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GENE30005 Human and Medical Genetics > Human Genome (1,26,27,28,34,35,36) > Flashcards

Human Genome (1,26,27,28,34,35,36) Flashcards

1
Q

What cannot be found through DTC genotyping?

a. Response to drugs
b. Whether you carry a certain allele
c. Accurate predictions for developing a disease
d. Ancestral information

A

c. Accurate predictions for developing a disease

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2
Q

What can reduce warfarin metabolism?

a. ARG to CYS mutation at AA 144
b. Duplicated rs1799853
c. Excess cytochrome P4 50
d. ARG to TRP mutation at AA 98

A

a. ARG to CYS mutation at AA 144

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3
Q

What is not part of the Snyderome?

a. Transcriptome,
b. Proteome,
c. Metabolome
d. T lymphocytes

A

d. T lymphocytes

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4
Q

• DTC genotyping companies may provide health reports indicating disease susceptibility.

A

F

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5
Q

What is not used to calculate heritability in humans?

a. Looking at correlations in identical twins Vs non-identical twins
b. Using parent offspring regression
c. Analysing dizygotic twins raised in different environments
d. Looking at correlations between full siblings and half siblings

A

c. Analysing dizygotic twins raised in different environments

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6
Q

What is a feature of parent offspring regression?

a. The mid parent phenotypic value is compared with that of the offspring
b. The slope of the line represents environmental influence
c. The steeper the slope, the lower the heritability
d. It measures broad sense heritability

A

a. The mid parent phenotypic value is compared with that of the offspring

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7
Q

What is false about GWAS?

a. It assumes SNPs are disease causing or in linkage disequilibrium with it
b. It can only be used for monogenic disorders
c. Loci are identified using SNPs with the phenotype in population sample
d. It uses Association mapping and Linkage disequilibrium mapping

A

b. It can only be used for monogenic disorders

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8
Q

What is true about linkage disequilibrium?

a. It involves the correlation of alleles at the same locus in a population
b. It is usually seen in polymorphisms that are physically far apart
c. When LD occurs, a tag SNP can be used to show LD blocks
d. It is not used in GWAS

A

c. When LD occurs, a tag SNP can be used to show LD blocks

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9
Q

What was NOT involved in association studies used for macular degeneration?

a. 96 cases, 50 controls
b. 116,204 SNPs and Affymetrix chips
c. Pedigrees generated due to the early onset of disease
d. HAPMAP data was used to identify the region containing the variant

A

c. Pedigrees generated due to the early onset of disease

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10
Q

What did GWAS reveal about macular degeneration?

a. SNPs occur in the complement factor H gene
b. Those homozygous at the specific SNP had an increased risk of AMD by 50%
c. It supported the fact that reduced inflammation causes AMD
d. The disease only has environmental risk factors such as smoking

A

a. SNPs occur in the complement factor H gene

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11
Q

What was not part of the GIANT consortium?

a. 180,00 people’s genotypes
b. 180 genes
c. 19 genes which arose independently
d. 90% of phenotypic variation was accounted for

A

d. 90% of phenotypic variation was accounted for

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12
Q

Unexplained heritability that arises from GWAS would not be explained by:

a. Epigenetic effects
b. Rare alleles with high penetrance
c. Epistasis
d. Linkage disequilibrium holes

A

b. Rare alleles with high penetrance

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13
Q

• Heritability describes phenotypic variation due to genotypic variation (H2=VG/VP).

A

T

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14
Q

• HAPMAP can be used to identify and catalogue gene similarities and differences in human beings and was carried out without using SNPS.

A

F (need SNPs)

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15
Q

• In a Manhattan plot, if a SNP demonstrates Hardy Weinberg equilibrium, it is discarded.

A

F

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16
Q

• In 2008, dbGaP contained 44 studies of 28 diseases.

A

T

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17
Q

• By 2011, dbGaP contained 1617 published studies relating to 249 traits.

A

T

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18
Q

• Common polymorphism can explain 45% of total variation (56% of heritability) when it comes to height.

