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4.1 Molecular Biology > Shane 3.2 (AI): Molecular Diagnostics - Mendelian Disorders > Flashcards

Shane 3.2 (AI): Molecular Diagnostics - Mendelian Disorders Flashcards

1
Q

What percentage of live births are affected by Mendelian diseases?

A

0.4%

This statistic highlights the prevalence of Mendelian disorders in the general population.

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2
Q

How many Mendelian diseases have been identified?

A

> 7,400

This figure includes all known Mendelian diseases cataloged in genetic databases.

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3
Q

How many Mendelian diseases have been solved since 2008?

A

> 2000

This significant progress reflects advancements in genetic research and technologies.

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4
Q

What is the first successful application of exome sequencing in Mendelian disorders?

A

Discovery of the gene for Miller syndrome (MIM 263750)

This case marked a milestone in the use of exome sequencing for rare genetic disorders.

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5
Q

What is the role of DHODH mutations in Mendelian disorders?

A

Key enzyme in the pyrimidine de novo biosynthesis pathway

Understanding this role can help in diagnosing certain genetic conditions.

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6
Q

What is a significant challenge in solving very rare Mendelian disorders?

A

Limited sample size

Finding causative mutations can be difficult when only a few individuals are affected.

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7
Q

How many patients are needed to solve a Mendelian disorder?

A

At least 3 patients

This requirement underscores the importance of having enough data for genetic analysis.

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8
Q

What technological advancement has led to a huge increase in solved Mendelian disorders since 2008?

A

Whole genome sequencing

This technology has revolutionized the identification of genetic causes of diseases.

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9
Q

True or False: There is only one single gene involved in Mendelian disorders compared to multiple genes in cancer.

A

True

This distinction is important in understanding the genetic basis of different types of diseases.

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10
Q

What is the purpose of whole exome sequencing (WES) in Mendelian disorders?

A

To identify pathogenic variants responsible for genetic conditions

WES focuses on the coding regions of the genome, which are most likely to contain disease-causing mutations.

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11
Q

How many SNPs are typically found in an individual exome?

A

20-30,000 SNPs

This number excludes synonymous SNPs, which do not affect protein function.

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12
Q

What is the typical reduction in the number of variants after filtering for pathogenic variants?

A

Reduced to 100-500 pathogenic variants

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13
Q

What can sequencing 2 or 3 affected individuals achieve in variant identification?

A

Can reduce it down to one variant gene

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14
Q

What is the significance of filtering fastq files in WES?

A

Filters out low-quality sequences with a Q score below 20

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15
Q

What is variant calling in the context of WES?

A

The process of identifying variants in the sequenced data

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16
Q

What is dbSNP?

A

A public database that contains information on SNPs

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17
Q

What challenges are associated with identifying de novo variants?

A

They are harder to identify as parents won’t have the condition

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18
Q

True or False: Whole exome sequencing can only identify variants that parents also have.

A

False

De novo variants arise spontaneously and are not present in the parents.

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19
Q

Fill in the blank: The process of filtering out common variants helps to focus on _______ variants.

A

potentially pathogenic

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20
Q

What is the name of the first child saved by Next Generation DNA Sequencing?

A

Nicholas Volker

He was saved in 2011

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21
Q

At what age did Nicholas Volker start experiencing health issues?

A

Age 2

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22
Q

What severe health problem did Nicholas Volker face after a cut?

A

It did not heal, leading to many injuries and sepsis.

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23
Q

How many surgeries did Nicholas Volker undergo?

A

Over 100 surgeries.

24
Q

What major surgery did Nicholas Volker have related to his digestive system?

A

Colon removal.

25
Q

What genetic mutation was identified in Nicholas Volker through Exome Sequencing?

A

Mutation in the XIAP gene.

26
Q

What condition resulted from the mutation in the XIAP gene?

A

Immune dysregulation syndrome.

27
Q

What type of disease did Nicholas Volker develop as a result of his condition?

A

Early-onset, rapidly progressing inflammatory bowel disease.

28
Q

What treatment did Nicholas Volker receive after the identification of his condition?

A

Bone marrow transplant of cells taken from umbilical cord blood.

29
Q

What was the initial misdiagnosis of Nicholas Volker’s condition?

A

Inflammatory bowel disease (IBD).

30
Q

What is the function of the XIAP gene?

A

X-linked inhibitor of apoptosis.

31
Q

How does the XIAP gene mutation affect the immune system?

