Which Human Tumor Cell Line/Sample Genomes Have Been Already Sequenced Completely?

Question

[Fred Fleche]

Hello,

I am looking for genome (from cell lines or patient samples) that have been fully characterized thanks to the Next Generation Sequencing (NGS) methods. I already know the following instances:

• NCI-H209 cell line

• 22 Human Glioblastoma Multiforme
  samples

• a first Acute Myeloid Leukaemia with minimal maturation (AML-M1) sample

• a second Acute Myeloid Leukaemia with minimal maturation (AML-M1) sample

So if you know other papers/ressources I would be glad if you could share it with others.

Thanks in advance,

Fred

[Giovanni M Dall'Olio]

This question is very interesting, but maybe the title can be refined. what about something like 'Which human cell line genomes have been already sequenced completely?', if I understood the question correctly.

[Giovanni M Dall'Olio]

do you refer to human genomes only?

[Fred Fleche]

Question 1: Yes I refer to human geneomes. Question 2: You are right I will give it a try.

[Fred Fleche]

[?]

[?]

[Fred Fleche]

Question 1: Yes I refer to human genomes only.

[Fred Fleche]

Question 2: You are right I will give it a try.

[Chris Miller]

Are you referring only to deep coverage, whole-genome sequencing? If not, many genomes and cell lines have been assayed for rearrangements using low-coverage with paired-end sequencing, and others have had whole-exome sequencing done.

[Fred Fleche]

Yes I am referring only to deep coverage, whole-genome sequencing

[Fred Fleche]

@Chris : Yes I am referring only to deep coverage, whole-genome sequencing.

Answer 1

[Yuri]

There were recently a paper from Nelson's lab at UCLA on full sequencing of U87 GBM cell line.

Clark et al, U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line, PLoS Genetics, 2010.

Answer 2

[Giovanni M Dall'Olio]

A company called Complete Genomics has released the genomes of two cancer pairs.

[Larry_Parnell]

Cancer-normal pairs of genome data may not be that easy to find because of IRB restrictions on data release.

Answer 3

[Fred Fleche]

• COLO-829 cell line
• 96 human glioblastoma samples

[Chris Miller]

a) The TCGA (GBM) is up to something like 150 samples now, but they aren't doing whole genome resequencing at this point. The first draft resequenced 600 selected genes, and they're bumping that number up, but still using targeted capture.

[Yuri]

AFAIK, TCGA project does not do full sequencing yet, only genes of interest.

Answer 4

[Hanif Khalak]

These cancer genomes are coming out fast - including a study which sequenced 25 breast cancers last December.

Even more amazing, seems like a huge international consortium is underway to sequence 25,000 cancer genomes(!).

I'm kind of curious as to how this data will be made accessible - it doesn't seem like GenBank/DDBJ/EMBL are really keeping up with all the data...