Positional cloning - genes in critical region

Question 1

How would we identify the genes in the critical region in pre-human genome project times?

Answer 1

Develop probes from markers identified to be in the critical region and use those to screen a library of clones. Then sequence the clones identified by the probes and identify any genes

Question 2

How would we identify the genes in the critical region now in post-human genome project times?

Answer 2

Go to a database and input the flanking markers of the critical region, then the database will identify any genes between them

Question 3

Why do we need to be cautious while predicting genes using a database?

Answer 3

Only as good as the algorithm used to predict them. It might’ve gotten some wrong or missed some

Question 4

What do we do once we know which genes are in the critical region?

Answer 4

Use other databases to learn everything about those genes and rank them in order of priority

Question 5

How do we select candidate genes to look for mutations in first?

Answer 5

1. Look if expression data is consistent with disease phenotype
2. Consistent function with disease phenotype
3. Any paralogs or orthologs?

Question 6

Would we sequence every exon in the critical region?

Answer 6

No, start at the top of the list and work down

Question 7

What is an ancestral haplotype?

Answer 7

Most common shared haplotype between affected individuals in a kindred

Question 8

How can the ancestral haplotype be used to narrow down the critical region for the disease gene even more?

Answer 8

Look for affected individuals that don’t have parts of the ancestral haplotype, or look for unaffected individuals that have parts of it

Question 9

What do we call affected individuals that don’t have parts of the ancestral haplotype or unaffected individuals that have parts of it?

Answer 9

Key recombinants

Question 10

What is chromosomal abnormality assisted gene identification?

Answer 10

The use of a subtle chromosomal abnormality that can be seen with cytogenetics to identify the disease gene

Question 11

Why do we need to be careful with chromosomal abnormality assisted gene identification?

Answer 11

The abnormality might not be causing the disease phenotype. It could just be a coincidence

Question 12

How do we do chromosomal abnormality assisted gene identification?

Answer 12

Use a database to identify any genes near the abnormality, prioritize them, then examine them further