Genomics Methods 1

Question 1

What is a a SNP

Answer 1

A variation at a single base pair in the genome. Commonly used as genetic markers a least 1 % of the population

Question 2

What is the difference between a SNV and a SNP

Answer 2

SNV is not common where a SNP is common

Question 3

What is high thorughput

Answer 3

millions of probes on the array that target the complementary sequence in the genome

Question 4

What are studies that have used SNP arrays

Answer 4

Locke compared single nucleotide polymorphisms and copy number variants between wild cuaght and laboratory bred mice

ancestry DNA 23 and me

Question 5

What are some charactersitcs of SNPS

Answer 5

May be within coding or non coding regions of a gene as well as intergenic regions may have advantageous neutral or disadvantageous effects may influnce phenotype can be uses as a measure of genetic relatedness

Question 6

What are CNVs

Answer 6

Chromosomal segments at least 500 bases in length that vary in the number of copies from human to human can either be delted duplicated can encompass genes leading to altered phenotype

Question 7

What does SNP signal intenstiy measure on an array

Answer 7

The strength of hybridization between the DNA sample and allele specefic probes used to dertemine the genotype AA AB BB

Question 8

What is a microarray used for in genomics

Answer 8

Genotype thousands to millions of SNPs at once by measuring hybridization at each proble location

Question 9

What is an allele-specific probe

Answer 9

A short DNA sequence on the array that binds only to a specefic SNP ( One probe for A one for G)

Question 10

What happens if the sample DNA does not match the probe sequence

Answer 10

It does bind strongly producing weak signal allowing genotype discrimination

Question 11

What does proximal medial distal mean in probe binding

Answer 11

These refer to the position of the SNP within the probe sequence probes differ by when the SNP sits relative to the probe ends

Question 12

Why do arrays use multiple probes per SNP

Answer 12

To increase accuracy by testing binding at different positions and accounting for sequence context

Question 13

What is genome fragmentation, and why is it done

Answer 13

Breaking DNA into smaller pieces to allow efficient hybridization to array probes

Question 14

What is step one of the SNP array

Answer 14

Sample collection from ear lung blood or tail

Question 15

What is step 2 DNA isolation and prep

Answer 15

Restrictive enzymes will cut the dna add the adaptors and PCR the PCr amplicons are then pooled and fragment and biotin end label and denaturation

Question 16

What is Nspl and Styl

Answer 16

Nspl cuts at the 5’RCATGY3’ where R=A or G and Y=T or C Styl cuts at 5’CCWWGG3’ where W = A or T

These restriction enzyme recognition sites are degenerate sequences when more than on nucleotide is possible at a particular position

Question 17

What do adapters recognize after restrction enzyme digestion

Answer 17

Overhands produeced by Nspl and Styl are ligated to the ends of the digest DNA fragments

Question 18

What is used in PCR amplification

Answer 18

Primers that recognize the adaptor sequence are unsed in PCR amplifciation

Question 19

What is then done with the PCR amplfication

Answer 19

Fragementation biotin end labeling and denaturing fragments are labele using biotion at the 3’ end of the fragment

Question 20

What do you do after biotin end labeling

Answer 20

Denaturation hybrdize to array and wash off any unbound DNA arrays are scanned and flournces intensties are interpeted into SNP agentoype and CNV calls

Question 21

What are genotype calls based on fluorescent intensities

Answer 21

AA or BB would be homozygous
AB Heterozygous
No call is unknown

Question 22

What is an example of a duplication event

Answer 22

The genomic region (e.g., Exon 1–Exon 2) is copied an extra time, increasing its copy number. On SNP arrays, this appears as increased signal intensity for both SNP probes and invariant genomic probes (IGPs), because more DNA fragments hybridize to that region.

Question 23

What are the different states when in reference to CNV using SNP

what is nullizgous

Answer 23

Sate of 0 - nullizygous amorphic complete loss
State of 1- hemizygous only one from a parent CN state of 3 or 4 you are getting a greater signal intensity than expected than you have more than one copy
Loss is 0 or 1

Question 24

Can you use IGPS for CNV calling too

Answer 24

Yes it works the same

Question 25

What represents a probe dessert

Answer 25

The centromeric repetitive non-genic regions of the centromere

Question 26

Do arrays provide information on the location of the duplication

Answer 26

NO

Question 27

How could we detect the CNV using FISH

Answer 27

Fluorescently labelled probe Hybridizes to a complementary sequence Assay is performed on metaphase spreads Cells in metaphase burst onto a microslide This provides the copy number and the location

Question 28

What are the application of SNP arrays

Answer 28

Detect variants at SNP loci; call SNP genotype Detect copy number variants Genome-wide linkage analysis, genome wide association studies Determine SNPS and CNVs associated with susceptibility to disease and drug resistance

Question 29

What is the advantages of genotyping arrays in comparison to NGS

Answer 29

Lower cost hundreds, not thousands Less labour-intensive sample preparation Less intensive bioinformatics is involved during analysis Good fit for population-based surveys (large number of samples screened) Must follow up with a validation assay to confirm findings

Question 30

What are some limitations of genotyping arrays

Answer 30

Less coverage Sampling of the genome could potentially miss important information in other areas (heritability, variants) Need another method to identify all genetic determinants of complex traits Array design is biased towards better-studied populations

Question 31

What is the Illumina Infinium PsychArray

Answer 31

Has high resolution High throughput