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Genomic Biology > Final > Flashcards

Final Flashcards

1
Q

What are the three “types” of diseases?

A
  1. acquired (cancer)
  2. infectious
  3. inherited
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2
Q

What are the 3 types of different ways that a genetic disease can be inherited?

A
  1. Autosomal
  2. X/Y linked
  3. mitochondrial
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3
Q

What is the difference between monogenic and polygenic?

A

monogenic: one gene involved (Mendelian)
polygenic: multiple genes involved

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4
Q

What are the consequences of mutations in coding/non-coding/regulatory regions?

A

coding: could affect the proteins being built
noncoding: affects amount of gene expression
regulatory: disrupt transcription factor binding sites

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5
Q

Define haplotype

A

group of closely-linked genes that tend to be inherited as a block

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6
Q

What are 2 reasons we would want to know what gene causes a disease?

A
  1. screening purposes
  2. druggable targets
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7
Q

What is a polygenic risk score?

A

provide a measure of your disease risk due to your frequency of SNPs

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8
Q

What are 3 biases with GWAS?

A
  1. self reporting
  2. location of data collection
  3. sample type
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9
Q

What is trio sequencing and how is it useful?

A

sequencing genome of mother, father, and offspring
- able to tell if SNP in question is inherited from a parent

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10
Q

What do microarrays measure for in GWAS?

A

hetero(yellow) /homozygosity (red, green)

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11
Q

whole exome sequencing better at detecting _________________ than whole genome sequencing?

A

novel variance

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12
Q

Why is exome sequencing advantageous?

A

Takes less time since only the usable (exons) are sequenced

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13
Q

What does a Manhattan plot show?

A

shows the significance of the associations between each genetic variant (SNP)

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14
Q

What is the purpose of GWAS?

A

identify a genotype (gene) associated with a phenotype (disease)

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15
Q

How was CFTR gene identified via positional cloning and Sanger sequencing?

A

positional cloning was able to identify which chromosome the gene was on and comparative genomic narrowed the location down

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16
Q

What is a current treatment for people with CF and the CFTR gene and how does it work?

A

Trikafta; opens up ion channel to reduce mucus

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17
Q

Is heterozygous or homozygous mutations worse?

A

heterozygous

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18
Q

The phenotypic severity of SNPs varies considerably, depending on the _____________ of the SNP relative to gene sequences and the genomic background of the individual

A

location

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19
Q

What is the Mendelian Inheritance of Man (MIOM)?

A

record of all genes that are autosomal dominant, autosomal recessive, X/Y linked, and mitochondrial

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20
Q

What is a katyotype?

A

normal number or chromosomes

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21
Q

What is cytogenetics?

A

study of chromosomes

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22
Q

What is aneuploidy?

A

abnormal number of chromosomes

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23
Q

What are 3 aneuploidies that we discussed in class?

A
  1. Down Syndrome (trisomy 21)
  2. Edwards syndrome (trisomy 18)
  3. Patau Syndrome (trisomy 13)
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24
Q

Trisomys are usually the result of ______________

A

non-disjunction (mispaired chromosomes during replication)

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25
Q

When are chromosome abnormalities typically detected?

A

in utero

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26
Q

Chromosomal instability syndromes are caused by mutations in DNA repair pathways and are associated with high rates of ________________

A

cancer

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27
Q

Cancer is a disease of the __________ in which cells divide uncontrollably

A

genome

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28
Q

What is an example of a chromosomal instability disease?

A

Ataxia telagiectasia

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29
Q

What are the three tissues of origin for cancers?

A
  1. carcinomas (90%)
  2. blood (9%)
  3. sarcoma (1%)
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30
Q

What tissue are carcinomas?

A

skin, lungs, gut

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31
Q

what tissue are sarcoma?

A

bone, fat

32
Q

What is an example of acquired mutation causing cancer?

A

chemical
radiation

33
Q

How do pathogens cause cancer?

A

interfere with genome

34
Q

What is Helicobactor pylari?

A

pathogen that causes stomach cancer

35
Q

mutations that lead to transformation are associated with what 3 types of genes?

A
  1. oncogenes
  2. tumor supressor genes
    3.apoptosis related genes
36
Q

what are oncogenes?

A

promote cell growth

37
Q

what do tumor suppressor genes inhibit?

A

cell growth

38
Q

What are the 6 hallmarks of cancer?

A
  1. self- sufficiency in growth signals
  2. insensitivity to anti-growth signals
  3. evading apoptosis
  4. limitless replication
  5. angiogensis (new blood vessels)
  6. mustastasis (maligenant growths)
39
Q

What are driver mutations v. passenger mutations?

