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4.1 Molecular Biology > Shane 4(AI): Molecular Diagnostics - Panels > Flashcards

Shane 4(AI): Molecular Diagnostics - Panels Flashcards

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1
Q

What is NGS technology primarily used for in clinical laboratories?

A

Diagnostic testing for hereditary disorders, risk screening for hereditary cancers, therapeutic decision-making for somatic cancers

NGS stands for Next Generation Sequencing, a powerful tool in genomics.

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2
Q

What percentage of applications in clinical laboratories does NGS technology represent?

A

13%

This percentage reflects the usage of NGS technology in specific diagnostic applications.

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3
Q

Fill in the blank: NGS technology is used mainly in _______ sequencing.

A

[target gene panel]

Target gene panel sequencing focuses on specific genes of interest, aiding in precise diagnostics.

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4
Q

What is Target Panel Sequencing?

A

A select set of genes or gene regions with known or suspected associations with disease or phenotype under study

It can involve preselected gene panels or custom designed panels.

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5
Q

What are the advantages of using Target Panel Sequencing?

A
  • Time-saving
  • Cost-reducing
  • Easier data management

It allows multiple genes to be assessed across many samples in parallel.

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6
Q

How does Target Panel Sequencing compare to Whole Genome Sequencing (WGS)?

A

It produces smaller, more manageable data sets

This makes analysis easier compared to WGS.

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7
Q

What types of gene panels can researchers use?

A
  • Preselected gene panels
  • Custom designed panels

Researchers can request companies to create custom panels as needed.

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8
Q

Fill in the blank: Target Panel Sequencing can assess multiple genes across many samples in _______.

A

parallel

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9
Q

True or False: Target Panel Sequencing is more expensive than running multiple separate assays.

A

False

It reduces costs associated with running multiple assays.

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10
Q

What is the first step in the Targeted Gene Panel Sequencing Workflow?

A

Sample DNA isolation

This process takes approximately 2 hours.

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11
Q

What types of samples can be used in the Targeted Gene Panel Sequencing Workflow?

A

Blood, Saliva, Dried Blood Sample (DBS), Cheek swab

These samples require only a small amount of DNA, about 50-100 nanograms.

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12
Q

What is used to prepare the library in the sequencing process?

A

120 RNA nucleotide probes

This method is similar to exome sequencing.

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13
Q

What is the function of the biotin tag on the probe?

A

Identified by streptavidin

This allows for the capture of target genes of interest.

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14
Q

What is the total time taken from DNA isolation to analyzed result in the workflow?

A

Almost a week

This includes sample preparation, sequencing, and data analysis.

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15
Q

How long does the DNA hybrid capture and sequencing process take?

A

92 hours

This is a significant portion of the overall workflow.

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16
Q

What is the final step in the Targeted Gene Panel Sequencing Workflow?

A

Analysis and interpretation

This step follows data management and takes an additional time.

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17
Q

What technology is used to capture the target genes of interest?

A

Sequencing technologies

These technologies can vary based on the specific sequencing method chosen.

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18
Q

Fill in the blank: The Targeted Gene Panel Sequencing Workflow is an example of _______.

A

target enrichment

This involves selectively capturing and sequencing specific genes.

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19
Q

What type of beads are used in the Targeted Gene Panel Sequencing Workflow?

A

Magnetic beads

These are used to facilitate the capture of target genes.

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20
Q

True or False: The total time for the sequencing workflow is less than a week.

A

False

The entire process, from DNA isolation to analysis, takes almost a week.

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21
Q

What is target enrichment in molecular diagnostics?

A

Regions of interest captured by hybridization to biotinylated probes and isolated by magnetic pulldown.

Target enrichment is used to focus sequencing efforts on specific genomic regions.

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22
Q

What is the range of regions that target enrichment can capture?

A

20 kb - 62 Mb depending on experimental design.

This variability allows for flexibility in targeting different genomic areas.

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23
Q

What is amplicon sequencing?

A

Regions of interest PCR amplified using highly multiplexed oligo pools.

This method allows for the simultaneous sequencing of multiple targets.

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24
Q

How many targets can be sequenced at a time using amplicon sequencing?

A

26 - 1536 targets.

This extensive multiplexing capability makes amplicon sequencing efficient for large-scale studies.

