User: lamteva.vera

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lamteva.vera120
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Posts by lamteva.vera

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Is the impact of a frameshift mutation restricted to the exon in which it occurs
... An interesting example of the consequences of frameshift mutation: "This duplication of one nucleotide in BRCA2 is denoted c.9253dupA at the cDNA level and p.Thr3085AsnfsX26 (T3085NfsX26) at the protein level. The normal sequence, with the bases that are duplicated in braces, is GAAAAAA[A]CAGG. The ...
written 7 weeks ago by lamteva.vera120
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Is the impact of a frameshift mutation restricted to the exon in which it occurs?
... Is the impact of a frameshift mutation restricted to spoiling the exon in which it occurs but not the intronic sequences or next exones? ...
frameshift mutation written 7 weeks ago by lamteva.vera120 • updated 7 weeks ago by WouterDeCoster24k
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Comment: C: dbSNP not using hg19?
... There is no hg20 assembly, you've messed it with hg38. https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/ ...
written 9 weeks ago by lamteva.vera120
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Comment: C: Should the carrier screening test be restricted to a list of clinically proven p
... ACMG [recommends][1] confirmation testing for all NGS-reported variants, so to keep it right, Sanger confirmation is inevitable: "FP rates for most NGS platforms in current use are appreciable, and therefore it is recommended that all disease-focused and/or diagnostic testing include confirmation ...
written 10 weeks ago by lamteva.vera120
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Should the carrier screening test be restricted to a list of clinically proven pathogenic variants?
... Our lab is going to offer a targeted gene panel as a preconception screening test for couples. We will not access and report variants classified as "benign", "likely benign" and "of unknown significance". As for "pathogenic" and "likely pathogenic" variants, after variant classification we will ...
carrier screening forum clinical report ngs written 10 weeks ago by lamteva.vera120 • updated 10 weeks ago by Kevin Blighe11k
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Answer: A: Sanger sequencing is no longer the gold standard?
... To everybody interested in the topic: have a look at [this][1] article. [1]: https://www.ambrygen.com/assets/pdf/sanger/sanger_confirmation_paper.pdf ...
written 10 weeks ago by lamteva.vera120
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Comment: C: Sanger sequencing is no longer the gold standard?
... Thanks for the reply, Kevin! The conception of "downsampling a single sample and recalling variants on the subsamples (and then finding consensus variants)" is new to me, could you please provide some details? Update: ah, I see now, this is some unique part of your pipeline. ...
written 10 weeks ago by lamteva.vera120
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Forum: Sanger sequencing is no longer the gold standard?
... > Sanger sequencing is no longer the gold standard, ... because > there is potential for allele dropout due to polymorphic positions > under primers or unknown heterozygous deletions. When this happens, > the sequencing may either miss variants or may erroneously assign > homozygosity ...
sanger ngs verification forum written 10 weeks ago by lamteva.vera120 • updated 10 weeks ago by tjduncan100
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Comment: C: BQSR: when it is applicable?
... Thanks for taking time to explain! 1. Based on your explanation and the [post][1]: Is it an oversimplification and misunderstanding that BQSR automatically assigns poor quality to the (presumably true) variants that are absent in dbSNP (thus potentially excluding them from further consideration)? ...
written 11 weeks ago by lamteva.vera120
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Comment: C: BQSR: when it is applicable?
... Dear John, could you (or someone else reading this thread) please explain in more detail: how does the sequencer's *error rate* linked to *SNP rate* based on dbSNP and how these numbers are used to predict the applicabitily of BQSR? ...
written 11 weeks ago by lamteva.vera120

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