Final Review
DNA amplification
thermocycler program uses two denaturation stages one at 94C and one at 90 to save time
De Novo Sequencing
Used to generate a DNA sequence for which no prior info is know
Resequencing
Sequencing of DNA followed by the comparison to a reference sequence
Used in clinical diagnosis
2 Steps in PCR product purification for sequencing
remove PCR primers
Remove dNTPs
Enzyme digest - ExoSAP for PCR purification
Exonuclease - destroys primers
Shrimp alkaline phosphatase hydrolyzes dNTPs to remove the phosphates so they cannot bind to other dNTPs.
Column PCR product purification
Silica gel membrane in column binds the DNA that is the correct length and everything else flows through
Fluorescent DNA sequencing
separation of fluorescently labelled, extended fragments of DNA using capillary electrophoresis for the determination of sequence
Components of enzyme digest in PCR purification for sequencing
Exonuclease to destroy primers
Shrimp alkaline phosphatase (SAP) hydrolyzes dNTPs so can’t bind
Column PCR product purification for sequencing
Silica gel column binds the DNA in the range desired and the primers and impurities flow through
Bi-Directional Sequencing
higher accuracy
confirm variants results are accurate,
identifies secondary structures
Components of the terminator ready reaction mix 2 things
Nucleotides with diTP instead of dGTP which prevents base compression
Each ddNTP has a dye that emits a unique wavelength when excited by light
Primer Design Sanger - PCR primer with Sequencing tail
M13 is added to the 5’ end
allows for single MM in the FWD and RVS reactions
Primer Design Sanger - PCR primer is the Sequencing primer
use a PCR primer as the sequencing primer
can result in excess pipetting
Primer Design Sanger - Nest sequencing primer
primer binds within the PCR product (eliminates non specifics)
Sequencing product purification - Gel Column
Sephadex spheres separate products based on weight - the leftover dyes are caught in the pores
fast but dye blobs present
Sequencing product purification - BigDye Xterminator
Solution has an insoluble phase to capture the ddNTPs and stabilize the sample
requires special vortex
Sequencing product purification - Ethanol
precipitation with EDTA and ethanol then incubate and wash
slow
Capillary Electrophoresis Settings for Sanger
50 cm Capillary - separates up to 800 bp of sequence
POP7 - intermediate polymer
Spectral Calibration with Z dye
Minimal overlap, no dips or irregularities
peaks are separate and distinct
ordered
Blue, green, yellow red
3 rules of nucleotide number in HGVS
nucleotide 1 is the A of ATG
5’ of the A is -
3’ of the stop codon is *
Intron naming in HGVS
total nucleotide divided in half
nt in first half are numbered in reference to the last exon
nt in the second half are numbered in relation to the downstream exon
3 keys points about RNA
contains ribose
uracil instead of thymine
RNA has OH at carbon position 2
RNA isolation methods - Trizol and Phenol
lyse cellular and nuclear membranes
add chloroform
centrifuge
precipitate RNA with EtOH
RNA isolation methods - RNA kits
Column Chromatography uses silica membrane with high salt to bind the big RNAs and then can be eluted
consider - column can clog and DNA must be sheared prior to loading
Ideal Quantitation values for RNA
absorbance at 260nm
260/280 - 1.8-2.1
260/230 - 2.0
Ideal quality bands for RNA
Quality
28S band at 4.7kb
18S band at 1.9kb
rRNA
many sizes - form the large subunit of ribosome while associating with other proteins
tRNA
inverted four leaf clover shape with anticodon in the bottom loop - carry AA to ribosome
hnRNA
heterogeneous RNA rapidly degraded
snRNA
small nuclear ribonucleoprotein only in the nucleus and splice the hnRNA
mRNA
100-10,000bp
found in cytoplasm and is translated into proteins
siRNA
dsRNA
small interfering RNA silences genes
Uses of QF-PCR
Rapid aneuploidy detection SCREEN for prenatal diagnosis - must be confirmed with ultrasound findings to be reported
screens for 13,18,21,X/Y
What does qf-pcr amplify
Amplifies polymorphic markers called short tandem repeats which can be separated by fragment analysis to detect copy number
Short tandem Repeats qfpcr
Polymorphic loci of 2-7nt repeats that are inherited in different numbers from each parents
