Question: Woman Sequenced With 454 Technology?
1
gravatar for Biomonika (Noolean)
7.4 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

Hi guys,

I am wondering if there was any female human genome sequenced with 454 technology. In this list:

http://www.eyeondna.com/2009/09/21/people-whove-had-their-genomes-sequenced/

I have found only one woman (!), Marjolein Kriek, sequenced with Illumina. Any suggestions? Thanks.

454 • 1.8k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 7.4 years ago by Biomonika (Noolean)3.1k
1

It's probably unintended but 'some woman' sounds awkward here and a bit downgrading.

ADD REPLYlink written 7.4 years ago by Leonor Palmeira3.7k

definitely unintened, thinking about how to modify :/

ADD REPLYlink written 7.4 years ago by Biomonika (Noolean)3.1k

Just click on 'edit', you can always edit your own posts and comments.

ADD REPLYlink written 7.4 years ago by Leonor Palmeira3.7k

It should be "any" instead of "some", that would fix the grammar and sounds less awkward. I'd ask: "I am wondering if there was any female human genome sequenced with 454 technology" sounds a bit more technical

ADD REPLYlink written 7.4 years ago by Michael Dondrup47k

thanks, I have fixed it this way.

ADD REPLYlink written 7.4 years ago by Biomonika (Noolean)3.1k

"any female human genome" .. would be better :)

ADD REPLYlink written 7.4 years ago by madkitty590
5
gravatar for Leonor Palmeira
7.4 years ago by
Leonor Palmeira3.7k
Li├Ęge, Belgium
Leonor Palmeira3.7k wrote:

In 2008, Marjolein Kriek was the first woman having her complete genome sequenced. I believe she was the fifth human being sequenced (not a very good sex-ratio there). And I still find it a bit uncomfortable to know that James Watson's genome had been sequenced the year before (knowing the controversy and the accusations of sexism surrounding the use of Rosalind Franklin's data to build the model of the DNA molecule). In the end, it was also a big technological race between 454 pyrosequencing (James Watson), Illumina (Marjolein Kriek) and the Celera company (Craig Venter).

Anyway, you might want to have a look at the female samples in the 1000 Genomes Project.

ADD COMMENTlink written 7.4 years ago by Leonor Palmeira3.7k

Thanks for the answer. Still seems to be a long way to go:) At this page ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20111108_samples_pedigree/20111108_1000genomes_samples.xls I have found NA07346 sample, which should be sequenced using 454. However, after downloading first fastq file from this page ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA07346/sequence_read/, all reads are 36 bp long, which sounds like Solid. Hmm. Will keep searching. Thanks.

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by Biomonika (Noolean)3.1k
1

Have you tried looking here : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ ? humanb36female.fa.gz contains the female human genome reference assembly used in the 1000 Genomes Project.

You can also get the mapped reads for each individual in BAM format here : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA07346/alignment/

What are you looking for exactly?

ADD REPLYlink written 7.4 years ago by Leonor Palmeira3.7k

I am looking for female 454 genomic data, similiar to this http://www.ncbi.nlm.nih.gov/sra?term=SRX000113. Will check your links in a minute.

ADD REPLYlink written 7.4 years ago by Biomonika (Noolean)3.1k
1

This might be what you are looking for : http://www.ncbi.nlm.nih.gov/sra?term=%28%28%28%28%28%28female%29%20AND%20human%29%20AND%20454%29%20NOT%20microbiome%29%20NOT%20metagenome%29%20NOT%20male%29 You'll see that in 'Sample' description, there is a 'sex' attribute which is set to 'female' for these samples.

Some of these results are discussed in this Science paper : http://www.sciencemag.org/content/318/5849/420.long

ADD REPLYlink written 7.4 years ago by Leonor Palmeira3.7k
5
gravatar for Jeroen Van Goey
7.4 years ago by
Jeroen Van Goey2.3k
Ghent, Belgium
Jeroen Van Goey2.3k wrote:

A quick Google search didn't turn anything up, so I wrote an e-mail to 454 customer support. This is the reply I got:

Dear Jeroen,

To our knowledge, no female human genomes have been completely sequenced using 454 Sequencing technology. A few male human genomes have been sequenced:

The complete genome of an individual by massively parallel DNA sequencing David A. Wheeler et al. (2008) Nature 452: 872-876

Complete Khoisan and Bantu genomes from southern Africa. Schuster SC et al. (2010) Nature 463(7283): 943-7.

Katie Montgomery

International Marketing Manager

454 Life Sciences, a Roche Company

ADD COMMENTlink written 7.4 years ago by Jeroen Van Goey2.3k
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