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Genomics > epigenetic & RNA-sequencing & NIPT > Flashcards

epigenetic & RNA-sequencing & NIPT Flashcards

1
Q

What is Non-Invasive Prenatal Testing (NIPT)?

A

NIPT is a method that analyzes cell-free fetal DNA in maternal blood to detect chromosomal abnormalities in the fetus.

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2
Q

What is the principle behind NIPT?

A

NIPT detects changes in the copy number of fetal DNA in maternal plasma to identify chromosomal abnormalities such as trisomies 21, 13, and 18.

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3
Q

How does NIPT analyze fetal DNA?

A

It uses statistical modeling (e.g., normal distribution) to assess the proportion of abnormal fetal DNA in maternal blood.

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4
Q

What are the common applications of NIPT?

A

NIPT is primarily used to screen for conditions like Down syndrome (trisomy 21), trisomy 18, and trisomy 13.

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5
Q

What are some limitations of NIPT?

A

Limitations include technical errors due to GC bias and the need for a reference genome from non-repetitive regions to improve detection accuracy.

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6
Q

What is the sensitivity and specificity of NIPT?

A

NIPT has a sensitivity and specificity exceeding 99% for detecting common trisomies like Down syndrome (trisomy 21).

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7
Q

Why is it important to use a reference genome in NIPT?

A

Using a reference genome helps improve the accuracy of detecting chromosomal abnormalities by providing a baseline for comparison.

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8
Q

What are some risks associated with invasive prenatal testing methods?

A

Invasive methods like amniocentesis carry risks such as miscarriage and infection, which NIPT helps to avoid.

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9
Q

Who should consider undergoing NIPT?

A

Pregnant women over 35 or those with an increased risk of chromosomal abnormalities are recommended to consider NIPT as part of their prenatal care.

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10
Q

What should be done if an NIPT result is positive?

A

A positive NIPT result should be followed by genetic counseling and possibly invasive diagnostic testing to confirm the findings.

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11
Q

What are some genetic disorders that can be tested using NIPT?

A

Disorders include microdeletion syndromes like Prader-Willi syndrome, Angelman syndrome, and various monogenic diseases.

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12
Q

What does an elevated molecular count indicate in NIPT?

A

An elevated molecular count from chromosomes indicates the presence of an extra copy, suggesting conditions like trisomy.

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13
Q

What is the significance of GC correction in NIPT?

A

GC correction eliminates biases that can affect the accuracy of read counts and improve detection sensitivity for chromosomal abnormalities.

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14
Q

What is ChIP-Seq?

A

ChIP-Seq (Chromatin Immunoprecipitation Sequencing) is a method used to analyze protein-DNA interactions, specifically to identify binding sites of transcription factors and to find motifs within the genome.

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15
Q

What is the purpose of ChIP-Seq?

A

The purpose of ChIP-Seq is to analyze transcription factor binding sites and discover conserved motifs in the genome.

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16
Q

What are the main steps in ChIP-Seq?

A

The main steps in ChIP-Seq include sample preparation, immunoprecipitation of DNA-protein complexes, and sequencing of the purified DNA.

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17
Q

What is peak calling in ChIP-Seq?

A

Peak calling is the process of identifying regions in the genome with significant enrichment of reads, indicating potential binding sites of transcription factors.

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18
Q

What does motif discovery involve in ChIP-Seq?

A

Motif discovery involves analyzing identified peaks to find conserved sequences that indicate binding preferences of transcription factors.

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19
Q

What is RNA-Seq?

A

RNA-Seq (RNA Sequencing) is a technique used to study differential gene expression and perform transcriptome analysis.

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20
Q

What is the purpose of RNA-Seq?

A

The purpose of RNA-Seq is to analyze which genes are actively expressed under specific conditions or treatments.

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21
Q

What are the main steps in RNA-Seq?

A

The main steps in RNA-Seq include library preparation (RNA extraction and cDNA conversion) and high-throughput sequencing.

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22
Q

What type of analysis does RNA-Seq provide?

A

RNA-Seq provides differential expression analysis, identifying genes that are upregulated or downregulated between different conditions.

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23
Q

What is a Position Weight Matrix (PWM)?

A

A Position Weight Matrix (PWM) is a computational tool used to evaluate the similarity between sequences and target regions, scoring from 0 (no similarity) to 1 (perfect match).

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24
Q

How does PWM help in genomic analysis?

A

PWM helps quantify how well a sequence aligns with known motifs, allowing researchers to assess potential binding sites for transcription factors.

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25
Q

What does RPKM stand for?

A

RPKM stands for Reads Per Kilobase of transcript per Million mapped reads.

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26
Q

What is RPKM used for?

A

RPKM is used to normalize RNA-Seq data to quantify gene expression levels, accounting for transcript length and total number of reads.

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27
Q

Why are ChIP-Seq and RNA-Seq important in genomics?

A

Both techniques enable comprehensive genomic analyses; ChIP-Seq identifies protein-DNA interactions while RNA-Seq provides insights into gene expression dynamics.

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28
Q

What is the de Bruijn graph used for in genome assembly?

