SNP Chip Lecture

Question 1

Whole genome sequencing captures

Answer 1

all variation- around 6M variants

Question 2

Benefits of SNP chips

Answer 2

lower number of variants but lower cost per sample

Question 3

Each assay costs around ____ to develop

Answer 3

$200,000

Question 4

How does Illumina Infinium chemistry work

Answer 4

small beads that have a unique barcode

Question 5

For each SNP, synthesize a 50 mer oligo that flanks the SNP

Answer 5

Probe

Question 6

Create a chip that has

Answer 6

microwells fabricated into the chip

Question 7

G and C

Answer 7

Green Bead

Question 8

A and T

Answer 8

red bead

Question 9

infinium I has how many probes

Answer 9

2

Question 10

infinium II has how many probes

Answer 10

1

Question 11

What is important to keep in mind when making decisions based on chip genotypes for any single SNP specifically

Answer 11

Higher error rates
0.5% but can add up with lots of samples

Question 12

best indicator of genotype quality

Answer 12

Call rate per SNP

Question 13

Best indicator of sample DNA quality

Answer 13

call rate per individual

Question 14

Photolithography

Answer 14

less expensive than generating a bead pool
allows you to screen potentially several million variants in a small number of individuals

Question 15

Variants that are polymorphic and assayable can be

Answer 15

used on lower density assays- which are lower cost

Question 16

Affymetrix technology

Answer 16

uses photolithography to synthesize oligos used to hybridize DNA to chip

Question 17

imputation

Answer 17

the statistical inference of unobserved genotypes

Question 18

how is imputation achieved

Answer 18

by using known haplotypes in a population

Question 19

Example of imputation

Answer 19

a stop sign is a common sign so if you see a blurry photo of a stop sign your brain can tell you what it is
but if you see an uncommon sign your brain will not be able to distinguish what it is

Question 20

What is low pass sequencing

Answer 20

shotgun sequence a human genome to 0.4x or 1x coverage, and use computational methods to ‘fill in’ anything we missed

Question 21

SNP array focuses on

Answer 21

variants