Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Genomics > Final Exam > Flashcards

Final Exam Flashcards

(71 cards)

Start Studying
1
Q

What is the basic unit of life?

A

The cell

There are roughly 37 trillion cells in the human body.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How many known cell types exist?

A

About 200 known cell types

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What percentage of a cell’s composition is water?

A

70% water

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is a stem cell?

A

A cell that can differentiate into any cell type

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is a type in cell biology?

A

A classification used to describe cells with similar characteristics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the four characteristics used to classify cell types?

A
  • Morphology
  • Gene expression profile
  • Function
  • Location
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is cell lysis?

A

The process where a cell’s membrane breaks down, releasing its internal contents

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are proteases used for in cell isolation?

A

To isolate the cell by dissociating tissue/proteins holding cells together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What does apoptosis refer to?

A

Programmed cell death, occurring as a normal part of an organism’s growth or development

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the difference between bulk RNA sequencing and single cell RNA sequencing?

A
  • Bulk RNA sequencing analyzes gene expression in a mixture of cells
  • Single cell RNA sequencing analyzes gene expression in a single cell or nucleus
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the three key advancements in single cell technology?

A
  • Integrated fluidic circuit
  • Nanodroplets
  • Barcoding
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What drives single cell RNA-seq technology adoption?

A
  • Cost
  • Ease
  • Data robustness
  • Experimental design
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the first step in single cell RNA sequencing data generation?

A

Lipid encapsulation of cells and transcription enzyme mix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a barcode in the context of single cell sequencing?

A

A unique nucleic acid sequence used to label and track individual cells or cell populations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the advantages of using nuclei over whole cells in single cell RNA sequencing?

A
  • Less stress and mitochondrial signal
  • Simpler sample processing logistics
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is clustering in the context of single cell data?

A

Grouping objects into groups that are more similar to each other based on gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the purpose of normalization in data processing?

A

To ensure data entries appear similar across all fields and records

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is a Nearest Neighbor Graph?

A

A graph by a set of points in metric space used for clustering

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is deconvolution in single cell analysis?

A

Estimating the proportion of a cell type present in a mixture of cells using single cell data

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is spatial transcriptomics?

A

Gene expression measures in a defined tissue space

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is comparative genomics?

A

A field of biological research comparing genome sequences of different or within species populations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is a phylogenetic tree?

A

A branching diagram that visually represents the evolutionary relationships based on genetic characteristics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the three advantages of using a pangenome?

A
  • More complete accounting of the genetic blueprint of a species
  • Improved sensitivity for detecting structural variants
  • Better ability to resolve complex structural variation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What does imputation refer to in genetics?

