Microarrays

Question 1

There are 2 methods for detecting Copy Number Variation (CNV). What’s the difference b/w Log R ratio (LRR) & B Allele Frequency (BAF)

• What each detects
• What each measures

Answer 1

LRR: - Detects copy number change (del/dup)
-Measures total signal intensity
BAF: - detects genotype (copy no. change OR uniparental disomy)
-Allelic intensity ratio of 2 alleles (A & B)

Question 2

What are Copy number variants

Answer 2

Deletion/duplication in DNA that cause genetic disease
•	Whole genome (aneuploidy)
•	Several genes 
•	Single genes
•	Exons

Question 3

Difference b/w Array-CGH & SNP-Arrays

• Reference DNA patient data is compared to
• Method of analyser

Answer 3

CGH: - patient data compared to normal reference control data
- Fragment of DNA fluorescently labelled & competitively hybridized onto array & read w/ fluorescent scanner
SNP: - Doesn’t use control reference DNA
- SNP allele frequency & absolute fluorescence lvls compared to averaged results of normal samples

Question 4

Difference b/w Array-CGH & SNP-Arrays

- What each can detect

Answer 4

Both (CGH & SNP): Genomic gains & losses

SNP: Copy neutral abberations like Regions of homogenicity (ROH) & Regions of loss homogeneity (LOH)

Question 5

What is the region of homogenicity?

Answer 5

Copy number neutral homozygosity 
In other words (if doesn’t make sense)
-	No Copy no. change (no del/dup)
-	Log R 0.00 (have 2 copies= normal)
-	No heterozygous BAF (either have 2 A allele or 2 B allele)

Question 6

Describe the 2 ROH diagnostic implications

Answer 6

1. Identity by decent: more homozygosity bc of ancestary (marriage w/in family)
2. Uniparental disomy(UPD): a) single (or couple) lrg ROH on same chromo. OR b) inheritance of 2 homologous chromo from one parent (ka Isodisomy)

Question 7

What is mosiacism

Answer 7

When an individual has 2+ cell lineages that have a different genotype (consist of abnormal & normal cells)

Question 8

How might mosaicism look on a microarray graph?

Answer 8

Extra BAF tracks representing the introduction of another cell line

Question 9

What are the QC parameters for

a) LogR Std Dev.
b) BAF Dev.
c) Cell rates (SNP)

Answer 9

a) LogR Std Dev. : <=0.16
b) BAF Dev.: <=0.04
c) Cell rates (SNP): >= 0.99

Question 10

What are the advantages of microarray? (4)

Answer 10

• Higher diagnostic yield than karyotyping
• Tissue culture not needed
• Quicker than karyotype
• Some automation

Question 11

What are the DIS-advantages of microarray? (4)

Answer 11

• Can’t detect heterodisomic UPD & sml variants
• Low level mosaicism (<10%) can be missed
• Time consuming to analyse & report
• Many CNV are novel w/ unknown clinical significance

Question 12

How are low copy repeats (LCR responsible for microdeletetion/microduplication

Answer 12

Low copy repeats (LCR) can cause DNA to misalign at meiosis or mitosis and result in deletions or duplications => predispose genomic arrangements by non-allelic homologous recombination (NAHR)