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Guest lectures Flashcards

Ancient DNA, RNAseq, Long read sequencing, metagenomics and binning, Genomic epidomiology, Canser-seq

1
Q

Ancient DNA:
What is a unique characteristic of ancient DNA (aDNA)?

A

It is usually heavily fragmented

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2
Q

Ancient DNA:
What is often a major challenge in analyzing aDNA?

A

Presence of modern DNA contamination

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3
Q

Ancient DNA:
What technique is crucial for authenticating aDNA sequences?

A

Analyzing post-mortem DNA damage patterns

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4
Q

Ancient DNA:
Why is endogenous DNA content important in aDNA studies?

A

Indicates the amount of DNA from the original organism

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5
Q

Ancient DNA:
What has been a major advancement in the field of aDNA research?

A

Use of Next-Generation Sequencing (NGS)

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6
Q

RNA-Seq:
What is the main purpose of RNA-Seq?

A

To analyze the expression levels of genes

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7
Q

RNA-Seq:
In RNA-Seq, what is the significance of a ‘count matrix’?

A

It shows the number of times each gene is sequenced

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8
Q

RNA-Seq:
Which of the following is a challenge in RNA-Seq data analysis?

A

Normalizing data for accurate comparisons

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9
Q

RNA-Seq:
What role does ‘differential expression analysis’ play in RNA-Seq?

A

It compares gene expression levels between conditions

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10
Q

RNA-Seq:
Why is ‘quality control’ important in RNA-Seq?

A

To ensure accurate and reliable sequencing data

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11
Q

Long Read Sequencing:
What is a key advantage of long-read sequencing over short-read sequencing?

A

Better accuracy for repetitive sequences

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12
Q

Long Read Sequencing:
What is one of the main challenges associated with long-read sequencing?

A

High error rate

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13
Q

Long Read Sequencing:
Which technology is known for providing long-read sequencing capabilities?

A

PacBio

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14
Q

Long Read Sequencing:
In the context of long-read sequencing, what is “phasing” used for?

A

Resolving haplotypes in a genome

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15
Q

Long Read Sequencing:
How does long-read sequencing benefit the study of structural variations in genomes?

A

It allows for better resolution of large and complex genomic rearrangements

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16
Q

Quantitative Metagenomics:
What is the primary focus of quantitative metagenomics?

A

Analyzing the genetic diversity in a microbial community

16
Q

Quantitative Metagenomics:
What does ‘alpha diversity’ refer to in metagenomics?

A

Diversity within a single sample

17
Q

Quantitative Metagenomics:
What is the significance of ‘rarefaction’ in quantitative metagenomics?

A

To normalize data for species richness

18
Q

Quantitative Metagenomics:
In metagenomics, what does the Shannon index measure?

A

Species richness and evenness

19
Q

Quantitative Metagenomics:
How is ‘beta diversity’ used in quantitative metagenomics?

A

To compare diversity across different environments

20
Q

Metagenomics Binning:
What is the primary goal of metagenomic binning?

A

To categorize DNA sequences into groups representing individual species or taxa

21
Q

Metagenomics Binning:
What is a common method used in metagenomic binning?

A

Composition-based binning

22
Q

Metagenomics Binning:
How does abundance-based binning work in metagenomics?

A

By looking at the relative abundance of sequences across samples

23
Q

Metagenomics Binning:
What challenge does metagenomic binning help to address?

A

Separating and categorizing complex mixtures of DNA from environmental samples

24
Q

Metagenomics Binning:
Why is assessing bin quality important in metagenomics?

A

To ensure accurate species identification

25
Q

Genomic Epidemiology:
What is the primary purpose of genomic epidemiology?

A

To understand the spread of diseases through genetic analysis

26
Q

Genomic Epidemiology:
What is the primary purpose of genomic epidemiology?

A

It is used to trace the transmission pathways of infectious diseases

27
Q

Genomic Epidemiology:
How can genomic epidemiology aid in outbreak investigations?

A

Through genetic comparison of pathogen samples

28
Q

Genomic Epidemiology:
How can genomic epidemiology aid in outbreak investigations?

A

Interpreting vast amounts of genetic data

29
Q

Genomic Epidemiology:
How can genomic epidemiology aid in outbreak investigations?

A

It has enhanced the ability to analyze pathogen genomes quickly and in detail

30
Q

Cancer Genomics:
What is a primary focus of cancer genomics?

A

Understanding genetic mutations that lead to cancer

30
Q

Cancer Genomics:
What role do tumor suppressor genes play in cancer development?

A

They prevent uncontrolled cell division

31
Q

Cancer Genomics:
How do oncogenes contribute to cancer?

A

By driving uncontrolled cell growth

32
Q

Cancer Genomics:
What is the significance of ‘driver mutations’ in cancer?

A

They directly contribute to cancer progression

33
Q

Cancer Genomics:
How has Next-Generation Sequencing impacted cancer genomics research?

A

By enabling detailed analysis of cancer genomes

NGS (4 decks)

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