Genomic Technologies: Sequencing, Mapping, and Functional Assays
Technologies that define contemporary genetics
Sequencing paradigms
Short-read sequencing remains powerful for variant discovery at scale, while long-read platforms improve assembly, phasing, structural variant detection, and haplotype reconstruction. Each technology has characteristic biases in read length, accuracy, throughput, and cost.
Major sequencing strategies
Short-read sequencing
- High throughput and mature analytics
- Strong for SNVs and small indels
- Limited in repetitive and highly rearranged regions
Long-read sequencing
- Superior for structural variation and assembly
- Useful for phasing and repeat-rich loci
- Typically higher per-base cost and distinct error modes
Functional genomics assays
Methodological caution
Every assay has batch effects, capture bias, and an implicit definition of signal. A good geneticist asks what the assay cannot see before interpreting what it can.
From association to mechanism
GWAS identifies statistical associations, but mechanism often requires fine-mapping, epigenomic annotation, saturation mutagenesis, reporter assays, perturb-seq, and causal modeling. The field is shifting from locus discovery toward functional dissection of variant effects in relevant cell states.
Which technique is best suited to identify chromatin accessibility at single-cell resolution?
Single-cell ATAC-seq measures chromatin accessibility in individual cells.
Correct answer: scATAC-seq
Why is phasing important in variant interpretation?
Allelic phase can change the biological meaning of multiple variants in a region.
Correct answer: Because it reveals whether variants are on the same or opposite homologs, which can determine compound heterozygosity, haplotypes, and regulatory interactions.
Typical modern functional-genomics workflow
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1
Map variants or candidate loci by sequencing or association.
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2
Prioritize candidates using annotation and evolutionary constraint.
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3
Perturb candidates using CRISPR, base editing, or epigenome editing.
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4
Read out the molecular or phenotypic response in relevant cell types.
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5
Validate the strongest causal hypothesis with orthogonal assays.
What is a major advantage of CRISPR screening over one-variant-at-a-time testing?
Pooled CRISPR screening enables scalable, parallel perturbation of many candidates.
Correct answer: It can interrogate many genes or regulatory elements in parallel