A

T

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19
Q

What was NOT a feature of the 1987 human RFLP map?

a. 1680 λ clones and 9 restriction enzymes were used
b. 393 polymorphic probes were mapped to 21 CEPH families
c. 50 individuals from the same pedigree were used
d. 23 linkage groups were derived

A

c. 50 individuals from the same pedigree were used

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20
Q

What does L(θ) = (1- θ)7 X θ mean?

a. There are 7 recombinant offspring
b. The maximum likelihood of θ is 0.7
c. There were 7 parental offspring and one recombinant
d. 1- θ represents the chance of recombination occurring

A

c. There were 7 parental offspring and one recombinant

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21
Q

What was not involved in sequencing the human genome by the publically funded consortium?

a. Gaps between contigs were filled in using southern blotting
b. A clone by clone strategy was used
c. The minimum overlapping tiles of clones were found
d. Each BAC was sub-cloned and shotgun sequenced

A

a. Gaps between contigs were filled in using southern blotting

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22
Q

What kind of clone was used to sequence the human genome?

a. YACs
b. Fosmids
c. Plasmids
d. BACs

A

d. BACs

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23
Q

What was involved in Celera’s sequencing of the human genome?

a. The method was slow but left few gaps
b. The entire genome was cloned in a phage vector
c. Overlapping end sequences were assembled into contigs by sequence comparison
d. Clones were sequenced at 28X coverage

A

c. Overlapping end sequences were assembled into contigs by sequence comparison

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24
Q

What is NOT part of the 1000 genome project?

a. 2500 diploid genomes from 27 populations
b. Each genome has 28X coverage
c. The samples are mostly anonymous and don’t give information about phenotype
d. Many participants are in trios (parents and child)

A

b. Each genome has 28X coverage

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25
Q

The average human has:

a. >10,000 SNPs per kb
b. 50-100 non-synonymous differences to reference genome
c. 340-400 loss of function variants
d. Less than 5 variants implicated in inherited disorders

A

c. 340-400 loss of function variants

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26
Q

• Physical mapping is the best kind of mapping to indicate translocation and chromosome banding patterns.

A

F (cytological)

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27
Q

• CEPH family’s involve 3 generation pedigrees, many children per family and the creation of immortalised cell lines.

A

T

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28
Q

• When determining maximum likelihood, if phase is not known, the overall probability is the probabilities of alternate phases.

A

T

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29
Q

• A LOD score (Z) measures how much more likely observed θ is than free recombination (θ=0.5).

A

T

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30
Q

• Adding more families to a linkage mapping study can decrease the LOD score.

A

F

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31
Q

• Chromosomes can be sorted and isolated using FACs.

A

T

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32
Q

• Gametic phase cannot be guessed using reference to a larger data set.

A

F

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33
Q

• Imputation requires a reference genome and for the individual variant to first be scored.

A

F

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34
Q

What is true about the battle between genomicists and expressionists in regards to the human genome project?

a. Genomocists focus on the functional units or coding regions
b. Expressionists sample the genome in a non-biased manner
c. Expressionists can identify alternate transcripts in genes
d. Genomicists can get information on tissue specific expression

A

c. Expressionists can identify alternate transcripts in genes

35
Q

What is correct about ESTs?

a. DNA from specific tissue is used to make a RNA cloning library
b. All cDNA inserts use the same primers and the 5’ and 3’ ends are sequenced only
c. The ESTdb has a low level of redundancy and artefacts
d. Sequences of cDNA clones that overlap are ignored

A

b. All cDNA inserts use the same primers and the 5’ and 3’ ends are sequenced only

36
Q

The UNIGENE database is beneficial because:

a. It ignores genes within introns
b. It selects for repetitive sequences
c. It ignores alternative splicing
d. It identifies transcribed genes and their boundaries

A

d. It identifies transcribed genes and their boundaries

37
Q

What is NOT involved in a microarray?

a. It scans genome wide gene expression
b. mRNA can be isolated from different cells, tissues and compare mutants and Wildtypes
c. The method requires labelled RNA probes
d. The intensity of the stain relates to the abundance of expression

