Moderator: Biomed
Biomed ♦ 4.3k
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Research Fellow, National Human Genome Research Institute
Posts by Biomed
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... Thanks for the thoughtful response. The chip in question is designed to be used in a primary care setting. Meaning that it is intended to serve as a diagnostic tool for known disease associated snps (may not be the ultimate tool but a diagnostic tool that can point the lab in the right direction whi ...
written 16 months ago by
Biomed ♦ 4.3k
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... Good catch on HGMD version. I edited the question accordingly. ...
written 17 months ago by
Biomed ♦ 4.3k
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... I would like to design a SNP chip to be used in primary care/clinical setting. I have the ability to determine what markers to have on this custom designed chip. This is not going to be focused on a single disease group/phenotype and is meant to be used as a screening test, risk prediction tool and ...
written 17 months ago by
Biomed ♦ 4.3k
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... Could you expand the "produce good results (normally)"? For us the quality of the extraction is naturally of highest priority.
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written 2.7 years ago by
Biomed ♦ 4.3k
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... A colleague told me that phenol chloroform extraction is not the best and most contemporary way to extract DNA for exome sequencing. One of our sequencing center partners require us to extract DNA using this method. Is phenol chloroform extraction really less desirable and is there a better standard ...
written 2.7 years ago by
Biomed ♦ 4.3k
• updated
2.7 years ago by
Devon Ryan ♦ 71k
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Comment:
C: Conservation At Amino Acid Level
... You are right I am interested in amino acid-protein level conservation as well as base level conservation. Thanks for the answer.
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written 5.3 years ago by
Biomed ♦ 4.3k
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Comment:
C: Conservation At Amino Acid Level
... Hi Sean, yes the idea is to help prioritize variants but the problem arises when the nucleotide is not so well conserved yet there is stronger conservation at the amino acid levels. I suspect the methods that are based on nucleotide conservation will give a slightly different result in those cases.
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written 5.3 years ago by
Biomed ♦ 4.3k
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... We annotate exome variants with conservation status using sources like PhyloP, GERP but these query the nucleotide instead of the amino acid. As the nucleotide may not be conserved among species, but the amino acid can be we would like to annotate our variants with amino acid level conservation. Wha ...
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... Hi,
I would like to functionally validate a -not seen before- 3 bp deletion I found on a 5' UTR of a knoen disease causing gene. I looked at the UCSC browsers tracks for conservation and regulation and it seems like this region is both well conserved and has a lot of regulation signals associated wi ...
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... I couldn't get it to work. Nothing happens when I run the above command with the genbank xml of the human protein.
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written 5.4 years ago by
Biomed ♦ 4.3k
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