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• SSCP Analysis
○ unlike regular gel electrophoresis (in which double-stranded DNA
travel through the gel), the DNA strands in a SSCP test are
denatured, separated and run through a gel where they cannot
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reanneal. Only in this way can they form hairpin loops, and
hairpin loops can affect their speed through a gel.
○ Different mutations form different hairpin loops
(“conformations”) hence they are called single-strand
conformational polymorphism
○ To do the SSCP test, compare how a Test DNA (with hairpin
loops) vs. Control DNA (with hairpin loops) will run through the
gel!
○ Advantages vs. Disadvantages
Advantages: You can test many exons at once.
Disadvantages: Not all point mutations will affect
secondary structure.
• DHPLC Analysis
○ like SSCP except you hybridize a single-stranded mutant strand
with a normal strand, and they cause “kinks” that causes the
whole thing to run differently in the gel.
• CGH Analysis
○ It’s called Comparative Genomic Hybridization, because you are
comparing the mutant with the control ‘s genome, how they
compete with each other to hybridize to the array.
○ If much more Control DNA than the Test DNA hybridizes to the
BACs on the array then it means that there is no Test DNA at this
point of the chromosome, and therefore there is a deletion.
2. GENOMIC DISORDERS
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• Genomic Diseases
○ DiGeorge Syndrome = 22q11 deletion
○ α -thalassaemia = deletion of entire A-globin gene
○ Williams syndrome = deletion on chrom 7
○ Smith Magenis Syndrome = deletion of 17p11.2
○ Potocki-Lupski Syndrome = duplication of 17p11.2 (PLS)
○ HNPP = null mutation or deletion in PMP22 (also in 17p11.2)
(major component of myelin), AD
○ Charcot-Marie-Tooth = duplication in PMP22(also in
17p11.2), AD
• Williams Syndrome patients have heart problems, and large lips.
Remember they are very loquatious and their language ability beats
their cognitive abilities.
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4. METABOLIC DISORDERS
• AMINO ACID METABOLISM DISORDERS – mainly autosomal
recessive, because missingenzyme
○ Hypophenylalanemia: via BH4 or PKU. Can’t turn
phenylalanine into tyrosine.
○ Alkaptonuria: homogentistic acid oxidase deficiency.
○ OCA1 – can’t turn tyrosine into melanin.
○ Homocystinuria – can’t turn Methionine into Cysteine (via
CBS) à MR, Osteoporosis
○ Maple Syrup Urine Disease –Defect in ketoacid
decarboxylase. Excrete VLI in urine. Common among
Mennonites. Mnemonic: Think of Mennonites making maple
syrup.
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• XIST and BF
○ XIST inactivates X chromosome by turning it into a
heterochromatin.
○ BF blocks XIST from inactivating Xa. This is why X chromosome
in guys are not inactivated.
6. EPIGENETICS
• Sperm and egg are methylated. When sperm and egg combine, they
start demethylating until implantation. As somatic cells, methylation
begins again and is maintained every time DNA replicates.
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• Uniparental disomy of entire genome (not just a few genes) can lead to
hydatidiform moles (ovarian teratoma)
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○ Note in the diagram that PHP1A has both AHO and PTH
resistance.
○ Note that PHPIB is due to imprinting defect, not mutation.
• PHP vs PPHP
○ PHP1a = AHO w/ PTH
resistance
○ PHP1b = PTH resistance
w/o AHO
○ PPHP = AHO w/o PTH
resistance
7. LINKAGE ANALYSIS
8. POPULATION GENETICS
9. MULTIFACTORIAL DISEASES
• SOD1 mutation causes ALS, but CNTF +/- can affect the age of onset
(but only if there is already a SOD1 mutation to begin with)
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• Heritability
○ H=0 means disease is completely environmental.
○ H=1 means disease is completely genetic.
○ Most multifactorial diseases have Heritability of 0.4-0.7
• Celiac Disease
○ HLA-DQ2/8 = a gene responsible for celiac disease.
○ However, Celiac disease is multifactorial!
○ Using sibpair analysis, they found that a mutation on chrom 6 was
not the only defect responsible but also a mutation on chrom 19!
○ Found disease in gene Myo9B of chrom 19!
• Hirschsprung Disease
○ RET normally causes neural crest cells to migrate to intestines à
but a mutation in RET causes Hirschsprung Disease.
○ Whereas RET is dominant gene, EDNRB is recessive. EDNRB is
responsible for a lot of cases of Hirschsprung disease among
Mennonites!! Mnemonic: Think of two mennonite fellas named
“Ed-n-Rob”
○ Lots of ways these responsible genes can interact. So mutation to
some of them or all of them can cause problems large and small.
○ In summary, RET, SOX, and EDNRB is to blame for Hirschsprung
Disease. (Mnemonic: Think about Ed and Rob watching a Red Sox
Game and they see a giant doodoo in the stadium bathroom)
• A lot more guys get Hirschsprung Disease than girls. If a girl has it,
then chances are her genes are “bad enough” for her siblings to have
a higher chance to get it as well (vs. if she were a guy).
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