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25
What is a key feature of amplicon sequencing?
PCR primers are designed to the gene of interest. ## Footnote This specificity allows for targeted amplification of desired regions.
26
Fill in the blank: Target enrichment captures regions of interest through hybridization to _______.
[biotinylated probes]
27
True or False: Amplicon sequencing can only sequence up to 26 targets at a time.
False. ## Footnote It can sequence between 26 and 1536 targets simultaneously.
28
What type of PCR is used in amplicon sequencing?
Multiplex PCR. ## Footnote This allows for the amplification of multiple regions in a single reaction.
29
What is the purpose of enrichment in molecular diagnostics?
To increase the concentration of targeted nucleic acid sequences ## Footnote Enrichment techniques help to isolate specific DNA or RNA sequences from a complex mixture.
30
What software is used to create custom oligonucleotide capture?
DasigStudio ## Footnote DasigStudio allows for the design and optimization of oligonucleotide probes.
31
What type of probes are used in the enrichment workflow described?
Biotin-labelled probes ## Footnote These probes are specifically designed to bind to targeted regions of interest.
32
What is hybridization in the context of molecular diagnostics?
The process of binding biotinylated probes to targeted nucleic acid regions ## Footnote Hybridization is a critical step in isolating specific sequences for further analysis.
33
What type of beads are used for enrichment in the workflow?
Magnetic beads coated with streptavidin ## Footnote These beads facilitate the capture of biotinylated probes through strong binding.
34
What is the role of streptavidin in the enrichment process?
To bind to biotinylated probes and facilitate their capture ## Footnote Streptavidin has a high affinity for biotin, making it effective for isolating target sequences.
35
Fill in the blank: The company is tasked to add the ______ to the probe.
biotin ## Footnote Biotin is a vital component for the functionality of the probes in enrichment.
36
What percentage is mentioned in the workflow context?
12% ## Footnote This could refer to a specific yield or efficiency related to the enrichment process.
37
What are predesigned targeted sequencing panels used for?
They are used for various areas including cancer, recessive paediatric onset diseases, and cardiac conditions.
38
What type of conditions do predesigned panels specifically target?
They target cancer, recessive paediatric onset diseases, and cardiac conditions.
39
What percentage of recessive conditions is covered by the CF comprehensive panel?
12%
40
What is included in the comprehensive panel?
It targets all genes associated with genetic disorders.
41
True or False: All known mutated genes are included in the comprehensive panel.
True
42
Fill in the blank: Comprehensive panels are available for a wide variety of _______.
[cancers]
43
What is the purpose of the Trusight® One Panel?
To provide comprehensive sequencing of every gene associated with clinical phenotypes. ## Footnote This panel targets a wide range of genes linked to various diseases.
44
How many genes are targeted in the Cancer Panel of Trusight?
401 genes associated with known clinical phenotypes. ## Footnote This panel is designed for cancer predisposition testing.
45
What is the cumulative target region size for the Cardio Panel?
244 kb. ## Footnote This panel focuses on inherited cardiac conditions.
46
What is the library prep time for the Trusight panels?
1.5 days. ## Footnote This is the time required for enrichment-based library preparation.
47
How many genes does the Trusight Inherited Disease Panel target?
552 genes related to severe, recessive pediatric diseases. ## Footnote This panel is aimed at detecting genetic conditions in children.
48
What is the DNA input required for the Trusight panels?
50 ng. ## Footnote This is the minimum amount of DNA needed for sequencing.
49
What is the number of samples that can be run in a MiniSeq run for the Cancer Panel?
3 samples. ## Footnote Limited by the sequencing capacity of the system.
50
What type of sequencing system compatibility is there for the Trusight panels?
MiniSeq, MiSeq, NextSeq, and HiSeq series. ## Footnote These systems are compatible for running different Trusight panels.
51
Fill in the blank: The Cardio Panel targets genes related to _____ inherited cardiac conditions.
17 inherited cardiac conditions. ## Footnote This panel is specifically focused on genetic heart diseases.
52
True or False: The Trusight One Panel can sequence only 3 patient samples in one run.
True. ## Footnote Due to the extensive sequencing involved.
53
What is the number of probes used in the Cancer Panel?
30,000 probes. ## Footnote This high number allows for detailed genetic analysis.
54
What is the primary purpose of the TruSight HLA V2 Sequencing Panel?
HLA typing ## Footnote HLA typing is crucial for transplantation compatibility.
55
How long does the sample-to-report process take with the targeted sequencing panels?
Less than 40 hours with less than 4 hours hands-on time.
56
What types of samples are compatible with the targeted sequencing panels?
FFPE samples ## Footnote FFPE stands for formalin-fixed paraffin-embedded samples, commonly used in histopathology.
57
What is the variant detection sensitivity for the TruSight Tumor 15 panel?
Detects variants down to 5% allele frequency.
58
What is the focus of the TruSight Myeloid panel?
Somatic mutations in myeloid malignancies.
59
What is the variant detection sensitivity for the TruSight Myeloid panel?
Detects variants down to 59% allele frequency.
60
How many genes does the TruSeg Amplicon Cancer Panel target?
Targets 48 genes.
61
What are mutation hotspots in the context of the TruSeg Amplicon Cancer Panel?
