User: lamteva.vera

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lamteva.vera160
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Ukraine, Kyiv
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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 2.0 years ago by lamteva.vera160
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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 2.0 years ago by lamteva.vera160 • updated 2.0 years ago by WouterDeCoster42k
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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 2.1 years ago by lamteva.vera160
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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 2.1 years ago by lamteva.vera160
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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 2.1 years ago by lamteva.vera160 • updated 2.1 years ago by Kevin Blighe52k
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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 2.1 years ago by lamteva.vera160
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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 2.1 years ago by lamteva.vera160
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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 2.1 years ago by lamteva.vera160 • updated 2.1 years ago by tjduncan250
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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 2.1 years ago by lamteva.vera160
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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 2.1 years ago by lamteva.vera160

Latest awards to lamteva.vera

Popular Question 3 months ago, created a question with more than 1,000 views. For Is the impact of a frameshift mutation restricted to the exon in which it occurs?
Appreciated 21 months ago, created a post with more than 5 votes. For BQSR: when it is applicable?
Popular Question 21 months ago, created a question with more than 1,000 views. For Is the impact of a frameshift mutation restricted to the exon in which it occurs?
Popular Question 21 months ago, created a question with more than 1,000 views. For Amplicon sequencing: how to handle adapters and primers?
Popular Question 21 months ago, created a question with more than 1,000 views. For Sequence length distribution after adapter trimming
Popular Question 21 months ago, created a question with more than 1,000 views. For Soft-clipping primer sequences in targeted sequencing: approaches and tools
Popular Question 21 months ago, created a question with more than 1,000 views. For How long does it take to build a pipeline?
Popular Question 21 months ago, created a question with more than 1,000 views. For How to handle off-target regions in amplicon panel analysis?
Popular Question 21 months ago, created a question with more than 1,000 views. For Sanger sequencing is no longer the gold standard?
Popular Question 21 months ago, created a question with more than 1,000 views. For BQSR: when it is applicable?
Student 21 months ago, asked a question with at least 3 up-votes. For BQSR: when it is applicable?
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