A

c. The method requires labelled RNA probes

38
Q

What is false about the GEO project?

a. The database is robust and versatile
b. The database has information on the whole genome including non-coding regions
c. Annotations are accurate due to MIAME guidelines
d. The data base is very user friendly for queries

A

b. The database has information on the whole genome including non-coding regions

39
Q

A feature of RNA sequencing is:

a. The reads are very long
b. Read depth can be used to quantify data
c. It is less sensitive than microarray due to the minimum threshold for expression
d. It is dependent on the creation of a cDNA probe library

A

b. Read depth can be used to quantify data

40
Q

What was NOT found through ENCODE?

a. There are nearly 100 promoter and enhancer regions in the human genome
b. modENCODE for c.elegans and d.melanogoster
c. 75% of the human genome is transcribed
d. Information of transcriptomics, protein binding and methylation

A

a. There are nearly 100 promoter and enhancer regions in the human genome

41
Q

DNAse 1 hypersensitivity assay:

a. Involves in vivo cell culturing, digestion with endonuclease and RNA sequencing
b. Will show higher sensitivity for locations of the genome with lots of protein bound
c. Revealed that 3600 of 2.9million sensitive sites are found in all cells
d. Involves the DNAse1 enzyme that cuts DNA that is wrapped around histones

A

c. Revealed that 3600 of 2.9million sensitive sites are found in all cells

42
Q

• Tiling arrays involve a 25-mer oligo probe made every 35nt across the non-repeated component of the genome.

A

T

43
Q

• Affymetrix synthesised chips by a cheap laser/mirror method and NimbleGen synthesised chips by expensive photolithography.

A

F

44
Q

• There are less protein coding transcripts than actual genes.

A

F

45
Q

• The number of protein coding genes has decreased whilst the number of long non-coding genes has increased over the past 5 years.

A

T

46
Q

• ENCODE found that for 15 cells lines, 75% of the genome is transcribed and 62% of transcripts are processed.

A

T

47
Q

• On a DNAse 1 hypersensitivity assay, peaks of sensitivity relate to areas of DNA where cutting cannot occur due to protein binding.

A

F

48
Q

• A DNAse 1 hypersensitivity assay cannot provide information on DNA/transcription factor structural relationships or polymorphisms.

A

F

49
Q

• In ChIP seq, antibodies bind specific DNA binding proteins and can be used to map where transcription factors bind.

A

T

50
Q

What is not a feature of a microarray?

a. Glass slides are coated with poly-lysine
b. DNA clones are spotted on with metal pins
c. Fluorescently labelled DNA hybridises with DNA clones
d. The amount of DNA is interpreted after gel electrophoresis

A

d. The amount of DNA is interpreted after gel electrophoresis

51
Q

How can differential expression be measured using microarray?

a. 2 colour hybridisation measure two RNA samples separately and superimposes the images
b. Single colour hybridisation requires that all RNA samples be hybridised to the same slide
c. 2 colour hybridisation uses the same colour dye to label RNA samples and fluorescence intensity is compared to controls
d. Single colour hybridisation labels RNA in two colours to represent the wild-type and disease state

A

a. 2 colour hybridisation measure two RNA samples separately and superimposes the images

52
Q

What is correct about Chip technology?

a. It can only be used on protein samples
b. Affymetrix synthesises chips by photolithography and this is expensive
c. Nimblegen synthesis chips by laser/mirror and this is expensive and produces short 25nt oligoNTs
d. The cheapest chip synthesis method is silicon synthesis and this is carried out by illumina

A

b. Affymetrix synthesises chips by photolithography and this is expensive

53
Q

What is FALSE about bead based array technology like Illumina?

a. The probes include 24000 known genes and 24000 hypothetical genes
b. Each gene is represented once
c. The probe is a 50base gene-specific probe with a 29base Address and hybridises to cDNA made from total RNA
d. Biotin labelled cDNA can be bound by fluorescently labelled streptavidin after binding specific probes

A

b. Each gene is represented once

54
Q

Put the general protocol for expressing a human genome by microarray in order.