Regions in frequently mutated cancer genes.
62
What is the total number of amplicons in the TruSeg Amplicon Cancer Panel?
212 amplicons.
63
What is the minimum required input DNA for the TruSight Myeloid panel?
150 ng for gDNA.
64
Which sequencing systems are compatible with the targeted sequencing panels?
MiniSeq, MiSeq, and NextSeq systems.
65
What is the total number of samples that can be processed per run for the TruSight Tumor 15 panel?
42 samples/run.
66
Fill in the blank: PCR Amplicon Based Library Prep is generally more _______.
targeted.
67
True or False: The TruSight panels can only process fresh samples.
False.
68
What is the total number of amplicons for the TruSight Tumor 15 panel?
250 amplicons.
69
What is the main advantage of using PCR-based library preparation for sequencing?
Higher specificity and targeted amplification.
70
What is the total number of genes targeted by the TruSight Myeloid panel?
54 genes.
71
What does the Illumina TruSight One comprehensive panel cover?
Covers 4813 genes having known association with clinical phenotypes ## Footnote This panel includes all exonic regions harbouring disease-causing mutations.
72
What databases were used to identify the genes in the Illumina TruSight One panel?
Identified based on info in Human Gene Mutation Database, OMIM, GeneTests.org ## Footnote These databases provide valuable information about genetic mutations and their clinical implications.
73
In what settings is the Illumina TruSight One panel analyzed?
Analyses all genes currently reviewed in clinical research settings ## Footnote This ensures that the panel is up-to-date with the latest research findings.
74
How can the Illumina TruSight One panel be utilized in clinical laboratories?
Could be used for any disease focused sub-panel testing after being completely validated in the clinical laboratory ## Footnote Validation in clinical laboratories is essential for ensuring accurate and reliable results.
75
When is the Illumina TruSight One panel typically used?
Used when you're not really sure what the mutation is/what the condition is ## Footnote This panel allows for comprehensive analysis when the specific genetic issue is unclear.
76
What is the primary function of VariantStudio?
Software application for analysing and interpreting variant data ## Footnote It aggregates information from multiple databases to streamline annotation.
77
What type of file does VariantStudio import for data interpretation?
VCF - variant call file ## Footnote This file format is essential for the software to analyze genetic variant data.
78
What does VariantStudio enable in terms of variant classification?
Options for analyzing variant data to enable classification and reporting of actionable variants ## Footnote This functionality is crucial for clinical decision-making.
79
True or False: Illumina provides VariantStudio with their machines.
True ## Footnote This integration allows users to utilize the software seamlessly with Illumina's hardware.
80
What does VariantStudio do with the analysis of variant data?
Does all the analysis for you ## Footnote This feature simplifies the workflow for users by automating complex processes.
81
Fill in the blank: VariantStudio aggregates information from a collection of _______ to streamline annotation.
databases ## Footnote This aggregation helps to provide comprehensive insights into genetic variants.
82
What is the NCBI Reference Sequence Database commonly referred to as?
RefSeq ## Footnote RefSeq provides a comprehensive, accurate representation of reference sequences for genomes, transcripts, and proteins.
83
Which database is known for providing information on genetic variants?
dbSNP ## Footnote dbSNP is a database that catalogs single nucleotide polymorphisms (SNPs) and other genetic variants.
84
What software is mentioned for analyzing genetic variants?
VariantStudio Analysis Software ## Footnote VariantStudio is used for analyzing and interpreting genomic data.
85
What does the Catalogue of Somatic Mutations in Cancer (COSMIC) provide information about?
Known disease association ## Footnote COSMIC focuses on the catalogue of somatic mutations in human cancer.
86
Which database contains information about genetic conditions and their inheritance patterns?
Online Mendelian Inheritance in Man (OMIM) ## Footnote OMIM is a comprehensive database of human genes and genetic disorders.
87
What is ClinVar used for?
Information on the clinical significance of genetic variants ## Footnote ClinVar aggregates information about variant interpretations and their clinical significance.
88
True or False: The databases used in molecular diagnostics are relatively new.
False ## Footnote The databases have been around for a long time, contributing to their reliability.
89
Fill in the blank: The information about known disease associations is obtained from the _______.
COSMIC ## Footnote COSMIC provides insights into somatic mutations associated with cancer.
90
What does the term 'functional impact' refer to in molecular diagnostics?
The effect of a variant on protein function, indicating variants that are likely deleterious. ## Footnote Functional impact is assessed to determine how a genetic variant may affect the biology of the organism.
91
What is the significance of 'allele frequency' in genetic studies?
It provides the frequency of a variant within a population. ## Footnote Allele frequency helps in understanding how common a variant is among different individuals.
92
Define 'conserved sequence' in the context of genetic variation.
Denotes sequence similarity if the variant occurs between species, providing phylogenetic information and evolutionary context. ## Footnote Conserved sequences are important for identifying functionally important regions of DNA that are preserved across species.