A

dirver: Mutations that provide a selective growth advantage, and thus promote cancer development

passenger: those that do not are termed passenger mutations

40
Q

How does radiation treat cancer?

A

induces DNA damage to initiate apoptosis

41
Q

How does chemotherapy treat cancer?

A

induces DNA damage to initiate apoptosis

42
Q

How does alkylating agents treat cancer?

A

crosslink DNA and replication
- damaging DNA preventing replication

43
Q

How does antimetabolites treat cancer?

A

chemically resemble nucleotides, tricking cancer cells into using its drug

44
Q

How does antimicrotubules treat cancer?

A

inhibit microtubule function which block cell cycle

45
Q

What 3 molecules are involved in triple negative breast cancer?

A
  1. estrogen receptor (ER)
  2. progesteron receptor (PR)
  3. HER2
46
Q

What is Estrogen Receptors targeted with in breast cancer for treatment?

A

tamoxifen

47
Q

What is the advantage to personalized medicine for cancer treatment?

A

affect healthy cells less and cells involved in cancer more

48
Q

______________ chemotherapy then surgery is given for breast cancer patients but only works 50% of time

A

neoadjuvant

49
Q

What is the purpose of single cell sequencing for tumors?

A

it distinguishes different cell types in tumor tissue

50
Q

How does single cell sequencing work?

A
  1. disassociate single cells of tumors
  2. one cell per plate
  3. add one barcode per plate
  4. mix
  5. NGS
51
Q

What is intratumor heterogeneity?

A

individual cells can accumulate thier own mutations

52
Q

What are the 2 reasons for chemoresistance?

A
  1. chemoresistant cells were there all along
  2. chemo caused them
53
Q

what are 3 challenges of gene therapy?

A
  1. how do we get in new DNA
  2. need to understand problem
  3. need to be very specific (safety)
54
Q

What are 3 things that work best for gene therapy? (1 genes and 2 diseases)

A

heritable genes
monogenic disease
tissue specific disease

55
Q

what is an advantage and disadvantage of in vivo gene therapy?

A

advantage: it’s easier to target internal organs. It’s also less complicated, since cells don’t need to be removed from a person at all.
disadvantage: they require very precise delivery of genetic material to the damaged area of the body.

56
Q

What is an example of a lentivirus?

A

AID

57
Q

What are 3 reasons lentiviruses are useful?

A
  1. infects dividing/non-dividing cells
  2. permanently integrates into host
  3. carries long pieces of DNA
58
Q

what is a disadvantage of lentiviruses?

A

inserts randomly into genome and inserts some of its own DNA

59
Q

what is an example of a lentivirus used to treat B-thalassemia (hemoglobin issue)?

A

Zynteglo

60
Q

What are 3 advantages of Adeno-assocaited viruses? (AAV)

A
  1. non pathogenic
  2. infected dividing/non-dividing cells
  3. integrates into 1 place
61
Q

what is a disadvantage of Adeno-assocaited viruses? (AAV)

A

can only carry small pieces of DNA

62
Q

what is an example of a AAV used to treat spinal muscular atrophy by providing SMN1?

A

Zolgensma

63
Q

Who was the first person to die from a clinical trial involving gene therapy?

A

Jesse Gelsinger

64
Q

What disease did Jesse Gelsinger have?

A

OTC deficiency causes a build up ammonia

65
Q

What did the death of Jesse do?

A

reformed informed consent

66
Q

Is ex vivo or in vivo better for treating blood disorders?

A

ex vivo

67
Q

What are CAR T cells?

A

T cells that detect cancer

68
Q

What are CAR T cells build with?

A

suicide switches (injected to kills CAR T cells)

69
Q

Why is forensics so concerved?

A

link to law

70
Q

What are the 3 goals of forensics?

A
  1. establish paternity
  2. identify remains
  3. identify suspects
71
Q

What is DNA finger printing?

A

identifying a series of short tandum repeats (STR)

72
Q

What are short tandum repeats?

A

repeats on codons that can be used in DNA finger printing to identify people based on how many repeats they have

73
Q

DNA fingerprinting uses ___________ electrophoresis

A

capillary

74
Q

What is genetic geneology?

A

using publicly available genetic data base to find relatives (gold state killer)

75
Q

What is a method to identify tissue?

A

microarrrays (look at transcriptomics)

76
Q

How is measuring microbiomes useful?

A

each person has a unique microbiome
tell time of death

Genomic Biology (6 decks)

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