Next generation sequencing
How many DNA molecules are produced in each cluster?
4000
There are two ways to perform an assembly depending on whether you know the reference sequence or not. What are they called?
Alignment and De Novo assembly
What are the possible applications of NGS?
All of these options
Why do we skip the fragmentation part when we are sequencing ancient dinner like the sample?
Because the DNA is already partially degraded
How could the DNA molecules bind to the adopter on the flow cell?
Because the sequences are complementary
In what format as the sequencing file stored?
FASTQ
What is the purpose of the adapter?
For the PCR primers to bind to it
Since we are working with ancient DNA, we need to be able to identify whether it has been contaminated with modern human DNA. Which characteristic below is not found in ancient DNA?
It is structured into very long strands
MOUTH - By caring two C alleles for Rs3827760, the ancient Greenlandic man's teeth are most likely to be...?
Shovel shaped
What is currently happening?
The DNA molecules are now binding with the adopters On the flow cell
After bridge PCR amplification, half of the DNA strands are washed away. Why?
To sequence clusters of clonal DNA
What is the next step after and repair?
Adding adenine to the 3' end of the Strand
EYES - The ancient Greenlandic man carries two C alleles for Rs1129038. What is the most likely color of his eyes?
Brown
EARS - This man carries two T alleles for Rs17822931, what is the most likely phenotype for this SNP?
Dry earwax
What is the first step you need to do to prepare the bone sample for DNA sequencing?
Extract the DNA
Now that we have performed the PCR amplification and accumulated enough DNA, what is the next step?
Generating clusters
We only run PCR amplification for 10 - 12 cycles which is much lower than usual 30 cycles. What is the reason for this?
Minimizing errors introduced in replication
SKIN - Having G instead of A in SNP Rs142665 for results in the ancient Greenlandic man having ...?
Non-light skin
When sequencing ancient DNA, what is the next step in the sample preparation after we have extracted the DNA from the bone?
Perform end-repair
The Phred scale describes a probability of error when calling a base. A quality score of 40 means that the probability of an incorrect base call is one in...?
10,000
How many clusters do you think we have in one closer?
200 million
What is the name of the process that is currently shown in the animation?
Bridge PCR
Which section describes a sequence quality?
D
HAIRS - Having the base G in SNP Rs6152 results in an increase pop up ability of ...?
Developing baldness
In the next generation sequencing, each of the bases is tagged with a... So that we can specifically identify them.
Fluorophore
How many pictures are taken for every single base addition
Four
When we are sequencing only from One Direction, the process is also called?
Single end sequencing
Which enzyme is used in the sequencing process?
T4 DNA polymerase
What is the purpose of the end repair procedure?
To create blunt ended strands
Why do we need an adenine overhang?
To ensure that the adaptors bind specifically
In the secondary data analysis, we assemble all the reads and try to interpret the data. What should we do first before starting the secondary analysis?
Trim out the adapters
There are many advantages of using the next generation sequencing and technique as compared with the Sanger sequencing, for example?
We can sequence many DNA molecules in parallel