Genetics / genomic pattern · BEGINNER LESSON
LD block
An LD block is a stretch of DNA where nearby sites show nonrandom association, called linkage disequilibrium, across the region. In practice, different studies define the block boundary differently, so an LD block is a model-based region rather than a single universal cutoff.
What it is
Linkage disequilibrium, or LD, means that alleles, which are DNA variants at a site, are associated with each other more often than expected by chance. An LD block is a region of DNA where this association stays strong across many nearby markers, so the region can be treated as a unit for some analyses. In human studies, similar regions are also called haplotype blocks because a small number of haplotypes, which are common combinations of variants on one chromosome, can summarize much of the observed variation. [1,2]
[2] Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome [3] Haplotype blocks and linkage disequilibrium in the human genome - Nature Reviews Genetics
How it is measured and identified
Researchers measure LD with statistics such as D' and r^2. D' describes how strongly alleles are associated relative to the maximum possible for the observed allele frequencies, while r^2 describes how much variation at one site can be explained by variation at another. Some block methods call a region a block when most pairwise LD values exceed a chosen threshold, such as D' above 0.8 or r^2 above 0.4; other methods use haplotype diversity, meaning they ask whether a small number of haplotypes explains most of the variation. [0,1]
[1] Characterisation of the genomic architecture of human ... [2] Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
How the block idea works biologically
Blocks are thought to reflect the history of recombination, which is the exchange of DNA between chromosomes during meiosis. Many historical recombination events can break up LD between regions, while stretches with fewer breaks can remain more internally associated. However, LD is not determined by physical distance alone: patterns vary across the genome, and different regions can have very different block structure. [0,2]
[1] Characterisation of the genomic architecture of human ... [3] Haplotype blocks and linkage disequilibrium in the human genome - Nature Reviews Genetics
Why the definition is limited
There is no single agreed definition of an LD block. Different thresholds and different statistics can produce different numbers of blocks, different block lengths, and different coverage of the genome. Studies also note that denser marker maps, larger sample sizes, and common variants tend to give shorter blocks, and that D' can be biased upward in small samples or with rare alleles, so comparisons between studies need caution. [0,2]
[1] Characterisation of the genomic architecture of human ... [3] Haplotype blocks and linkage disequilibrium in the human genome - Nature Reviews Genetics
SEE THE IDEA
How an LD block is identified
Sites close together on a chromosome that can be tested for association.
A value such as D' or r^2 summarizes how strongly pairs of sites are associated.
If enough pairs pass a chosen threshold, the region is called a block.
The block summarizes local inheritance patterns, often for haplotypes or association studies.
Markers are measured with an LD statistic; a threshold-based rule then groups them into a block.
An LD block is not directly observed as a physical object; it is inferred from pairwise association patterns in DNA data.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.