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Old 08-27-2012, 03:46 PM   #1
nilshomer
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Default Who is doing clinical sequencing here?

Hello all, it would be fun to see who at seqanswers.com is doing clinical sequencing. Perhaps we can also compile a list of companies offering ClinSeq or Clinomics, with possibly entries in the wiki.

Feel free to post here announcing your involvement, or post a company that is offering or planning to offer these services or products, though keep the advertising to a minimum.
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Old 08-27-2012, 04:38 PM   #2
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I do.
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Old 08-28-2012, 04:53 AM   #3
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We need to define "clinical sequencing" with more precision.

I am sure many (most?) of us sequence human samples that come from clinic (or otherwise) for research purposes (the results can't officially become part of patient medical record since sequencing happens in a non-CLIA certified lab).
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Old 08-28-2012, 07:08 AM   #4
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What does it mean by clinical sequencing? Does it mean the sequencing step must be CLIA?
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Old 08-28-2012, 10:30 AM   #5
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We are doing clinical sequencing projects, but we are not CLIA yet.
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Old 08-28-2012, 10:45 AM   #6
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Are there any academic centers that have received CLIA certification for NGS?
A quick google search appears to show only commercial providers.
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Old 08-28-2012, 10:46 AM   #7
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Yes there are. For example BCM does this in Houston.
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Old 09-13-2012, 12:25 PM   #8
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We offer CLIA NGS for human exome projects at EdgeBio. If you want more information please contact us at [email protected]
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Old 09-25-2012, 10:36 PM   #9
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Quote:
Originally Posted by EdgeBio View Post
We offer CLIA NGS for human exome projects at EdgeBio. If you want more information please contact us at [email protected]
Great! How many x differences in pricing between CLIA and non-CLIA?
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Old 09-28-2012, 06:44 AM   #10
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Great! How many x differences in pricing between CLIA and non-CLIA?
I sent you a PM.
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Old 09-28-2012, 07:17 AM   #11
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Default LMM at partners healthcare

We offer clinical diagnostic services through next-gen sequencing for a handful of diseases. We do the sequencing in our own CLIA certified lab. Visit us at http://pcpgm.partners.org/lmm
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Old 09-28-2012, 11:49 AM   #12
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Pathogenius offers molecular microbiology sequencing services. They are CLIA and CAP certified. http://www.pathogenius.com/
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Old 11-05-2012, 11:16 PM   #13
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Illumina clinical lab was the first to offer CLIA genomes
We were the first CLIA lab to do WGS clinical interpretation starting almost 3 years ago.
Most national clinical genetics labs use NGS for panels and their are multiple labs in the US offering CLIA certified exomes.
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Old 07-12-2013, 01:15 AM   #14
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We are doing clinical sequencing in a CPA accredited lab NHS lab in the UK - our cancer panel is live and we will shortly be introducing other disease focused panels. We also have a big grant to introduce whole genome and exome sequencing into the NHS....exciting times!

http://www.oxford-translational-mole...ostics.org.uk/
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Old 07-20-2013, 11:45 AM   #15
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Hi
I want to do WGS of 2 samples of human. I have 2 sequencer Hiseq2000 in main facility. I have experience of Analysing of Illumina data. But the problem is that I am not sure about the following:
1. replication / replicates
2. depth coverage
3. best stretegies
4. Kits / reagents

May I ask this forum, if you can give me guideline on the sequencing for Whole Genome. Since this field is developing very fast, I dont want to any mistake and asking here. I have funding and sequencer (freely available), just need to buy kits and reagents. Please tell me how can I design best for WGS.
Thank you, (my English is not good so please ignore English mistakes)
jp.

Quote:
Originally Posted by gnomemics View Post
We are doing clinical sequencing in a CPA accredited lab NHS lab in the UK - our cancer panel is live and we will shortly be introducing other disease focused panels. We also have a big grant to introduce whole genome and exome sequencing into the NHS....exciting times!

http://www.oxford-translational-mole...ostics.org.uk/
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Old 07-20-2013, 02:10 PM   #16
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Quote:
Originally Posted by jp. View Post
Hi
I want to do WGS of 2 samples of human. I have 2 sequencer Hiseq2000 in main facility. I have experience of Analysing of Illumina data. But the problem is that I am not sure about the following:
1. replication / replicates
2. depth coverage
3. best stretegies
4. Kits / reagents

May I ask this forum, if you can give me guideline on the sequencing for Whole Genome. Since this field is developing very fast, I dont want to any mistake and asking here. I have funding and sequencer (freely available), just need to buy kits and reagents. Please tell me how can I design best for WGS.
Thank you, (my English is not good so please ignore English mistakes)
jp.