A

It causes a huge amount of inflammation in the colon.

32
Q

What type of research was conducted to understand Nicholas Volker’s condition?

A

Research in mice.

33
Q

What publication reported the case of Nicholas Volker?

A

Worthey et al. Genet Med. (2011) 13:255-62.

34
Q

When can cell-free fetal DNA be detected in maternal blood?

A

4-5 weeks after gestation

This early detection allows for non-invasive prenatal testing.

35
Q

What percentage of circulating DNA in maternal blood is typically fetal?

A

4-10%

This percentage increases as the pregnancy progresses.

36
Q

What is the role of cell-free fetal DNA in prenatal testing?

A

Targeted detection of mutations

It serves as a non-invasive alternative to invasive procedures.

37
Q

What procedure is being replaced by cell-free fetal DNA testing?

A

Amniocentesis

Cell-free fetal DNA testing is considered safer and less invasive.

38
Q

What is the sensitivity of whole genome sequencing in detecting trisomies?

A

99%

This high sensitivity makes it an effective screening method.

39
Q

Which trisomies are commonly detected through whole genome sequencing?

A
  • Down’s (Chromosome 21)
  • Chromosome 18 (Edwards Syndrome)
  • Chromosome 13 (Patau Syndrome)

These conditions are serious chromosomal disorders that can be identified early.

40
Q

Fill in the blank: Up to _______ of circulating DNA in the mother is fetal.

A

10%

This percentage can vary with pregnancy progression.

41
Q

True or False: Cell-free fetal DNA testing can easily detect chromosomal disorders.

A

True

This method is effective in identifying various chromosomal abnormalities.

42
Q

What is cell-free (cf) DNA?

A

DNA isolated from plasma, often used in prenatal testing.

Cell-free DNA refers to fragments of DNA that circulate in the bloodstream, which can be analyzed for genetic conditions.

43
Q

In the study, how many pregnant women were involved?

A

11 pregnant women.

The study focused on pregnant women carrying fetuses with specific chromosomal abnormalities.

44
Q

What chromosomal abnormalities were detected in the study?

A

Sub chromosomal duplications, deletions, translocations, mosaicism, and trisomy 20.

These abnormalities can indicate various genetic disorders in the developing fetus.

45
Q

What method was used to detect chromosomal abnormalities?

A

Next-generation sequencing of maternal plasma.

Next-generation sequencing allows for rapid and comprehensive analysis of genetic material.

46
Q

True or False: All microdeletions, duplications, translocations, and trisomy 20 were detected blindly.

A

True.

‘Blindly’ indicates that the testing was done without prior knowledge of the specific abnormalities present.

47
Q

Fill in the blank: The study by Srinivasan et al. was published in AJ Hum _______.

A

Genet.

AJ Hum Genet refers to the American Journal of Human Genetics.

48
Q

What is the significance of detecting fetal subchromosomal abnormalities non-invasively?

A

It allows for early diagnosis without risk to the fetus.

Non-invasive methods reduce the potential for complications associated with invasive testing procedures.

49
Q

What percentage of the human genome consists of exons?

A

1% of human genome

Exons are the coding regions of genes that are expressed.

50
Q

What percentage of disease-causing mutations are found in the exome?

A

85%

The exome refers to the portion of the genome consisting of exons.

51
Q

Agilent SureSelect hybridizes DNA with what?

A

Biotinylated RNA baits

This technique is used for capturing specific DNA sequences for analysis.

52
Q

How many samples were used in the Cancer Genome Atlas?

A

11,000 samples

The Cancer Genome Atlas is a project that cataloged genetic mutations responsible for cancer.

53
Q

EGFR mutations are treated with what type of inhibitors?

A

Small molecular inhibitors/protein kinase inhibitors

These inhibitors target the Epidermal Growth Factor Receptor (EGFR) involved in cancer cell growth.

54
Q

Name three drug names used for treating EGFR mutations.

A
  • Getinib
  • [Other drug names can be added here]
  • [Other drug names can be added here]

Specific drugs targeting EGFR mutations may vary.

55
Q

What was the first rare Mendelian disorder solved using whole exome sequencing (WES)?

A

Miller syndrome

Miller syndrome is a genetic disorder characterized by specific physical abnormalities.

56
Q

Why is fetal DNA sequencing possible for genetic disorders?

A

Cell-free fetal DNA is detected in maternal blood

This technique allows non-invasive prenatal testing for genetic conditions.

4.1 Molecular Biology (21 decks)

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