Term
| What is a BAC Array-CGH and how do you perform one? |
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Definition
Label genomic DNA - Cy3/Cy5
Co-hybridize test genome and reference against an array of genomic (BAC) clones
Look for BACs with discordant representation in the two genomes |
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Term
| What are the strengths and weaknesses of the Array-CGH? |
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Definition
| Genome wide but no structural basis of change, and cant detect balanced changes, i.e. inversions |
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Term
| How do you perform paired end-sequencing? |
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Definition
Select 3kb fragments of human DNA
End sequence
Compare paired end-sequences with genome sequence assembly - any differences between the two are structural variants array-cgh could not discover |
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Term
| In paired end sequences, what does it mean if the end-sequences are closer than 3kb, further apart than 3kb, or from the same strand of assembly |
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Definition
from expanded allele
from deleted allele
fragment crosses inversion boundary |
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Term
| What are the most common cause of copy number variants (CNVs)? |
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Definition
| deletions or duplications |
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Term
| How can you identify very recent selection? |
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Definition
| analyse genomes for regions with excess singleton variants |
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Term
| When did humans and chimpanzees split? |
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Definition
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Term
| How do you figure out two-locus genetic distance? |
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Definition
| (Difference in frequency of allele 1 in pop A and pop B)^2+(difference in frequency of allele 2 in pop A and popB)^2 = two locus genetic difference ^2 |
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Term
| What is principal component ananlysis? |
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Definition
| Condense trends in frequencies- show correlation between genetic similarity and geographical proximity (No one would ever have guessed this) |
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Term
| What evidence suggests the out of africa theory? |
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Definition
| genetic distance measures, trees of sewuence constructed from fully sequenced mtDNA, SNP typing in Y chromosome |
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Term
| Why is it difficult to study ancient DNA and which part should you study? |
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Definition
| DNA badly damaged - C-U mutations, and contamination from modern human DNA - study mtDNA, as although just as degraded, starts off at a high copy number |
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Term
| How much is the average amount of Neanderthal DNA in humans? |
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Definition
| 1.5-2%, around 30% of Neanderthal DNA in total is preserved |
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