotherapy dose and schedule by Norton-Simon modeling. Breast Disease.
• sarapata2013-comparison-tumor-growth-models — Sarapata (2013): A comparison and catalog of intrinsic tumor growth models. HMC Senior Thesis.
• sottoriva2015-big-bang-model — Sottoriva et al. (2015): A Big Bang model of human colorectal tumor growth. Nature Genetics.
• hassan2024-comparative-study-tumor-growth — Hassan & Al-Saedi (2024): Comparative study of tumor growth based on single species models. BIO Web of Conferences.
• graham2017-measuring-cancer-evolution — Graham & Sottoriva (2017): Measuring cancer evolution from the genome. The Journal of Pathology.
• pcawg2020-pan-cancer-analysis — PCAWG Consortium (2020): Pan-cancer analysis of whole genomes. Nature.
• bakir2023-tracerx-metastasis — Al Bakir et al. (2023): The evolution of NSCLC metastases in TRACERx. Nature.
• bozic2010-driver-passenger-model — Bozic et al. (2010): Accumulation of driver and passenger mutations during tumor progression. PNAS.
• bozic2013-combination-therapy — Bozic et al. (2013): Evolutionary dynamics of cancer in response to targeted combination therapy. eLife.
• bozic2016-clonal-subclonal-passenger — Bozic et al. (2016): Quantifying clonal and subclonal passenger mutations in cancer evolution. PLOS Computational Biology.
• conticello2008-aid-apobec-family — Conticello (2008): The AID/APOBEC family of nucleic acid mutators. Genome Biology.
• petljak2022-apobec3-mechanisms — Petljak et al. (2022): Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature.
• dananberg2024-apobec-cancer-review — Dananberg et al. (2024): APOBEC mutagenesis in cancer development and susceptibility. Cancers.
• haig2004-genomic-imprinting-kinship — Haig (2004): Genomic imprinting and kinship: How good is the evidence? Annual Review of Genetics.
• falls1999-genomic-imprinting-disease — Falls et al. (1999): Genomic imprinting: Implications for human disease. The American Journal of Pathology.
• monk2019-genomic-imprinting-disorders — Monk et al. (2019): Genomic imprinting disorders. Nature Reviews Genetics.
• patten2014-evolution-genomic-imprinting — Patten et al. (2014): The evolution of genomic imprinting. Heredity.
• wilkins-haig2003-function-genomic-imprinting — Wilkins & Haig (2003): What good is genomic imprinting? Nature Reviews Genetics.
• extended-brain-2026-haig-genetic-text — Extended Brain (2026): The genetic text: How David Haig reimagines evolution as interpretation. Extended Brain (Substack).

Concepts (27)

Foundational

• clonal-evolution — The overarching Darwinian theory of tumor development.
• branching-process-model — Mathematical scaffolding unifying the Bozic-Nowak trilogy; δ = d/b, μ reconciliation, survival probability.
• clonal-expansion — Proliferation of a cell lineage bearing a fitness-affecting mutation.
• intratumor-heterogeneity — Genetic and phenotypic diversity within a single tumor.
• subclonal-architecture — Composition and phylogenetic structure of tumor subclones.
• branching-evolution — Divergent clonal lineages from a common ancestor.
• neutral-evolution — Clonal diversity from mutation and drift without selection.
• punctuated-evolution — Rapid bursts of genomic change rather than gradual accumulation.
• clonal-sweep — A fitter subclone expanding to dominate the population.
• intermediate-clones — Transient low-frequency subclones bridging pre- and post-sweep states; why they’re invisible and why they matter.

Selection and Fitness

• driver-mutation — A mutation conferring selective fitness advantage.
• passenger-mutation — A neutral mutation with no fitness effect; hitchhikes on expansions.

Growth Kinetics

• gompertzian-growth — Decelerating tumor growth model; constrains clone detectability and neutrality inference.

Genomic Alterations

• genetic-instability — Acquired propensity for elevated mutation and mitotic error.
• chromosomal-instability — Ongoing chromosome segregation errors producing aneuploidy.
• chromothripsis — Catastrophic shattering of chromosomes in a single event; early clonal, 22.3% pan-cancer.
• whole-genome-duplication — Tetraploidization event enabling subsequent diversification.
• metastasis — Spread of cancer to distant sites; an evolutionary process.

Mutational Processes

• mutational-signature — Characteristic mutation pattern reflecting a specific DNA damage/repair process.
• APOBEC-mutagenesis — C>T and C>G at TpC dinucleotides from AID/APOBEC cytidine deaminase activity.
• kataegis — Localized hypermutation colocalizing with rearrangement breakpoints.
• molecular-clock — Passenger mutation accumulation as a temporal record of tumor evolutionary history; enables relative timing of branching, drivers, CNAs, and mutational process shifts.

Imprinting and Epigenetics

• genomic-imprinting — Parent-of-origin-specific gene silencing; functional haploidy at imprinted loci and its consequences for clonal evolution.
• loss-of-imprinting — LOI as an epigenetic driver mechanism; biallelic activation of growth promoters without sequence change.

Methods

• subclonal-reconstruction — Computational inference of clonal composition from sequencing data.
• variant-allele-fraction — Proportion of reads carrying a variant; surrogate for clone abundance.
• cancer-cell-fraction — Proportion of cancer cells carrying a mutation; VAF corrected for purity and copy number.

Clinical

• therapy-resistance — Emergence of resistant clones under therapeutic selective pressure.

Entities (2)

• TRACERx — Prospective multi-region sequencing study tracking cancer evolution through therapy.
• PCAWG — Pan-Cancer Analysis of Whole Genomes; 2,658 cancers across 38 types.

Concept Vocabulary

• _concept-vocabulary — Full extracted concept list with planned wikilink targets.

Comparisons