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IMF-102-02-0001-en	Why must controls in molecular methods follow the whole chain from specimen to data, not just the final readout?	Extraction, amplification, labelling, sequencing and filtering each create a representation that can selectively lose or enrich material, so the signal may not match the molecule in the original specimen.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0002-en	What do extraction blanks and spike-in molecules each monitor, and why does the choice of extraction kit matter?	Blanks reveal reagent contamination and spike-ins monitor recovery; different kits can produce systematic differences that resemble biology.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0003-en	Why is end-point PCR poorly quantitative, and how does quantitative PCR estimate starting template instead?	After reagents saturate, accumulated product no longer tracks the starting amount; quantitative PCR monitors fluorescence during amplification and uses the threshold-crossing cycle, if efficiency and baseline handling are valid.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0004-en	Why does deeper sequencing coverage not guarantee accurate variant detection?	More observations per position improve detection of low-frequency variants, but depth cannot repair systematic mapping or amplification bias.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0005-en	Why might Sanger sequencing miss a variant carried by only a minority of the DNA molecules?	Sanger sequencing produces a consensus signal, so low-frequency variants can be missed; it remains useful for small regions and for confirmation.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0006-en	Why does a genome-wide association signal not by itself identify the causal variant?	Through linkage disequilibrium the associated marker may only tag the functional change; replication and fine mapping narrow credible variants, and functional experiments test mechanism.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0007-en	After genome editing produces a phenotype, how can target function be separated from editing artefact?	Rescue experiments or independent guides are required, because off-target editing, mosaicism, large rearrangements and p53-related selection can also accompany editing.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0008-en	Why can an apparent expression change in bulk RNA sequencing be ambiguous?	Bulk sequencing averages across cells, so the change may reflect altered expression within a cell type or a changed mixture of cell types.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0009-en	Why can transcript abundance not be read directly as protein abundance or activity?	Translation, degradation, localisation, cleavage, phosphorylation and complex formation intervene between transcript and functional protein.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0010-en	Why is identifying a feature in untargeted metabolomics uncertain, and what raises confidence?	One metabolite can yield several ions, adducts or fragments, and different molecules can share mass; confidence rises with accurate mass, retention, fragmentation and comparison with authentic standards.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0011-en	In single-cell RNA sequencing, why should dropout of a gene or a new cluster not be taken at face value?	Dropout reflects limited sampling rather than true absence, and clusters emerge from analytic choices, so they need markers, anatomy, function and independent validation.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0012-en	Why is pathway enrichment a hypothesis generator rather than evidence that a pathway is active?	Its result depends on the background gene set, database definitions and selection threshold; and using the same data to select and test a pattern is circular.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0013-en	Why can computational correction not rescue a study in which batch is confounded with disease group?	When batch and group coincide, technical and biological signal cannot be reliably separated; randomising samples across batches with bridge controls prevents more bias than later correction.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending
IMF-102-02-0014-en	Why does a molecular signature that classifies samples well not establish mechanism, and what builds strong inference?	A signature can classify without identifying mechanism; strong inference adds validation in independent material, localisation to relevant cells, perturbation in a suitable system and connection to human phenotype.	Integrated Medical Foundations; chapter 102, TTS module 2; https://theisegoria.github.io/medical-textbook/integrated-medical-foundations-expanded-english.md; module SHA256 at export: 49f97f53a8492d636836fe79b64a49f3dc58260bbaa77e2623888fa6a6257528; editorial review pending	imf lang::en chapter::102 module::102-02 review::pending