HeLa Genome

Question 0

Why is the sequence available only through controlled-access database?

Answer 0

-family objected to it

Question 1

What is HeLa genome important in research?

Answer 1

• cells grow well and at a fast rate

- distributed without restriction

Question 2

What sequencing techniques were used in the study?

Answer 2

• Illumina sequencing- shot gun sequencing, can be 70-150 nucleotides long
• RNA-seq: high throughput method
• Fosmid: isolates clones and sequences them by themselves one at a time
• PacBio: sequence single molecule at a time (watch video), small well is called zero mode wave guide (ZMW), can take 10,000
• ChIa-Pet: sequences ligated ends

Question 3

Do SNVs explain why HeLa cells are highly tumerogenic?

Answer 3

• total #of SNVs are not higher in a HeLa cell compared to healthy people
• only 10% were rare
• PPV are not unique to HeLa
• PPA were uniquie to HeLa
• ran GO analysis on PPA and found no enriched in HeLa genome
• NO!

Question 4

What is GO enrichment analysis?

Answer 4

• genes are given word descriptors for biological processes

- process are enriched if p>0.01

Question 5

What are halpotypes

Answer 5

…

Question 6

What is LOH and how does it arise?

Answer 6

• loss of heterozygosity

- arises from mitotic nondisjunction that happens in cancer cells

Question 7

What is the predominant copy number for HeLa?

Answer 7

• copy #:3, 30-68%

Question 8

How might deletions contribute to tumorigenicity?

Answer 8

• loss of whole genome information

Question 9

How has HeLa genome changed in different isolates?

Answer 9

• are all the same, all were contaminated by HeLa cells

- were named differently because they were thought to be different but they were all the same

Question 10

What viral genome is integrated into the HeLa genome?

Answer 10

• HPV-18 was inserted into chromosome 8

Question 11

How were ChIA-PET and RNA-seq used to provide evidence for one of the proposed mechanisms?

Answer 11

• chromatin interaction analysis by paired end tag sequencing
• RNA pol II binds to DNA
• fix chromatin with formaldehyde, sonicate
• ImmunoPrecipitate with antibody to RNA pol II
• ligate ends with adaptors
• sequence ligated ends
• look for distant regions that have been ligated together
• RNA-seq was used to analyze MYC locus
• HPV and MYC are interacting and increasing expression