A

The de Bruijn graph is used to assemble sequences by finding Eulerian paths from k-mers.

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29
Q

What are the 4-mers for the reads {ACCATTC, ATTCCAA}?

A

The 4-mers are: ACCA, CCAT, CATTC, ATTC, TTCC, TCCA, CCAA.

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30
Q

What are the k-1 mers for the reads {ACCATTC, ATTCCAA}?

A

The k-1 mers (3-mers) are: ACC, CCA, CAT, ATT, TTC, TCC, CAA.

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31
Q

How is the de Bruijn graph created from k-1 mers?

A

Connect k-1 mers as nodes; directed edges represent overlaps of one nucleotide.

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32
Q

What is the reconstructed sequence S1 from the reads?

A

The sequence S1 is ACCATTC.

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33
Q

What biological questions can ChIP-seq address?

A

ChIP-seq can study gene regulation, transcription factor binding, and epigenetic modifications.

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34
Q

What is a transcription factor binding motif?

A

A transcription factor binding motif is a short DNA sequence where transcription factors bind to regulate gene expression.

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35
Q

How can TF binding motifs be represented?

A

TF binding motifs can be represented as position weight matrices (PWMs) or consensus sequences.

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36
Q

How can we predict TF binding sites using PWMs?

A
  1. Construct PWM from known motifs. 2. Scan DNA sequence for matches. 3. Score matches based on PWM values.
37
Q

What does a ChIP-seq data analysis workflow include?

A

Workflow includes sample preparation, immunoprecipitation, sequencing, data processing, peak calling, and motif analysis.

38
Q

What is epigenetics?

A

Epigenetics is the study of heritable changes in gene expression without altering DNA sequence.

39
Q

What are three epigenetic regulatory mechanisms?

A
  1. DNA methylation: Addition of methyl groups affects gene expression. 2. Histone modification: Chemical changes to histones alter chromatin structure. 3. Non-coding RNAs: RNAs that regulate gene expression post-transcriptionally.
40
Q

What are the steps for prioritizing functional mutations?

A
  1. Identify mutations from sequencing data. 2. Annotate mutations with databases. 3. Assess mutation impact on protein function. 4. Evaluate population frequency and disease association. 5. Prioritize based on functional relevance and experimental validation.
41
Q

What is a differentially methylated region (DMR)?

A

A DMR is a genomic region where DNA methylation levels differ significantly between conditions or samples.

42
Q

What is bisulfite sequencing?

A

Bisulfite sequencing is a method that converts unmethylated cytosines to uracils, allowing for the analysis of DNA methylation patterns.

43
Q

What is three-letter alignment in bisulfite sequencing?

A

Three-letter alignment converts all cytosines in reads and the reference genome to thymine, simplifying the mapping process.

44
Q

How does three-letter alignment affect methylation detection?

A

It loses the distinction between methylated and unmethylated cytosines, which can affect the accuracy of methylation analysis.

45
Q

What is the Msuite program?

A

Msuite is a toolkit for analyzing DNA methylation data, including quality control, read alignment, and methylation calling.

46
Q

What are the key features of Msuite?

A

Msuite supports multiple alignment modes and provides tools for quality control and visualization of methylation data.

47
Q

How does Msuite handle bisulfite-treated sequences?

A

It uses a three-letter mode to accurately process methylation data from bisulfite sequencing.

48
Q

What challenges does bisulfite sequencing present?

A

It complicates read mapping due to the conversion of unmethylated cytosines to thymine, leading to potential mismatches in alignment.

49
Q

What is the output of bisulfite sequencing analysis?

A

The output includes information about read alignment, methylation status of cytosines, and genomic coordinates.

50
Q

What are some applications of detecting differentially methylated regions?

A

Applications include studying gene regulation, cancer research, and understanding epigenetic modifications in various biological processes.

51
Q

What is long non-coding RNA (lncRNA)?

A

lncRNA is a type of RNA that does not code for proteins but plays a crucial role in regulating gene expression and chromatin structure.

52
Q

How do lncRNAs affect chromatin structure?

A

lncRNAs can modulate chromatin structure by influencing nucleosome positioning and chromosome looping, thereby regulating genome activity.

53
Q

What is the role of miRNA in gene regulation?

A

miRNAs bind to the 3’ untranslated region (3’ UTR) of target mRNAs to down-regulate their expression by inhibiting translation or promoting degradation.

54
Q

Why are miRNAs primarily located in the 3’ UTR?

A

miRNAs are localized in the 3’ UTR because this region allows effective binding and regulation of mRNA stability and translation.

55
Q

What happens when miRNAs bind to the 3’ UTR?

A

“Binding of miRNAs to the 3’ UTR leads to translational repression and destabilization of the target mRNA reducing protein synthesis…”

56
Q

What is the significance of hydrogen bonding in RNA interactions?

A

“Hydrogen bonding is crucial for base pairing between miRNAs and their target mRNA sequences facilitating regulatory interactions.”

57
Q

How does methylation differ from hydrogen bonding in RNA?

A

“Methylation involves adding a methyl group to DNA or RNA affecting gene expression stability while hydrogen bonding stabilizes base pairing during transcription translation.”

