Genetics Lecture 1

Question 1

Summarize the basic principles of PCR

Answer 1

PCR: polymerase chain reaction- amplify DNA or RNA from a small sample, rapid, inexpensive, 1. Denature (uses Taq polymerase that can survive the temperature 95 C of denaturing cycle) 2. Annealing 3. Extension

Question 2

types of single nucleotide variants in the protein coding region of genes

Answer 2

silent- switch one base and no change in amino acid
nonsense- switch one base and have a stop codon
missense- switch one base and get a new amino acid
frameshift- deletion of a base and frameshift of other bases results in new amino acid

Question 3

cystic fibrosis

Answer 3

autosomal recessive disease, common in Caucasian and Ashkenazi Jewish populations, due to CFTR gene

Question 4

ACOG/ACMG

Answer 4

American college of obgyn and genetics recommend mutation panel for cystic fibrosis carrier testing that includes 23 mutations in CFTR gene (targeted by PCR)

Question 5

deltaF508; W1282X

Answer 5

accounts for 70% of CF mutations in Caucasian; accounts for 46% of CF mutations in Jewish people

Question 6

why not sequence the entire CFTR gene in everyone?

Answer 6

cost, time, novel sequence variants, CF screening panel is designated to detect only those mutations associated with classical CF

Question 7

If a woman is a CF carrier the physician would recommend…

Answer 7

partner get tested

Question 8

hereditary breast and ovarian cancer syndrome

Answer 8

autosomal dominant with incomplete penetrance

Question 9

BRCA1 and BRAC2

Answer 9

genes that if mutated increase risk of familial breast cancer and ovarian cancer

Question 10

How do you sequence for mutations in the BRCA1 and BRAC2?

Answer 10

need to sequene the entire coding regions (exons)

Question 11

DNA sequencing

Answer 11

allows examination of DNA up to 500 bases and can detect single base changes as well as small insertions and deletions

Question 12

target DNA sequencing

Answer 12

when the mutation is known, quick, less expensive, few mutations associated with the disease, can test for individual mutations or sequence selected exons

Question 13

gene sequencing

Answer 13

mutations are unknown, more expensive/longer, interpretation can be more complicated, targeted mutation is negative

Question 14

For single nucleotide/ small insertions and deletions you would use which method of DNA sequencing

Answer 14

PCR

Question 15

For large indels and whole or partial gene deletions/duplications you would use which method of DNA sequencing

Answer 15

deletion duplicatoin analysis

Question 16

For genome rearrangements you would use which method of DNA sequencing

Answer 16

cytogenetic karyotyping, FISH

Question 17

whole exome sequencing (WES)

Answer 17

sequencing of the coding region (exons) of all the known human genes

Question 18

whole genome sequencing (WGS)

Answer 18

sequencing the whole genome, a lot of the genome we don’t know what it does

Question 19

massively parallel (nexGen) sequencing

Answer 19

start with DNA, chop into small fragments, select fragments using hybridization, once you have selected fragments they become annealed, PCR process, aligned to reference genome sequence

Question 20

heterozygous variant

Answer 20

shows massively parallel (nexGen) sequencing results showing differences

Question 21

WES and WGS

Answer 21

increased information is not always better, difficult to interrupt

Question 22

there are a lot of variants in a genome even in “normal” people usually located in

Answer 22

intergenic regions (noncoding introns) and have no medical implications

Question 23

5 -class scale for pathogenicity

Answer 23

“benign until proven otherwise” benign, likely benign, variant of uncertain significance, likely pathogenic, pathogenic

Question 24

Variant of uncertain significance (VUS)

Answer 24

rare variants are common, most genetic variants have little or no clinical effect

Question 25

linkage

Answer 25

genetic linkage is a violation of mendels law of independent assortment

Question 26

linkage disequilibrium

Answer 26

refers to non-random association fo alleles in the population

Question 27

Southern

Answer 27

DNA

Question 28

Northern

Answer 28

RNA

Question 29

Western

Answer 29

Protein