This calculator can help with the coverage calculations: http://support.illumina.com/download...alculator.ilmn
and a tech note to go with it: http://res.illumina.com/documents/pr...alculation.pdf
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Old 07-21-2013, 01:57 AM   #17
jp.
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I thank you for providing kind valuable info. My samples are from human origin Paired-End-HiSeq2000 and I have to pay for reagents cost only because HiSeq2000 is just free to use, in my case, budget is not a problem.
Therefore, I like to ask few more question;
1. How many replicates are required for whole genome sequencing ?
I am thinking to go for 3 biological replicates + 3 technical replicates per sample i.e. 1 samples = (1 x 3) 3 = 9. Is it enough ? or I should increase the replicates ?
2. What is the best depth coverage, 30X or more ?
3. How can I increase depth coverage ?
4. What is best library size, 150 or 250 or higher?
5. Can I use single-cell DNA/RNA on Paired-End-HiSeq2000 ?
Thank you very much in advance
(I am sorry for asking very preliminary question here but nobody answers my question, every body want something back to give me the answers or just said, figure it out. There is nobody in my location to help/guide a beginner).
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Old 07-21-2013, 06:27 AM   #18
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Quote:
Originally Posted by jp. View Post
I thank you for providing kind valuable info. My samples are from human origin Paired-End-HiSeq2000 and I have to pay for reagents cost only because HiSeq2000 is just free to use, in my case, budget is not a problem.
Therefore, I like to ask few more question;
1. How many replicates are required for whole genome sequencing ?
I am thinking to go for 3 biological replicates + 3 technical replicates per sample i.e. 1 samples = (1 x 3) 3 = 9. Is it enough ? or I should increase the replicates ?
2. What is the best depth coverage, 30X or more ?
3. How can I increase depth coverage ?
4. What is best library size, 150 or 250 or higher?
5. Can I use single-cell DNA/RNA on Paired-End-HiSeq2000 ?
Thank you very much in advance
(I am sorry for asking very preliminary question here but nobody answers my question, every body want something back to give me the answers or just said, figure it out. There is nobody in my location to help/guide a beginner).
You need to describe your experiment more fully to get valid answers. Different coverage is required for different applications. If you're trying to call SNPs as either heterozygous or homozygous, you need much less coverage than if you are trying to find mutations present at a frequency of say 5% in a tumor sample. Read length depends on your application too. For example, if you're calling mutations then all else being the same longer reads may be better as they will be easier to align, assuming the quality doesn't tail off too much at the ends. However, if you're doing expression analysis where it is the number of reads that matters moreso than the specific coverage of any given base, longer reads won't help as much (although they may help if you're looking for different isoforms). These might be the reasons people want you to give "something back" to get the answers.
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Old 07-24-2013, 07:27 AM   #19
jp.
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Thank you so much for your valuable info. I have studies a bit and wish to ask few more things.
I wish to sequence whole genome to study SNPs, mutations. I will also use for expression study. I have to sequence transcriptom, So I will do RNA-seq for expression and mutation. I also want to compare the expression data from RNA-seq with Whole Genome Seq. I am thinking to compare this whole genome with hg19 and then compare RNA-seq with hg19 and my whole genome seq. Overall, I will do complete analysis. I also want to build my own reference whole genome which I will use as a hg19 and vice versa.
1. Do I have to go for two different time sequencing of whole genome with normal coverage and longer and shorter reads ?
2. I wonder how hg19 is built, the same way I want to built my own. Is it built by sanger.

Expecting kind reply.
Thank you.


Quote:
Originally Posted by Heisman View Post
You need to describe your experiment more fully to get valid answers. Different coverage is required for different applications. If you're trying to call SNPs as either heterozygous or homozygous, you need ......
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Old 07-27-2013, 11:53 PM   #20
jp.
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Thank you Heisman
Finally, I am going with 500 reads with >30X WGS. Is there any suggestion ?



Quote:
Originally Posted by Heisman View Post
You need to describe your experiment more fully to get valid answers. Different coverage is required for different applications. If you're trying to call SNPs as either heterozygous or homozygous, you need much less coverage than if you are trying to find mutations present at a frequency of say 5% in a tumor sample. Read length depends on your application too. For example, if you're calling mutations then all else being the same longer reads may be better as they will be easier to align, assuming the quality doesn't tail off too much at the ends. However, if you're doing expression analysis where it is the number of reads that matters moreso than the specific coverage of any given base, longer reads won't help as much (although they may help if you're looking for different isoforms). These might be the reasons people want you to give "something back" to get the answers.
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