58
Q

What are some biological functions of lncRNAs?

A

“lncRNAs regulate gene expression influence chromatin remodeling involved cellular processes like differentiation response stress.”

59
Q

What mechanisms do miRNAs use to regulate gene expression?

A

“MiRNAs use mechanisms such as mRNA degradation translational repression interference RNA-binding proteins control gene expression.”

60
Q

What is impact genetic variants in 3’ UTR?

A

“Genetic variants in 3’ UTR can alter miRNA binding sites affecting mRNA stability translation efficiency may lead changes gene expression.”

61
Q

What percentage transcripts non-coding RNA (ncRNA)?

A

“Non-coding RNA accounts approximately 98% all transcripts.”

62
Q

What are main types RNA cells?

A

“Main types RNA include rRNA (over 90%) tRNA mRNA (which has poly-A tail).”

63
Q

What whole transcriptome sequencing?

A

“Whole transcriptome sequencing analyzes all RNA transcripts sample including coding non-coding RNAs.”

64
Q

What coding RNA sequencing?

A

“Coding RNA sequencing specifically targets mRNA contains poly-A tail gene expression analysis.”

65
Q

What RPKM?

A

“RPKM stands Reads Per Kilobase transcript Million mapped reads; normalizes read counts single-end sequencing.”

66
Q

“What FPKM?”

A

“FPKM stands Fragments Per Kilobase transcript Million mapped fragments; normalizes read counts paired-end sequencing.”

67
Q

“What primary difference between RPKM FPKM?”

A

“RPKM normalizes based reads while FPKM accounts fragment counts avoid double counting paired-end data.”

68
Q

“What does differential gene expression analysis identify?”

A

“It identifies genes show significant differences expression levels between different sample groups.”

69
Q

“What do x-axis y-axis represent differential expression plot?”

A

“The x-axis represents log fold-change (logFC) while y-axis represents significance (P-value).”

70
Q

“What alternative splicing?”

A

“Alternative splicing allows single gene produce multiple mRNA isoforms including excluding certain exons.”

71
Q

“What long non-coding RNAs (lncRNAs)?”

A

“lncRNAs non-coding RNA transcripts longer than 200 nucleotides regulate gene expression chromatin structure.”

72
Q

“What lincRNAs?”

A

“lincRNAs subset lncRNAs do not overlap protein-coding genes transcribed intergenic regions.”

73
Q

“How lincRNAs identified?”

A

“LincRNAs identified filtering length (>200 nucleotides) depth ensuring do not overlap known protein-coding genes.”

74
Q

“What significance annotation identifying lncRNAs?”

A

“Annotation assesses coding potential identifies open reading frames distinguish between coding non-coding regions.”

75
Q

“What purpose cell sorting single-cell sequencing?”

A

“Cell sorting isolates individual cells analysis allowing detailed study cellular heterogeneity.”

76
Q

“What three main cell sorting strategies?”

A

“The three main strategies droplet encapsulation FACS Fluorescence-Activated Cell Sorting microfluidics.”

77
Q

“What droplet encapsulation?”

A

“Droplet encapsulation cost-effective method isolating single cells tiny droplets oil sequencing.”

78
Q

“How FACS work?”

A

“FACS sorts cells based specific fluorescent markers allowing separation different cell types.”

79
Q

“What microfluidics cell sorting?”

A

“Microfluidics uses small channels manipulate fluids microscale similar FACS often compact efficient.”

80
Q

“What 10X Genomics platform used?”

A

“The 10X Genomics platform designed single-cell sequencing enabling high-throughput analysis individual cells.”

81
Q

“What happens during single-cell tagging?”

A

“Single-cell tagging involves amplifying RNA within oil droplet adding unique barcode identify each cell’s transcriptome.”

82
Q

“What techniques used clustering scRNA sequencing analysis?”

A

“Techniques include PCA Principal Component Analysis t-SNE t-distributed Stochastic Neighbor Embedding machine learning methods.”

83
Q

“What significance studying cell-cell interactions?”

A

“Understanding cell-cell interactions helps elucidate immuno-cell interactions roles receptors ligands cell surfaces.”

84
Q

“What trajectory inference analyze single-cell studies?”

A

“Trajectory inference analyzes differentiation pathways cells stem cell lineage evolution.”

85
Q

“What RNA velocity analysis?”

A

“RNA velocity analysis estimates future state cell based current transcriptional activity providing insights dynamic cellular processes.”

86
Q

“What components multi-omics single-cell study?”

A

“Multi-omics studies integrate data from DNA (epigenetics)

87
Q

“What two main types single-cell sequencing?”

A

“The two main types single-cell DNA sequencing scDNA-seq single-cell RNA sequencing scRNA-seq.”

88
Q

“What application single-cell sequencing?”

A

“It used study tissue heterogeneity cell-to-cell communication infer evolutionary trajectories cells.”

89
Q

“How single-cell sequencing help cancer research?”

A

“It identifies new mutations cancer cells explores evolution tumors analyzing individual cell genomes.”

Genomics (10 decks)

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