  1. Wash
  2. Scan slide/chip for fluorescence
  3. Analyse data for differences in intensity
  4. Isolate specific mRNA (tissue, cancer, control, disease)
  5. Make labelled cDNA
  6. Hybridise to microarray
A
  1. Isolate specific mRNA (tissue, cancer, control, disease)
  2. Make labelled cDNA
  3. Hybridise to microarray
  4. Wash
  5. Scan slide/chip for fluorescence
  6. Analyse data for differences in intensity
55
Q

What is NOT involved in a typical microarray experiment?

a. 2 treatment groups (wild type and disease state)
b. 3 replicates of each treatment group
c. The generation of 12 data points
d. 2 time points

A

c. The generation of 12 data points

56
Q

What is a feature of microarrays?

a. It is possible to measure 50,000 transcripts at once in one sample
b. The technology is outdated and now considered immature
c. It is difficult to gain accurate and reproducible results
d. The amount of transcripts is sufficient in providing definite data

A

a. It is possible to measure 50,000 transcripts at once in one sample

57
Q

What is correct about the ATP2A2 gene?

a. RT-PCR and iScan analysis of the gene yielded the same results
b. It has one main isoform
c. RT-PCR results conflicted iScan results as the 3’ UTR probe binding site was not revealed
d. iScan and PCR analysis demonstrated that it is not always necessary to know which part of a gene you are measuring

A

c. RT-PCR results conflicted iScan results as the 3’ UTR probe binding site was not revealed

58
Q

What is correct about RNAseq?

a. A cDNA library is generated from genomic DNA
b. It cannot detect all isoforms of a gene
c. It can produce redundant information for highly expressed transcripts
d. Low abundance transcripts can be detected without the need for multiple runs

A

c. It can produce redundant information for highly expressed transcripts

59
Q

• Lifestyle modifications cannot delay the onset of a complex disease.

A

F

60
Q

• “Home brew” Microarrays have a more restricted gene and probe library than commercial microarrays like illumina.

A

F

61
Q

• Genes with multiple isoforms can complicate and confound gene expression measurement.

A

T

62
Q

What is correct about using a candidate gene approach to study complex disease?

a. The approach is unbiased and can pick up many variants in the whole genome
b. Variant selection is independent of known biological functions
c. It is a biased approach and requires prior knowledge of the potential gene
d. The approach does not use case-control studies or phenotypic data

A

c. It is a biased approach and requires prior knowledge of the potential gene

63
Q

What is correct about using a GWAS approach to study complex disease?

a. It is an unbiased approach and covers the entire genome
b. In common diseases caused by common variants, each variant elicits a large effect
c. Information from linkage studies cannot be used
d. In common diseases caused by rare variants, each variant elicits a small effect

A

a. It is an unbiased approach and covers the entire genome

64
Q

In terms of GWAS studies:

a. Alleles that are identified by GWAS are always the causative alleles
b. Findings can be confirmed without the need for mechanistic studies
c. Studies cannot yet identify novel loci
d. Identified alleles can be in LD with the causative alleles

A

d. Identified alleles can be in LD with the causative alleles

65
Q

What is correct about sampling designs used to study complex disease?

a. Heritability can only be measured using an extended pedigree (Sib pairs, nuclear family, extended pedigree)
b. Heritability, Linkage and Association can be measured using Triads and Unrelateds
c. Linkage and association can be studied using triads
d. Sib pairs can only be used to measure linkage

A

c. Linkage and association can be studied using triads

66
Q

What is correct about the inheritance of type 2 diabetes?

a. Monozygotic twins show 35-58% concordance in acquiring the disease
b. The disease is not heritable and develops as a result of environmental factors like obesity
c. A child with two diabetic parents will have a 20% risk of developing diabetes
d. Dizygotic twins show 60% concordance in acquiring the disease

