Medical Genetics: Genetic Mapping and Cloning

Question 1

Linkage v. Association (3)

Answer 1

1. linkage is between loci
   associations exist between diseases and specific alleles
2. linkage must be studied in families;
   associations can be studied in unrelated persons
3. associations may imply a causal relationship; linkage does not

Question 2

Strategy: Functional Approach

Answer 2

based on the knowledge of the specific gene product (protein) involved in the disease
ex. Hemoglobin

Question 3

Strategy: Candidate Gene

Answer 3

based on the knowledge of the type of gene product involved in the disease.
*mapping not necessary

ex. For example, if a mutation in a ‘tyrosine kinase’ protein appears to be important in the pathogenesis of a disease, all known genes in the genome with a ‘tyrosine kinase’ domain could be evaluated for mutations in a set of affected and unaffected individuals

Question 4

Strategy: Chromosomal abnormality

Answer 4

show that the disease is consistently associated with a cytogenetic abnormality such as a deletion or translocation.

microdeletion syndrome
ex. Prader Willi Syndrome

translocation-

Question 5

Strategy: Positional Candidate (primary modern method)

Answer 5

1. map disease to a chromosomal region (inheritance linkage analysis)
2. survey plausible candidate genes in the region

ex. cystic fibrosis
ex. achondroplasia:
1. disease was mapped to short arm of chromosome 4 by linkage analysis
2. FGFR3 was known to be located in this region

Question 6

Strategy: Next Generation DNA Sequencing (NGS)

Answer 6

exome or linkage interval

Question 7

Exercise: Draw Products of Cross over

Answer 7

Take-Home: genes segregated independently if they are on different chromosomes or close on the same chromosome
50% Recombination: independent seg (no linkage)
0% Recombination: completely linked genes

Question 8

LOD score cut-offs

Answer 8

pro-linkage: 3 or more

con-linkage: -2 or less

Question 9

LOD= logarithm of odds

Answer 9

log (prob. of pedigree if linkage/ prob of pedigree if recombination)

Question 10

genetic and physical maps

Answer 10

genetic: based on recombination?
physical: cytogenetic

complete nucleotide sequence: 3 billion base pairs per haploid genome)

Question 11

next generation genome sequencing

Answer 11

Sequencing of exomes

The main strategies employed to identify a gene (or genes) with novel variants have been:

a. sequencing across multiple unrelated, affected individuals
b. sequencing multiple affected individuals from within a pedigree
c. sequencing parent–child trios; or comparing sequences of individuals from the extremes of the distribution for a quantitative phenotype.

More than 180 novel disease causing genes have been identified by now using this approach. A primary challenge of this technology is distinguishing between background polymorphisms and pathogenic mutations.