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chapter 10
GENETICS ODU
56
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Undergraduate 3
10/21/2015
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Term
A WILD TYPE HUMAN
 Definition
genome sequence does not exist
Term
DNA POLYMORPHISM
 Definition
sequence difference
the genome sequences of only 3 people reveal over 5 million differences
Term
MOST POLYMORPHISMS DO NOT INFLUENCE PHENOTYPE
 Definition
condons make up <2% of the human genome
many mutations in codons dont change the amino acid
deleterious mutations disappear from the population
Term
SINGLE NUCLEOTIDE POLYMORPHIS
 Definition
one base pair change
SNP
Term
DELETION INSERTION POLYMORPHISM
 Definition
short insertions or deletions of a single or a few base pairs
DIP
Term
SIMPLE SEQUENCES
 Definition
1-10 base sequences repeated 15-100 times in tandem
SSR
Term
COPY NUMBER VARIANTS
 Definition
large blocks of duplication or deletion with populations frequency of <1%
CNV
Term
COMPARISON OF HUMAN AND CHIMPANZEE GENOME
 Definition
reveals that SNP's that occurred since divergence of these species
Term
THE SECOND SINGLE BASE CHANGE IS
 Definition
polymorphic in humans
the C must be ancestral
the T is derived
Term
POLYMERASE CHAIN REACTION PCR
 Definition
method of making many copies of a target region
developed in 1985
faster and less expensive
extremely efficient
Term
2 OLIGONUCLEOTIDE PRIMERS DEFINE THE TArGET REGION
 Definition
one primer is complementary to one strand of DNA at one end
the other primer is complementary to the other strand of DNA at the other end
Term
3 STEPS IN EACH PCR CYCLE
 Definition
1) denature strands
2) base pairing of primers
3) polymerization of primers along templat
Term
EXPONENTIAL INCREASES
 Definition
in the amount of target DNA during PCR
Term
DETERMINING GENOTYPE BY SEQUENCING PCR PRODUCTS
 Definition
sickle cell anemia is caused by a SNP in the Hb beta gene
genotyping can identify carriers and homozygous individuals
Term
PCR BY PRODUCT SIZE
 Definition
target regions containing SSR's or DIP's can be amplified by PCR
the PCR products vary in size
Term
ANALYSIS OF HUNTINGTON DISEASE
 Definition
-autosomal dominant disorder
-normal allele has < 34 CAG repeats
-disease-causing alleles have 42 or more CAG repeats
Term
PRENATAL GENETIC DIAGNOSIS
 Definition
-genotyping fetal cells
- cells isolated by amniocentesis-fetal cells in amniotic fluid are extracted using a needle
Term
PREIMPLANTATION EMBRYO DIAGNOSIS
 Definition
-utilizes in vitro fertilization and PCR
- genotype embryos before placing in womb
Term
DNA POLYMORPHISM
 Definition
sequence difference
the genome sequences of only 3 people reveal over 5 million differences
Term
MOST POLYMORPHISMS DO NOT INFLUENCE PHENOTYPE
 Definition
condons make up <2% of the human genome
many mutations in codons dont change the amino acid
deleterious mutations disappear from the population
Term
SINGLE NUCLEOTIDE POLYMORPHIS
 Definition
one base pair change
SNP
Term
DELETION INSERTION POLYMORPHISM
 Definition
short insertions or deletions of a single or a few base pairs
DIP
Term
SIMPLE SEQUENCES
 Definition
1-10 base sequences repeated 15-100 times in tandem
SSR
Term
COPY NUMBER VARIANTS
 Definition
large blocks of duplication or deletion with populations frequency of <1%
CNV
Term
COMPARISON OF HUMAN AND CHIMPANZEE GENOME
 Definition
reveals that SNP's that occurred since divergence of these species
Term
THE SECOND SINGLE BASE CHANGE IS
 Definition
polymorphic in humans
the C must be ancestral
the T is derived
Term
POLYMERASE CHAIN REACTION PCR
 Definition
method of making many copies of a target region
developed in 1985
faster and less expensive
extremely efficient
Term
2 OLIGONUCLEOTIDE PRIMERS DEFINE THE TArGET REGION
 Definition
one primer is complementary to one strand of DNA at one end
the other primer is complementary to the other strand of DNA at the other end
Term
3 STEPS IN EACH PCR CYCLE
