Question 1 According to Dr. Roth, the bottleneck with genome seque...

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Question 1
According to Dr. Roth, the bottleneck with genome sequencing in terms of personalized medicine is in
The cost of sequencing
Not having emough genomes sequenced
Interpreting genomes
Sequencing technology is not advanced enough

Question 2
The Human Genome Project:
Was solely Canadian project
Was created from Craig Venter's DNA alone
Used many cell types
Was created from an average of several individuals

Question 3
The method most likely to be used to test for a pathogenic allele at a well-known location such as the BRCA1 gene would be
Whole Exome Sequencing
Genotyping
Whole Genome Sequencing
RNA sequencing

Question 4
Oftentimes the result of an experiment is considered statistically significant if the p value is less than 0.05 (0.05 is denoted alpha). For GWAS, the significance threshold is set to values more like 10° This is because:
GWAS is very conservative test
When you are doing so many tests. like with GWAS. the probability of finding significant result by chance is very high. so the p-value is adjusted to avoid false negatives
All statistical tests should set alpha to 10
When you are doing so many tests. like with GWAS. the probability of finding significant result by chance is very high. so the p-value is adjusted to avoid false positives

Question 5
The data from GWAS:
Indicate many suggestive loci that are part of the haplotype block associated with the variant
Indicates rare variants associated with disease
Indicate locus that is associated with the variant
Reveal the variant that causes disease unambiguously

Question 6
Most functional variants:
Are beneficial
Are deleterious
Are not subject to natural selection
Are neutral

Question 7
In burden of mutation analysis, the mutational make-up of cases and controls is
Cases deleterious mutations, controls neutral mutations
Cases: neutral mutations controls neutral beneficial mutations
Cases neutral + deleterious mutations, controls neutral multations
Cases deleterious mutations, controls beneficial mutations

Question 8
Sometimes, expressing the human version of a gene in yeast is sufficient for yeast growth when the native yeast copy of the gene is knocked out If so, a putative disease variant in that human gene can be tested for functionality by expressing it as the only copy of that gene in yeast This strategy is best classified as:
eQTLs
Acase control study
Trans-species complementation
Comparative genomics

Question 9
Africa has the greatest genetic diversity because
It is the oldest population and therefore more mutations have had time to accumulate
It is the youngest population and therefore there has been less time for selection to eliminate deleterious mutations

Question 10
The method Dr. Awadalla and his colleagues used to determine the human germline mutation rate was to:
Sequence sperm/egg and somatic tissue and count the difference in the number of changes between sperm/egg and the somatic tissue
Compare the sequence differences between an individual sequenced and the reference sequence. count those differences as the mutation rate
Sequence sperm/egg and somatic tissue and count the difference in the number of changes relative to the reference sequence
Sequence parent-child trios: mutations found in the child that are not present in either adult are de novo mutations

Question 11
One of the three pilot coverage strategies for the 1000 Genomes Project was to sequence two parent-child trios at very high coverage. The purpose of this was:
To look for genetic differences between these distinct trios
To develop new reference sequences
To identify disease alleles in those families
To test whether the bioinformatic tools were working properly

Question 12
The reason the 1000 Genomes Project could "get away with" low coverage of an individual was because they were testing many different individuals and looking at population level variation. When trying to identify a rare variant causing disease in a clinical environment, for example:
This would not be an effective strategy to employ because you need more confidence for variant calling mutation in an individual
This would be an effective strategy to employ because it's much more cost effective to have low coverage of genome
This would be an effective strategy to employ because you can easily identify the disease-causing variant

Question 13
The majority of variants identified in Phase 3 of the 1000 Genomes Project were:
Indels
Multiallelic SNPs
Biallelic SNPs
Structural variants

Question 14
Coverage, or the number of times a genome is sequenced is important because you can have more confidence when variant calling if the variant is present in few sequence reads
True
False

Question 15
Common variants are usually of small effect size because if they had large deleterious effect in early life they would probably have been eliminated from the population by natural selection
True
False

Question 16
In a GWAS, if the minor allele frequency at some positions is different between the cases and controls, it suggests that that variant is in the region of the variant contributes to disease
True
False

Question 17
Computational approaches to determining the effect of a rare variant include (select all that apply):
Modelling protein structure
Using comparative genomics
Using programs like PolyPhen2
Tiny robots called nanoswimmers that can swim through and survey blood

Question 18
A major achievement of the 1000 Genomes Project was improvements in pipelines for data processing This includes (select all that apply):
Improved "base calling (identifying the nucleotide base)
Improved identification of INDELs
Better tools to identify SNPs
Improved identification and removal of duplicates

Question 19
<blank> is a good choice to perform when a gene is frequently mutated in disease but the individual variants are rare:
Familial association analysis
twin study
Burden of mutation analysis
T-test
</blank>

Question 20
A common deleterious effect a new variant can have is:
interfering with proper protein folding
interfering with the process of transcription
interfering with diffusion processes
interfering with cell-cell communication

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