Lecture 26

Question 1

Personal Genomics

Answer 1

concerned with the sequencing and analysis of the genome of an individual

• employs different techniques
• -SNP analysis
• -exome or full genome sequencing

then genotype can be compare with the published literature to determine likelihood of trait expression and disease risk

Question 2

Predictive Medicine

Answer 2

the use of the information produced by personal genomics techniques when deciding what medical treatments are appropriate for a particular individual

ex. inherited medical genomics, cancer genomics, and pharmacogenomics

Question 3

Precision medicine

Answer 3

focused on a new taxonomy of human disease based on molecular biology

Question 4

What are some examples of genetic testing?

Answer 4

• Newborn screening
• Diagnisti testingn
• CArrier testing
• Predictive testing
• Pre-symptomatic testing
• pharmacogenetics

Question 5

newborn screening

Answer 5

targeted tests for recessive genetic disorders

ex. CF, sickle cell anemia

Question 6

diagnostic testing

Answer 6

confirmatory test or differential diagnosis testing for a symptomatic individual
ex. skeletal dysplasias

Question 7

carrier testing

Answer 7

targeted testing for asymptomatic individuals potentially carrying one or more recessive mutations
ec. Cf, Tay-Sachs

Question 8

Predictive testing

Answer 8

tests for variants causing or associated with disease or disorders with a hereditary component, usually with adult onset symptoms
ex. most cancers, cadiovascular disease, diabetes

Question 9

Pre-symptomatic testing

Answer 9

tests for variatnts causinf or associated with disease or disorders known to be inherited in the family, often with adult-onset symptoms
ex. huntington’s, alzheimer”s

Question 10

Pharmacogenetics

Answer 10

targeted tests for variants associated with pharmaceutical dosage choise or adverse reactions
ex. DNA tests, warfarin, carbamazepine

Question 11

What can be used to evaluate the validity of genetic tests?

Answer 11

• analytical sensitivity
• analytical specificity
• clinical sensitivity
• clinical specificity
• positive predictive value
• negative predictive value
• clinical utility
• personal utility

Question 12

analytical sensitivity

Answer 12

refers to the proportion of assays with the genotype that have a positive test result (false-negative rate of the assay)

Question 13

analytical specificity

Answer 13

refers to the proportion of assays without the genotype that have a negative test result (false-positive rate of the assay)

Question 14

clinical sensitivity

Answer 14

refers to the proportion of people with a disease who have a positive test results (false-negative rate of diagnosis)

Question 15

clinical specificity

Answer 15

refers to the proportion of people without a disease who have a negative test result (false-positive rate of diagnosis

Question 16

positive predictive value (PPV)

Answer 16

refers to the likelihood that a patient has the disease given that the test result is positive

Question 17

negative predictive value

Answer 17

refers to the likelihood that a patient does not have the disease given that the test result is negative

Question 18

clinical utility

Answer 18

refers to the value of the test for determining treatment, patient management and family planning

Question 19

personal utility

Answer 19

refers to the value of the test for personal and family choices

Question 20

23andMe

Answer 20

a privately held personal genomic and biotech company based in Mountain View, CA
- named for the 23 pairs of chromosomes in a normal human cell

Question 21

What are some examples of tests carried out by 23and Me?

Answer 21

36 genes tested for carrier status CF

• cancer
• sleep movement
• Ancestry
• shared family segments

Question 22

What does 23andMe analyze and with what technology?

Answer 22

uses Illumina HTS iSelect HD

- scans for ~600,000 SNPs

Question 23

What is Promethease?

Answer 23

• a literature retrieval system that builds a personal DNA report based on the scientific literature cited in SNPedia and a file of genotype (DNA) data
• customers of DNA testing services can use it to retrieve published data about their DNA completely independent of whichever company produced the data

Question 24

Why do genetic sequencing companies need to use Promethease?

Answer 24

in 2013, the FDA instructed 23andMe that they could not report outcomes with medical relevance unless they had FDA approval
- so it does what the companies essentially cannot

Question 25

SNPedia

Answer 25

a report that you can get from Promethease if you want more information about the SNP in question

Question 26

What kind of reports can you get from promethease?

Answer 26

• sequence variants with bad outcomes
• lymphoma potential
• Prostate cancer
• Cancer
• rare pharmacogenomic variants

Question 27

Why is 23andMe terrifying?

Answer 27

• real goal to hoard data?
• meant to be a front end for a massive information-gathering operation against an unwitting public
• –not the intention to be a medical device
• they reserve the right to use your personal information —including your genome- to inform you about events and try to sell you products and services
• attempts to recruit people who suffer from certain disease, such as Parkinson’s and a few types of cancer. simply though brute-force pattern matching
• –company has a chance of finding genetic causes of these ailments