the allele inherited from the mother and father at one locus are different creating unique genetic fingerprint
7 reasons microsatellites are used for analysis
Present in large numbers in the genome
Evenly spaced in genome
Alleles are inherited in a Mendelian manner
Highly polymorphic
Stable over multiple generations
Can be specific to certain populations
Size is Ideal for amplification (even in degraded samples)
Prenatal sample requirements for qfPCR
Optimized to work on low levels of DNA 1-10ng
1ml Amniotic fluid
0.2mg chorionic villus
Fetal blood (5ul)
Data interpretation of qfPCR
Peak areas of the different alleles for a single marker are compared to generate a ratio
amount of product is proportional to the amount of original target
Peak areas of the two alleles on a single marker are compared to each other to generate a ratio
PA1/PA2=ratio
ISCN for qfPCR
“rsa” tells region specific assay
rsa(X,13,18,21) x copy number
Uses of Microarray
investigate copy number changes throughout the entire genome using hybridization of patient DNA to probes on a slide with a detection system
2 Clinical applications microarray
Copy number changes
Genotype - SNP analysis
miccro array chip
solid substrate with assay material on it - used for single channel
Agilent with OGT platform manufacturing
uses an inkjet printer to place nucleic acid onto a glass substrate creating 60-mer oligo probes either depositing pre-synthesized cDNA or synthesizing base by base
Microarray - probe
series of nt for a complementary unique base pair with the genome are affected to the glass of the microarray
Microarray - feature
A large grouping of the same probe for a locus
Found around the array with each features representing a different area of the genome
Whole Genome Microarray
Equally distribute probes provide coverage of the whole genome
detects aneuploidies and large imbalances
target only Microarray
targets clinically relevant regions with high density of probes to ensure genes are well covered
detects small changes at the relevant gene
Targeted whole genome Microarray
provides coverage of the entire genome with increase coverage of target regions
CGH and SNP Microarray
Most clinically relevant
provides whole genome coverage with targeted coverage and loss of heterozygosity information via SNP probes
3 Consideration in array resolution
probe size
number of features
distance between probed loci
Probe Size in microarray resolution
smaller length = more specificity =high resolution
longer = lower resolution
Number of features in microarray resolution
Greater number of features = higher resolution
Distance between probes in microarray resolution
Smaller distance between loci = higher resolution
Quality Control Metrics for Microarray
DLR spread
red/green signal intensity
background noise
Signal to noise ratio
Reproducibility
array image
Microarray analysis - DLR spread
Measure the difference in Log 2 ratio between all pairs of probes on a chromosomes and expect them to be aligned
If DLR spread is too high it indicate variability between neighbouring results and makes it hard to call abnormalities
Microarray SNP analysis
SNP analysis gives insight into the genotype status of the patient to detect Loss of heterozygosity and mosaicism
SNP probe algorithm - microarray
only the DNA fluorescence is measure giving an intensity representative of how much alleles is bound - genotype is inferred by the comparing the intensity of the two features for each SNP (A vs B)
B alleles frequency plot
graph representing the presence of each genotype
can detect mosaicism at low levels 10-15%
How to calculate consanguinity
Add autosomal LOH segments >5Mb
Divide by size of autosomal genome
convert to percentage
Depth of coverage
how many times a base has been sequenced or read - a greater depth of coverage increases detection sensitivity and reliability of results
3 considerations for library prep of NGS
not using EDTA and chelating salt - inhibit enzymes
extract into EB, low TE or water
store at -20 do not freeze/thaw
2 types of fragmentation in NGS
Physical shearing
enzymatic digestion
Physical shearing in NGS
break the bond of DNA using focused acoustic, ultrasonic energy on the sample within the Covaris for unbiased fragmentation
Enzymatic Digestion fragmentation in NGS