93
What does 'disease association' indicate regarding a genetic variant?
Indicates whether a variant has been previously associated with disease. ## Footnote Understanding disease associations helps in identifying potential risk factors and understanding disease mechanisms.
94
What is the purpose of variant annotation in molecular diagnostics?
To provide annotations at variant, transcript, and gene levels for comprehensive assessment of the biological impact of genetic variation. ## Footnote Variant annotation helps in classifying variants and understanding their relevance in diseases.
95
What does the term 'transcript changes' refer to?
Predicts transcript changes resulting from the variant of interest, allowing segregation of synonymous from different types of alterations. ## Footnote This prediction is crucial for understanding how variants impact gene expression and function.
96
Fill in the blank: The variant study software provides annotations at the ______, transcript, and gene levels.
variant ## Footnote This multi-level approach enhances the understanding of genetic variations.
97
True or False: The variant study software can classify disease-relevant variants.
True ## Footnote Classifying variants is essential for identifying potential therapeutic targets and understanding genetic diseases.
98
What is the primary purpose of ClinGen?
To improve patient care through genomic medicine ## Footnote ClinGen aims to establish a genomic knowledge base that informs clinical decision-making.
99
How many people and institutions are involved in ClinGen?
>400 people from >90 institutions ## Footnote This collaboration enhances the breadth and depth of genomic data available.
100
What are the three critical questions that ClinGen is trying to answer?
1. Is this gene associated with a disease? 2. Is this variant causative? 3. Is this information actionable? ## Footnote These questions are essential for determining the clinical utility of genetic information.
101
What does the term 'pathogenicity' refer to in the context of genomic diagnostics?
The ability of a variant to cause a disease ## Footnote Pathogenicity is a key factor in assessing the clinical significance of genetic variants.
102
What is meant by 'clinical utility' in genomic medicine?
The relevance and applicability of genetic information in clinical settings ## Footnote Clinical utility helps determine whether genomic information can guide treatment decisions.
103
Fill in the blank: ClinGen's goal is to build a _______.
[genomic knowledge base] ## Footnote This knowledge base is essential for improving patient care and understanding genetic conditions.
104
What is the overall goal of ClinGen?
To build a genomic knowledge base to improve patient care ## Footnote ClinGen aims to enhance patient outcomes through genomic data sharing and standardization.
105
What types of data does ClinGen aim to share?
Genomic and phenotypic data ## Footnote Data is provided by clinicians and researchers for both clinical and research uses.
106
What is meant by standardizing clinical annotation?
Standardizing the interpretation of genomic variants ## Footnote This ensures consistency and reliability in how genetic information is assessed.
107
What does ClinGen implement for curating genes and variants?
Evidence-based expert consensus ## Footnote This process involves gathering expert opinions to ensure accurate gene and variant curation.
108
What is assessed regarding genes and variants in ClinGen?
The 'medical actionability' ## Footnote This refers to the potential impact of genetic findings on patient care and treatment decisions.
109
What is one of the purposes of disseminating knowledge in ClinGen?
For unrestricted use in the community ## Footnote This promotes wider access to genomic resources and information.
110
What is the total number of submissions in ClinVar?
405,000 submissions ## Footnote ClinVar contains submissions related to genetic variants and their interpretations.
111
How many unique variants are reported in ClinVar?
268,240 unique variants ## Footnote This number represents the different genetic variants submitted for interpretation.
112
How many submitters contribute to ClinVar and from how many countries?
642 submitters from 53 countries ## Footnote This indicates the global participation in contributing genetic variant data.
113
What are the five categories for interpreting variants in ClinVar?
* Pathogenic * Likely Pathogenic * Uncertain Significance * Likely benign * Benign ## Footnote These categories help classify the clinical significance of genetic variants.
114
What does ACMG stand for?
American College of Medical Genetics and Genomics ## Footnote ACMG provides standards and guidelines for the interpretation of genetic sequence variants.
115
What is the purpose of the ACMG standards and guidelines?
To provide a joint consensus recommendation for interpreting sequence variants ## Footnote These guidelines are crucial for ensuring consistency and accuracy in genetic variant classification.
116
What are the levels of evidence for classifying variants according to ACMG?
* Very Strong * Strong * Moderate * Supporting ## Footnote These levels of evidence assist in determining the classification of a variant as pathogenic or benign.
117
Fill in the blank: ClinVar is helpful at classifying different _______.
[mutations] ## Footnote ClinVar serves as a database for understanding the clinical significance of various genetic mutations.
118
True or False: Evidence must be heavily based to determine if something is benign or pathogenic.
True ## Footnote Adequate evidence is essential for accurate classification of genetic variants.

4.1 Molecular Biology (21 decks)

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