Next Gen Sequencing Flashcards

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1
Q

what is the key idea underlying next-generation DNA sequencing?

A

parallel observation of spatially separated sequencing reactions

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2
Q

what are the 2 main types of sequencing today?

A

short read and long read (both optical)

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3
Q

how to microarrays measures gene expression?

A

intensity

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4
Q

how do next gen sequencing measure gene expression?

A

sequences

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5
Q

what is the process that microarrays rely on?

A

hybridization of DNA to probe

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6
Q

what are some of the downsides of microarray?

A

no sequence level information, can miss mutations, search space is limited to probes on the array

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7
Q

which system is best for RNA sequencing?

A

microarray

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8
Q

what is the point of mutation detection?

A

detect single nucleotide variants compared to a reference genome

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9
Q

what are 3 problems that affect SNP calling?

A
  1. coverage (how many times you sequence the same strand with different reads)
  2. error rates (if error rate low, coverage reportings with be correct)
  3. ploidy
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10
Q

what is exome sequencing?

A

build sequence library based solely on genes that are expressed

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11
Q

why is exome sequencing helpful in the clinical setting?

A

can detect SNPs among patient with the same genetic disorder

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12
Q

what is the best way to perform exome sequencing?

A

microarrays with hybridization

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13
Q

what is the best way to detect mendelian diseases?

A

exome sequencing

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14
Q

what does methotrexate do?

A

inhibits parts of de novo pyrimidine biosynthesis

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15
Q

how many mutations are created each generation?

A

about 60

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16
Q

what is the paternal contribution to mutation rate?

A

90%

17
Q

what is the main way to non-invasively sequence a babies genome?

A

sequence mom and then dad’s genome, moms blood contains 13% babies genome

18
Q

how much percentage of a mother’s blood is cell-free DNA from baby?

A

13%

19
Q

what is a genome?

A

all genetic information from a single organism

20
Q

what is a metagenome?

A

all genetic information from a group of organisms

21
Q

what can the extended genotype influence?

A

obesity, disease susceptibility, decision making

22
Q

what is the extended genotype influenced by?

A

sex and body polarity

23
Q

what is a variant of unknown significance?

A

coding variant without an associated functional cause (disrupt protein function, stabilize mRNA)

24
Q

why is error rate so much higher in long read version of DNA sequencing?

A

because it is just focusing on one molecule instead of an entire genome