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Moderator: Biomed

gravatar for Biomed
Biomed ♦ 4.7k
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Bethesda, MD, USA
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10 years, 8 months ago
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Research Fellow, National Human Genome Research Institute

Posts by Biomed

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What would be the expected average coverage of a 384 multiplexed run on a Novaseq S4 flowcell?
... If we ran 384 samples multiplexed on a Novaseq 6000 using S4 chemistry (2x150 reads) using human samples, what would be the expected coverage for each sample? ...
novaseq coverage written 2.0 years ago by Biomed ♦ 4.7k • updated 2.0 years ago by ATpoint ♦ 42k
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Is it possible to multiplex mora than 384 samples on Novaseq 6000 for a very low pass (0.5-10x) WGS?
... Is it possible to multiplex mora than 384 samples on Novaseq 6000 for a very low pass (0.5-10x) WGS? ...
novaseq wgs written 2.0 years ago by Biomed ♦ 4.7k
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Comment: C: Is Clinvar the most comprehensive and reliable source of disease-causing genes a
... The question is about known-to-be disease-causing genes and variants like a nonsense variant in an ACMG 59 gene. I am not interested in genes and variants of unknown significance. I hope this clarifies the question. Thanks for the comment. ...
written 2.4 years ago by Biomed ♦ 4.7k
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Is Clinvar the most comprehensive and reliable source of disease-causing genes and variants?
... I am interested in finding a comprehensive (SNV +CNV) and reliable list of all known disease-causing genes and preferably also variants in those genes. Clinvar comes to mind as an obvious option but is it really the best source out there or should one combine the information found in clinvar with ot ...
clinvar disease-causing genetic-disease omim written 2.4 years ago by Biomed ♦ 4.7k
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Expired Illumina GSA chips
... A clinical lab I collaborate with, offered to give my lab some recently (less than 3-6 months) expired Illumina GSA chips for free. Has anyone used those chips for research (or other purposes) beyond their expiration dates, if so what has been your experience? ...
chip gsa snp written 2.4 years ago by Biomed ♦ 4.7k
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Comment: C: What are the resources to design the most comprehensive clinical SNP chip?
... 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 4.5 years ago by Biomed ♦ 4.7k
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Comment: C: How can design the most comprehensive "clinical" SNP chip?
... Good catch on HGMD version. I edited the question accordingly. ...
written 4.5 years ago by Biomed ♦ 4.7k
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What are the resources to design the most comprehensive clinical SNP chip?
... 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 ...
snp clinical primary care written 4.5 years ago by Biomed ♦ 4.7k
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Comment: C: What is the best way to extract DNA for exome sequencing?
... Could you expand the "produce good results (normally)"? For us the quality of the extraction is naturally of highest priority.  ...
written 5.8 years ago by Biomed ♦ 4.7k
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(Closed) What is the best way to extract DNA for exome sequencing?
... 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 ...
dna extraction written 5.8 years ago by Biomed ♦ 4.7k • updated 5.8 years ago by Devon Ryan ♦ 97k

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