A

a. Monozygotic twins show 35-58% concordance in acquiring the disease

67
Q

Why was exome sequencing used in The GWAS Mauritius Family Study of type 2 diabetes?

a. It provided increased power to study rare and private variants
b. It demonstrated the important regulatory regions at 12q24 responsible for fasting plasma glucose
c. To isolate common variants that are likely to be important in contributing to blood glucose levels
d. To understand why 95% of the variants types across 12q24 were polymorphic

A

a. It provided increased power to study rare and private variants

68
Q

What is a feature of GWAS associated SNPs?

a. Exonic SNPs can impact mRNA binding and stability
b. Intergenic SNPs can impact splicing and change protein structure
c. Intronic and flanking SNPs encode proteins and splicing enhancers
d. Intergenic SNPS can impact chromatin structure and methylation

A

d. Intergenic SNPS can impact chromatin structure and methylation

69
Q

What is FALSE about the study used to study how Epigenome wide DNA methylation might influence type 2 diabetes?

a. It was a case-control and 8 year follow up study which used about 25,000 participants
b. Relative risk was associated with methylation of TXNIP, SREBF1, PHOSPHO1, SOCS3 and ABCG1
c. Obesity increased the risk of developing diabetes and methylation was found to have no impact on risk
d. The genes associated with type 2 diabetes risk are resitant to methylation and all kidns of epigenetic modification

A

c. Obesity increased the risk of developing diabetes and methylation was found to have no impact on risk

70
Q

• Common alleles contribute more to a disease when considering abundance whilst rare alleles have larger individual effects.

A

T

71
Q

• Next generation sequencing cannot pick up small copy number variations (

A

F

72
Q

• Missing heritability is most likely to lie in low frequency variants.

A

T

73
Q

• The GWAS Mauritius Family Study of diabetes showed a region of interest on at 12q24.

A

T

74
Q

What is NOT a consideration in preimplanation diagnosis?

a. The process is often more invasive for the mother
b. The destruction of embryos can cause moral debate
c. The idea of saviour children is controversial
d. It means that the mother does not have to terminate a pregnancy

A

a. The process is often more invasive for the mother

75
Q

In regards to pre-implantation diagnosis:

a. The test is 100% reliable and false negatives or positives do not occur
b. Cells taken for biopsy always represent the entire embryo
c. Women do not need to undergo tests for chromosome abnormalities during the pregnancy
d. It is possible that none of the tested embryos will be normal

A

d. It is possible that none of the tested embryos will be normal

76
Q

Which is NOT a guideline that must be met to ensure that a disorder is appropriately selected for community screening?

a. The disorder must be rare
b. The consequences of failing to diagnose must be severe
c. Early treatment must be beneficial
d. There must be a reliable test available and systems to deal with counselling, treatment and patient follow up

A

a. The disorder must be rare

77
Q

Which statement is INcorrect?

a. Newborns in Victoria are screened for PKU, cystic fibrosis and congenital hypothyroidism
b. In cystic fibrosis, IRT levels may be elevated for reasons not due to CF
c. Guthrie cards are readily accessed on a public database
d. PKU is treatable when picked up early and screening for the disorder is therefore cost effective

A

c. Guthrie cards are readily accessed on a public database

78
Q

Genetic testing:

a. Is okay to carry out without the use of genetic counselling
b. Does not require informed consent
c. Can be carried out on those without autonomy
d. Should be performed for the benefit of the person being tested

A

d. Should be performed for the benefit of the person being tested

79
Q

• Genetic screening is only carried out on babies known to be at risk of a genetic condition.

A

F

80
Q

• Genetic testing is offered to all newborns regardless of family history.

A

F

81
Q

• Presymptomatic testing is for individuals at risk of developing a genetic disorder that is known to be in the family.

A

T

82
Q

• Genetic testing on children is always preferred.

A

F

83
Q

The NIH panel declares than no risk factors should be divulged to patients, regardless of potential to cause disease.

A

F (57. Some cancers, heart conditions)

GENE30005 Human and Medical Genetics (13 decks)

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