A

Statistical inference of unobserved genotypes using known haplotypes in a population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What is the significance of sensitivity in variant calling?
Trying to discover all the real variants
26
What is the significance of specificity in variant calling?
Trying to limit the false positives that creep in when filters get too lenient
27
What is the main purpose of SNP chips?
To genotype a large number of individuals cost-effectively
28
What is the call rate per SNP used for?
Best indicator of genotype quality
29
What is the call rate per individual used for?
Best indicator of sample DNA quality
30
What does GWAS stand for?
Genome Wide Association Study ## Footnote GWAS is used to detect associations between genetic variants and traits.
31
What is the purpose of whole genome sequencing?
To generate data and analyze genetic information ## Footnote Whole genome sequencing provides a comprehensive view of an organism's genetic makeup.
32
What is low pass sequencing?
A method that allows for genotyping a large number of individuals at a lower cost ## Footnote It can be used in GWAS to associate traits of interest.
33
What is a key limitation of association studies like GWAS?
Association does NOT equal causation ## Footnote This means that just because two variables are correlated does not imply one causes the other.
34
What are the characteristics of polygenic traits?
Traits influenced by multiple genes ## Footnote Polygenic traits are more complex and often show a range of phenotypes.
35
What determines the ability to detect associations in GWAS?
1. Number of loci 2. Effect size and allele frequency 3. Sample size 4. Nature of markers used 5. Heterogeneity of the trait ## Footnote Each factor influences the statistical power of the study.
36
What is linkage disequilibrium?
The non-random association of alleles at different loci ## Footnote It occurs when alleles at nearby loci are inherited together more often than expected by chance.
37
In a GWAS Manhattan Plot, what does the significance threshold indicate?
It distinguishes between significant and non-significant associations ## Footnote A higher number of participants can lead to clearer associations.
38
What are the critical properties of sequencing reads for genome assembly?
1. Length 2. Accuracy 3. Evenness of representation ## Footnote These factors affect the quality and success of genome assembly.
39
Define contig in the context of genome assembly.
A set of sequence reads that overlap to form a contiguous stretch of DNA sequence ## Footnote Contigs are essential for reconstructing the genome.
40
What does N50 represent in genome assembly?
The shortest contig length such that 50% of the bases are contained in contigs of that length ## Footnote A higher N50 value indicates better assembly quality.
41
What is a De Bruijn graph?
An assembly method that uses smaller sub-sequences (kmers) to find overlaps and build a graph ## Footnote This method is effective for assembling complex genomes.
42
What is the goal of a human pangenome?
To identify genetic variation within populations and individuals ## Footnote It incorporates multiple reference genomes to capture diversity.
43
What are the three A's in the context of pangenomes?
1. Assemblies 2. Alignments 3. Annotations ## Footnote These elements are crucial for understanding human variation.
44
What does BUSCO stand for?
Benchmarking Universal Single-Copy Orthologs ## Footnote It is used to assess genome completeness by comparing expected single-copy orthologs to the genome assembly.
45
True or False: The main determinant of how easy it is to assemble a genome is its size.
False ## Footnote The repeat structure of the genome is more significant than its size.
46
Fill in the blank: The ability to resolve repetitive sequences in genome assembly is improved with _______.
longer reads ## Footnote Longer reads provide more context for assembling complex regions.
47
48
What is the primary goal of the 1000 Genomes Project?
To build a resource to help understand genetic variation.
49
What are the two types of sequencing used in the 1000 Genomes Project?
Low coverage whole-genome sequencing and high coverage exome sequencing.
50
What is a pro of low coverage whole-genome sequencing?
Cost effective and allows large scale studies.
51
What is a con of high coverage exome sequencing?
Only sequences 2% of the genome.
52
Why are genotype likelihoods used in genetic studies?
To summarize the evidence for each genotype at biallelic sites.
53
True or False: Low frequency variants tend to be older mutations.
False.
54
What must happen for a mutation to remain in the population?
* The mutation must allow the individual to survive and reproduce. * The individual must transmit it to the next generation.
55
What does the False Discovery Rate (FDR) quantify?
The likelihood of making errors in variant calls.
56
What is the relationship between coverage and genotype accuracy?
The more coverage you have, the more accurate your genotype estimates will be.
57
What is RNA-seq used to study?
Gene expression and identify novel RNA species.
58
Fill in the blank: The most common method for RNA purification is _______.
Oligo-dT based purification.
59
What is the minimum number of biological replicates required for an RNA-seq experiment?
3.
60
What is GTEx and its goal?
Genotype Tissue Expression; to understand how genetic variants influence gene expression across various tissues.
61
What are eQTLs?
Expression quantitative trait loci; genetic loci that explain variation in expression levels of mRNAs.
62
What does ENCODE stand for?
Encyclopedia of DNA Elements.
63
What did ENCODE find about enhancer regions?
There are 5.6 times more enhancer regions than promoter-like regions.
64
True or False: Most disease variants are found in coding regions.
False.
65
What percentage of the genome is functional according to ENCODE?
80.4%.
66
What adds complexity to human genetics compared to simpler organisms?
An abundance of non-coding RNA and alternative splicing.
67
What is the significance of alternative splicing?
It allows for multiple versions of a gene to be produced.
68
What is the impact of gene length on normalization in RNA-seq?
Normalization by gene length is necessary when comparing expression levels.
69
What does differential gene expression (DGE) analysis investigate?
Differences in gene expression due to various factors, like viral challenges.
70
What is a common method for assessing the quality of RNA?
Using a Fragment Analyzer.
71
What is a primary reason for the proliferation of RNA-seq in biology?
Discovery and quantification of gene expression.

Genomics (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions