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Interpreting more genomic data

Below you can see another cluster diagram. The circles represent a group of people infected by with isolates which vary by zero SNPs. Each circle is joined by a line to the isolates which vary by one SNP. Black circles are added when isolates in blue circles vary by more than 1 SNP i.e. each black circle represents an additional SNP.

Dotted lines link isolates separated by more than one SNP (number of SNPs as shown).

The figure below shows the average numbers of SNPs separating pairs of TB isolates with strong epidemiological links (blue) and no known epidemiological links (red). Looking at the SNPs separating the isolates in the cluster among members of the recent migrant community, where do they fall on this distribution?

What does this tell us about possible transmission?

Note: None of the pairs of isolates differed by between 13 and 29 SNPs

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Feedback for Exercise 6

Look at the numbers of SNPs which separate the TB isolates in the cluster diagram; how do these fit on the distribution below?

The majority of the isolates at the top of the diagram differ by a small number of SNPs – the largest number separating any two isolates is 8 SNPs .

The majority of isolates at the top of the diagram are separated by less than 5 SNPs.

The isolates at the bottom of the diagram differ from each other and from those at the top of the diagram by many more SNPs – between 36 (from the 2005 isolate at the top to the 2007 isolate on the right) and 116 SNPs (from the 2005 isolate at the top to the 2007 isolate at bottom left).

What does this tell us about possible transmission?

You saw earlier in the case study that isolates which differ by less than 5 SNPs are very likely to be part of the same transmission chain, whereas isolates with more than 12 SNPs between them are much less likely to be directly transmitted. This means that the isolates shown in the bottom half of the diagram are very unlikely to be linked to those at the top as part of a transmission cluster but those at the top which are linked by less than 5 SNPs show good evidence of being linked.

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