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
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)
What are Copy number variants
Deletion/duplication in DNA that cause genetic disease • Whole genome (aneuploidy) • Several genes • Single genes • Exons
Difference b/w Array-CGH & SNP-Arrays
- Reference DNA patient data is compared to
- Method of analyser
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
Difference b/w Array-CGH & SNP-Arrays
- What each can detect
Both (CGH & SNP): Genomic gains & losses
SNP: Copy neutral abberations like Regions of homogenicity (ROH) & Regions of loss homogeneity (LOH)
What is the region of homogenicity?
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)
Describe the 2 ROH diagnostic implications
- Identity by decent: more homozygosity bc of ancestary (marriage w/in family)
- Uniparental disomy(UPD): a) single (or couple) lrg ROH on same chromo. OR b) inheritance of 2 homologous chromo from one parent (ka Isodisomy)
What is mosiacism
When an individual has 2+ cell lineages that have a different genotype (consist of abnormal & normal cells)
How might mosaicism look on a microarray graph?
Extra BAF tracks representing the introduction of another cell line
What are the QC parameters for
a) LogR Std Dev.
b) BAF Dev.
c) Cell rates (SNP)
a) LogR Std Dev. : <=0.16
b) BAF Dev.: <=0.04
c) Cell rates (SNP): >= 0.99
What are the advantages of microarray? (4)
- Higher diagnostic yield than karyotyping
- Tissue culture not needed
- Quicker than karyotype
- Some automation
What are the DIS-advantages of microarray? (4)
- 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
How are low copy repeats (LCR responsible for microdeletetion/microduplication
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)
