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:
So if you know other papers/ressources I would be glad if you could share it with others.
Thanks in advance,
Fred
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Fred Fleche
There were recently a paper from Nelson's lab at UCLA on full sequencing of U87 GBM cell line.
A company called Complete Genomics has released the genomes of two cancer pairs.
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Giovanni M Dall'Olio
Cancer-normal pairs of genome data may not be that easy to find because of IRB restrictions on data release.
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Fred Fleche
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.
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...
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Hanif Khalak
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do you refer to human genomes only?
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.
Question 1: Yes I refer to human geneomes. Question 2: You are right I will give it a try.
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Question 1: Yes I refer to human genomes only.
Question 2: You are right I will give it a try.
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.
Yes I am referring only to deep coverage, whole-genome sequencing
@Chris : Yes I am referring only to deep coverage, whole-genome sequencing.