Gene Mapping and Cloning

Question 1

Linkage analysis

Answer 1

Locates genes to regions of chromosomes, determines what genes may be inherited together, basic information about genome organization

Question 2

Mapping by recombination

Answer 2

Linkage depends on chromosomal location, chromosomes re-organize at meiosis, crossing over may separate linked alleles, distance between genes is important to linkage, multiple crossovers can occur between two chromatids in one meiosis

Question 3

Physical distance and linkage

Answer 3

Closer genes recombine less, distance is measured in centimorgans (cM), 1 cM = 1% of the chromosomes recombine between two genes

Question 4

Linkage phase

Answer 4

Important when following a gene in a family, which alleles of linked genes are on the same DNA strand as a mutated gene, can follow inheritance of linked marker rather than mutation, can screen more quickly

Question 5

Determining if genes are linked

Answer 5

Genes may be inherited together by chance with small numbers, cannot replicate results in other studies, genes can be located with enough individuals and markers, determine likelihood that gene or trait is linked to a number

Question 6

LOD score

Answer 6

Calculate likelihood that observed data fits a given hypothesis, compare that to likelihood genes are unlinked, likelihood ratio, odds that genes are linked, logarithm of odds is LOD score

Question 7

LOD score values

Answer 7

Score is a base-10 logarithm, positive or negative value, >3 is significant for linkage, -2 suggests no linkage

Question 8

Markers for mapping

Answer 8

Many genes mapped, need more than location to be useful, need polymorphisms to determine linkage phase of various markers

Question 9

Marker distribution

Answer 9

Markers are found at many locations on chromosome, degree of localization varies, recombination distance differs by sex

Question 10

Uninformative mating

Answer 10

Some combinations do not give enough information to determine linkage phase, same marker allele on both chromosomes, cannot follow through subsequent generations

Question 11

Linkage and time

Answer 11

Recombination will slowly separate mutation from linked markers, distribution will change over generations, will remain linked to nearby markers in most cases early on

Question 12

Linkage disequilibrium

Answer 12

Mutation and specific linked alleles inherited together, more likely person with mutant gene carries a specific allele at linked marker, recombination will separate mutation from marker, can give estimate of mutation’s age

Question 13

Markers through time

Answer 13

Recombination separates alleles over generations, more closely linked markers take longer, will eventually reach linkage equilibrium

Question 14

Association

Answer 14

Applies when linkage is not known or may not be a factor, some specific allele significantly increases risk of a person being affected, may be due to effect of allele rather than linkage disequilibrium

Question 15

Ankylosing spondylitis

Answer 15

Ossification of spinal disc, joints, and ligaments, 90% of patients have HLA-B27, <10% of population has B27 allele, only one factor, likely autoimmune disorder

Question 16

Genome wide association studies (GWAS)

Answer 16

Used to locate genes, many markers screened in one test, uses techniques like microarrays, screens many markers such as SNPs (single nucleotide polymorphisms), use haplotypes to reduce burden

Question 17

Chromosome anomalies

Answer 17

Changes to chromosome useful in mapping genes to small regions, series of deletions allow small common region to be identified, translocation breakpoints may be in a specific gene

Question 18

DNA libraries

Answer 18

Large collections of DNA clones, human DNA inserted into a vector, genomic and cDNA

Question 19

Genomic library

Answer 19

Made from chromosomal DNA, should have all DNA from an organism

Question 20

cDNA library

Answer 20

Should have copies of all genes expressed in a given tissue

Question 21

Candidate gene

Answer 21

DNA sequences that may be responsible for a given trait, identified by position and function, must fit various criteria before they are no longer just a candidate

Question 22

Positional candidate gene identification

Answer 22

Location is known, entire region sequenced, identify likely gene sequences

Question 23

Functional candidate gene identification

Answer 23

Know likely function and chromosome, look for gene which fit both

Question 24

Electing a candidate gene

Answer 24

Compare sequence of gene from normal and mutant individuals, look for expression in appropriate tissues, compare expression in mutant and normal, express gene to determine the gene product and its function