restriction endonucleases break both strands however where may be recognition site present leading to biases
4 steps in library prep for NGS
fragmentation
end repair
A tailing
adapter ligation
2 types of target enrichment in NGS
Hybrid capture
Amplicon based capture
5 steps in Hybrid capture for NGS
denature DNA
hybridize biotin to the targets
Capture target on bead
recover target
amplify
4 steps in Amplicon based capture in NGS
primer based PCR amplified regions of interest
produces amplicons
PCR and barcode adapter ligation with second PCR
Data of reads aligned to the reference
Size selection in NGS
fragments outside the desired range interfere with sequencing so should be removed by purification
3 methods of purification for NGS library
gel electrophoresis
bead based purification
double sided bead clean up
Double Sided bead clean up for NGS
lower ratio bead:DNA captures large fragments
wash
higher ratio bead:DNA captures wanted DNA leaves small fragments
Wash
Quality control steps in NGS
Bioanalyzer does automated electrophoresis to quantify library and asses fragment sizes
Sample Pooling considerations in NGS
all libraries can be pooled together if there are in the SAME size range and concentration
4 steps to load the NGS library
quantified by quantitative PCR
internal control added
denature with NaOH or heat and ice
load with reagents and buffer onto the flow cell
4 Channel base calling
4 channel requires 4 images after each cycles to capture a unique dye for each base
2 Channel base calling
Taking only 2 images after each cycles and can determine all 4 bases using computation
Pair end sequencing
After the first sequencing by synthesis the strand folds over hybridizes and DNA pol extends the reverse strand
5 benefits of paired end sequencing
more accurate
precise mapping
detect indels
remove duplicate artefacts
higher number of single nucleotide variation
Optimal read length
Median insert size should be 2x longer than read length so only a few bases overlap
Primary data analysis NGS
algorithm generates a base call with a quality metric
data is pooled and demultiplexed
Secondary Data analysis NGS
Read alignment by mapping position sequence to the reference and creates a map
variant calling programs determines single and multiple base pair variation
Tertiary Data analysis
Genetic variation put in a list with chromosome number, position and reference alleles
Ion Torrent Platform
Clonal amplification where DNA fragments are mixed into emulsion oil and beads, DNA fragments achor and are amplified
Clustering Quality
Cluster density
Cluster passing filter
Cluster density
how dense the clusters are on the flow cell expressed as cluster per mm
Cluster passing filter
measure of the number of clusters used for final data output, uses a digital filter to remove low quality clusters
Q score
measures sequencing accuracy by indicating the probability that a base is called incorrectly across the entire run and in each variant
Alignment process in secondary analysis
Input the patient generated file and reference genome
alignment platform/program
output as a binary alignment map
Depth of coverage NGS
Average number of times a base is sequenced
Breadth and Uniformity in NGS coverage
All regions have even coverage and are on target
Variant caller for secondary analysis
Determine where difference between the patient and reference exist and annotate
Background on BRCA1
Tumour suppressor gene involved in DNA repair 17q21.31
when inactive allows accumulation of defect causing cells to divide
Multiplex Ligation-Dependent probe amplification
relative method to detect copy number variations from one PCR based reaction
target gDNA quantity for MLPA
50-100ng must be accurate
parts of SALSA MLPA probes
PCR primer
stuffer sequence
hybridization sequence
Purpose of Q fragments for MLPA
Confirms quantity of DNA sample is sufficient
Ligation and DNA independent
Purpose of D fragments for MLPA
Determines adequate sample DNA denaturation
Ligation and DNA dependent
Benchmark/ligation fragment
used as a benchmark to compare the other CQ fragments and confirms the probe to target hybridization and ligation are complete
Ligation and DNA dependent
MLPA detection of known point mutations
probes designed for certain SNPs and only perfectly matched probes are ligated/amplified