User: lamteva.vera

gravatar for lamteva.vera
lamteva.vera120
Reputation:
120
Status:
Trusted
Location:
Ukraine, Kyiv
Last seen:
4 months, 4 weeks ago
Joined:
1 year, 7 months ago
Email:
l***********@gmail.com

Posts by lamteva.vera

<prev • 41 results • page 1 of 5 • next >
0
votes
2
answers
454
views
2
answers
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 months ago by lamteva.vera120
3
votes
2
answers
454
views
2
answers
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 months ago by lamteva.vera120 • updated 7 months ago by WouterDeCoster30k
0
votes
3
answers
4.4k
views
3
answers
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 8 months ago by lamteva.vera120
0
votes
1
answer
304
views
1
answers
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 8 months ago by lamteva.vera120
0
votes
1
answer
304
views
1
answer
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 8 months ago by lamteva.vera120 • updated 8 months ago by Kevin Blighe24k
1
vote
4
answers
750
views
4
answers
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 8 months ago by lamteva.vera120
1
vote
4
answers
750
views
4
answers
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 8 months ago by lamteva.vera120
29
votes
4
answers
750
views
12 follow
4
answers
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 8 months ago by lamteva.vera120 • updated 8 months ago by tjduncan170
1
vote
2
answers
959
views
2
answers
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 8 months ago by lamteva.vera120
2
votes
2
answers
959
views
2
answers
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 8 months ago by lamteva.vera120

Latest awards to lamteva.vera

Supporter 9 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1535 users visited in the last hour