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(6-10) Translational Medical Science > Trigger 9: Genomic technologies > Flashcards

Trigger 9: Genomic technologies Flashcards

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Biology 101 flashcards USMLE® Step 1 flashcards
1
Q

which is the oldest genomic technology

A

sanger sequencing (1977)

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2
Q

which is the newest genomic technology

A

single- molecular real time (SMRT) sequencing

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3
Q

name 6 forms of genomic technology

A
  • high microscope - G-banded karyotype - Array- CGH - SNP- array - Exome sequencing - genome sequencing
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4
Q

what is G banded karyotype testing

A

a technique used in cytogenetics to produce a visible karyotype by staining condensed chromosomes.

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5
Q

resolution of G banded karyotype

A

5-10Mb

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6
Q

number of loci probed in G banded karyotype

A

around 500

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7
Q

how large do the variants have to be to be to be detected

A

over 5Mb

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8
Q

how many variants detected per person using G banded karyotype

A

0 to 1

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9
Q

diagnostic yield and incidental findings in G banded karyotype

A

low

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10
Q

Array CGH

A

has the ability to explore all 46 chromosomes in a single test and to detect any DNA imbalance including extra or missing chromosomes and loss or gain of chromosome material much more precisely than conventional chromosome analyses (e.g. G banded karyotype)

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11
Q

resolution of Array- CGH

A

50-100kb

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12
Q

number of loci probed in Array- CGH

A

0.05- 2 million

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13
Q

What sort of variants detected in Array- CGH

A

copy number variants

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14
Q

copy number variants

A

a phenomenon in which sections of the genome are repeated

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15
Q

variants per person in Array- CGH

A

10-100s

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16
Q

diagnostic yield and incidential findings in Array-CGH

A

medium ability

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17
Q

resolution of light miroscope

A

entirre genome

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18
Q

number of probed loci in ligh microscopy

A

N/A

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19
Q

variants detected in light microscopy

A

aneuploidy / polyploid

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20
Q

how many variants per person detected by ligh microspcy

A

0 to 1

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21
Q

diagostic yiled and incidental finding ability of lght microscopy

A

low!

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22
Q

outline the Array CGH process

A
  1. Patient and control DNA are labeled with fluorescent dyes and applied to the microarray
  2. patient and control DNA compete to attach to the microarray
  3. the microarray scanner measures the fluorescent signal
  4. computer softwar analyses the date and generated plot (e.g. can see where copy number variant is different
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23
Q

example of array CGH result

A

shows differences between the amount of DNA (e.g. number of CNVs) in controls vis signature

24
Q

copy number variants are largest in what sorts of mutations

A

craniofacial and then autism

25
Q

SNP array

A

is a type of DNA microarray which is used to detect polymorphisms within a population.

26
Q

resolution of SNP array

A

10kb

27
Q

number of loci probed in SNP-array

A

0.1- 2 million

28
Q

variant detected in SNP array

A

common SNVs

29
Q

how many variants detected per person using SNP array

A

4 million

30
Q

diagnostic yield and incidental finding ability of SNP-array

A

medium high

31
Q

resolution of exome sequencing

A

1bp

32
Q

number of loci probed in exome seuquencing

A

50 million

33
Q

variants detected using exome sequencing

A

coding variants

34
Q

variants per person in exome seqeuncing

A

20,000

35
Q

diagnostic yeild and incidental findings of exome sequencing

A

high

36
Q

resolution of genome sequencing

A

1bp

37
Q

number of loci probed in genome sequencing

A

3 billion

38
Q

variants detected in genome sequencing

A

most variants

39
Q

variants per person in genome sequencing

A

4-5 million

40
Q

diagnostic yield and incidental finding ability of genome sequencing

A

highhhhh

41
Q

strongest genome technology

A

genome sequecing

42
Q

example of a light microscope

A
43
Q

G-banded karyotype

A
44
Q

Array-CGH

A
45
Q

SNP- array

A
46
Q

exome sequencing

A
47
Q

genome sequencing

A
48
Q

genotyping

A

determining which genetic variants are present in an individual genome

49
Q

genotyping uses

A

arrays

50
Q

array

A

only assay specific type of variants

51
Q

SNP-chip

A

determines genotype of specific SNPs on microarray

52
Q

array-CGH

A

determine copy number of scpeific regions on microarray

53
Q

Sequencers

A

only assay variants within sequenced regions

54
Q

role of sequencing

A

determining the order of baseparis in a region of DNA

55
Q

sanger sequencing

A

targets specific exons or a single genome

56
Q

next generation sequencing

A

targets multiple genes or whole genome

(6-10) Translational Medical Science (40 decks)

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