Utilizing the Co-segregation of a marker

with some disease allele

Using the disease phenotype to guess

at what gene(s) may underlie.

Really the final, definitive step of gene localization.

Markers narrow down to a couple genes, the exons of which are then sequenced.

What locus/loci are mutationally different in disease cases than wildtype (healthy patients)?

Using genetic techniques to modify genes, to

*Study expression

*Study structure/function relationships

*Study gene function (i.e. via knockouts)

Used for hybridized DNA detection

after RFLP

Detects RNA -

same technique as Southern / RFLP

Detects Proteins.

Same techniques as Southern, Northern Blots

Testing for presence of markers that are closely linked w/ disease alleles.

Esp. in families that have particular prevalence of the disease.

Allele-specific oligonucleotide probes.

Bind to specific alleles.

Normal ASO, Mutant ASO

Array-based Comparable Genomic Hybridization

(aCGH)

Array-based SNP genotyping (~10,000 loci),

reads SNPS, gives copy number (uniparental disomy),

and loss of heterozygosity in cancer cells

Most states require PKU, four others

*Mass spectometry can detect 70-90 diseases from newborns

*American College of Medicine recommends ~25 tests to be screened.

One percent recombination distance.

If A and B are 1 cM apart, their linkage will be

unbroken in 99% of the offspring

Loci occuring on same chromosome

(barring recombination)

Long-Of-The-Odds

Likelihood that two loci are linked at a particular recombination frequency, versus unlinked.

(An iterative measure as you get more info.)

LOD = log10( | Prob linked / Prob unlinked | )

Indicate two loci are not linked

at any recomb. frequency

Indicate linkage.

Where LOD score values peak along

axis of recombination frequencies

gives greatest odds that two markers are

linked at this distance.

ex./ if 6 kids and no recombinants,

Z = log10(2^6) = 1.8.

Conventionally, if Z >=3, 1000x likelihood of linkage.

Z =< 2 indicates no proof of linkage

Linked together on same chromosome, as in scenario

A| |A'

| |

B| |B'

Here, A is linked in coupling to B and in repulsion to B'

Autosomal Dominant,

CAG repeat that shows anticipation when inhereted from father

Expression from a single allele/chromosome is

insufficient for a normal phenotype

Mutation in one allele disrupts function of product from normal allele.

Often times in protein complexes, i.e. Marfan

Autosomal Dominant.

~1/3 are new mutations

Autosomal dominant

(Loss of function of one allele)

Autosomal Dominant

"Bird Bones"

Where autosomal recessive traits appear dominant

due to consanguinity in the pedigree

Becker's Muscular Dystrophy

Recessive X-linked,

BMD is milder clinical version.

Muscular dystrophy shows phenotypic diversity.

Duchenne's Muscular Dystrophy,

Recessive X-linked.

DMD is the more clinically severe form,

Muscular Dystrophy shows phenotypic diversity between the two forms.

Inactivation of the 2nd

X chromosome in females

X-linked Dominant,

due to runaway microsatellite on X chromosome.

Anticipation occurs in female gametes.

Chromosomal centromere roughly in

physical center of chromosome

Centromere is more toward one end

of the chromosome

Chromosome in which short arm is more of a

"stalk" on which satellite DNA sits

Chromosomes digested slightly before

staining with Giesma.

Dark bands are GC-rich "G-bands".

Light are G-negative.

Essentially the reverse of Giesma-banding;

AT-rich regions are stained

X0

(Phenotypically femal-ish)

Deformed 5th chromosome,

leading to mental retardation, head deformity.

"Cry of the cat" - make that sound

Fundamental Unit of Chromosome Packing,

chromatin subunit.

"Bead on a string"

Tightly compacted, darkly-stained bundles of genes

hardly ever expressed.

Effectively silenced by histones,

as in X-inactivation (Barr bodies)

Lightly stained regions of chromosomes,

containing most genes.

Free to be transcribed.

Short, Interspersed Elements (100-300 bp)

found in single copies at many locations in the genome

Long Interspersed Elements (5-7kB)

found in single copies at many locations in the genome

Joint Probability /

(Joint + Prior Probability)

Chromosome banding convention:

A(p/q)BC

A: Chromosome number

B: Chromosome zone (1 or 2)

C: Chromosome band, from centromere out.