C. Exome Seq. & Mendelian Disorders Flashcards

1
Q

What are the main objectives of re-sequencing?

A

a. Discovery of novel mutations (rare Mendelian disease)

b. Genotyping of known variants (shared within a population) ex. Breast-cancer genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Features of resequencing?

A

a. Straightforward: by mapping (to find the best match in ref. seq.)
b. High reproducible: by high-depth sequencing (~ 40X)
c. Effective diagnosis: replacing cumbersome biochemical methods used in clinics (ex. amniocentesis test - karyotyping)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How is resequencing straightforward?

A

by mapping (to find the best match in ref. seq.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How is resequencing highly reproducible?

A

High reproducible: by high-depth sequencing (~ 40X)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How does resequencing contribute to effective diagnoses?

A

Resequencing replaces cumbersome biochemical methods used in clinics (ex. amniocentesis test - karyotyping)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Minimal _____ coverage necessary for making reliable genotype calls (diploid)

A

Minimal 10X coverage necessary for making reliable genotype calls (diploid)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Which kinds of discordant reads support translocation-type of SVs?

A

?

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How to call variants and kinds of variants collected by re-sesequencing?

A

Each read as one observation: high coverage –> precise calls

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Small variants

A
SNPs (single nucleotide polymorphisms)
Small Indels (insertion- deletions)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Large variants

A

CNVs (copy number variations), SVs (Structural variations)

- Use of discordant paired-end reads to collect SVs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How to distinguish benign and severe as 4-5 million variants are found in each individual?

A

By exome sequencing, which reduces the cost of sequencing. But its set-up requires large investment.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is Exome?

A

Exome (protein-coding) + other identified genes (15 - 20 thousands)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

equilibrated frequency distribution (p, q, r, etc.) can be used for measuring base- position-specific selection pressure

A

MAF can be used

How well did you know this?
1
Not at all
2
3
4
5
Perfectly