 Definition
1) denature strands
2) base pairing of primers
3) polymerization of primers along templat
Term
EXPONENTIAL INCREASES
 Definition
in the amount of target DNA during PCR
Term
DETERMINING GENOTYPE BY SEQUENCING PCR PRODUCTS
 Definition
sickle cell anemia is caused by a SNP in the Hb beta gene
genotyping can identify carriers and homozygous individuals
Term
PCR BY PRODUCT SIZE
 Definition
target regions containing SSR's or DIP's can be amplified by PCR
the PCR products vary in size
Term
ANALYSIS OF HUNTINGTON DISEASE
 Definition
-autosomal dominant disorder
-normal allele has < 34 CAG repeats
-disease-causing alleles have 42 or more CAG repeats
Term
PRENATAL GENETIC DIAGNOSIS
 Definition
-genotyping fetal cells
- cells isolated by amniocentesis-fetal cells in amniotic fluid are extracted using a needle
Term
PREIMPLANTATION EMBRYO DIAGNOSIS
 Definition
-utilizes in vitro fertilization and PCR
- genotype embryos before placing in womb
Term
SSR LOCI ARE HIGHLY POLYMORPHIC
 Definition
many alleles exist in the populaiton
an individual person carries only 2 alleles at a given loci
Term
GENOTYPE IS DETERMINED BY PCR AT MANY SSR LOCI
 Definition
-13 pairs of PCR primers are labeled with fluorescent dyes
- probability that a person has the same alleles at 13 SSR loci is about 1 in 10 trillion
Term
CODIS DATABASE IS MAINTAINED BY THE FBI
 Definition
data from all 13 SSR loci
data can match DNA from crime scene to a person, or establish innocence
Term
MULTIPLEX PCR
 Definition
is used for DNA fingerprinting
Term
SHORT HYBRIDIZATION PROBES
 Definition
can distinguish single-base mismatches
Term
HYBRIDIZATION OF SHORT OLIGONUCLEOTIDES TO SAMPLE DNA'S
 Definition
-if there is not mismatch btwn probe and target, hybrid will be stable at high temp
-if there is a mismatch, hybrid will not be stable at high temps
Term
HYBRIDIZATION PROBES
 Definition
are used on micoarrays for genotyping
Term
ALLELE SPECIFIC OLIGONUCLEOTIDES
 Definition
are attached to a solid support
Term
PREPARATION OF GENOMIC DNA
 Definition
fragmented
adapter attached
amplified by PCR and denatured to make single stranded
fluorescent dye coupled to end of single stranded DNA
Term
FLUORESCENT OUTPUT
 Definition
is proportional to the number of copies of each allele
Term
ALLELIC HETEROGENEITY
 Definition
disease caused by different mutations in the same gene.
Term
COMPOUND HETEROZYGOTE
 Definition
individual with different mutant alleles of the same gene
Term
LOCUS HETEROGENEITY
 Definition
disease caused by mutation in one of 2 or more different genes
Term
GENOME SEQUENCING IS BECOMING ROUTINE
 Definition
sequencing an entire genome now costs about $5000
sequencing whole-exome is less expensive
Term
HIGH THROUGHPUT OR MASSIVELY PARALLEL SEQUENCING
 Definition
is like sanger sequencing with a few modifications:
- individual DNA molecules are anchored in place
-each base is identified before the next one is added
- increased sensitivity elimnates need for cloning or PCR
Term
GENOME SEQUENCING REVEALS A SEA OF VARIATION
 Definition
each individual differs at >3 million locations from the refseq human genome
Term
HOW CAN WE TELL WHICH POLYMORPHISM CAUSES A DISEASE?
 Definition
-transmission pattern
- predicted effect on protein function
- clues from other genome sequence
Term
SNP PATTERN IN A RARE DOMINANT TRAIT
 Definition
-except heterozygous polymorphism
-common variants are poor disease candidates
Term
SNP PATTERN IN A RARE RECESSIVE TRAIT
 Definition
-except affected individuals to be homozygotes or transheterozygotes
Term
PINPOINTING A DISEASE GENE
 Definition
requires a combination of approaches
- nic volker has a severe form of IBD
Term
PINPOINTING A DISEASE GENE MAY POINT TO A TREATMENT
 Definition
xiap also causes another disease (XLPD) that results in production of too many white blood cells.
-XLPD is treated w/ bone marrow transplant
-bone marrow transplant helped nic too
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