Danny Miller, MD, PhD
@danrdanny.bsky.social
CODA. Dad. Interested in genetics, long-read sequencing, and ultramarathon running. Assistant Professor at University of Washington. The command line is my happy place. https://millerlaboratory.com
The first 100 were R9, then we started generating data on both R9 and R10. ~150 total samples are R9, and the rest are R10. Should be about 380 samples online right now, and 500 up by the end of the month.
February 2, 2025 at 1:53 AM
The first 100 were R9, then we started generating data on both R9 and R10. ~150 total samples are R9, and the rest are R10. Should be about 380 samples online right now, and 500 up by the end of the month.
Such a beautiful place but so many contrasts that I will be processing for a long time. Did anything happen while I was gone? 🫠
January 25, 2025 at 11:41 AM
Such a beautiful place but so many contrasts that I will be processing for a long time. Did anything happen while I was gone? 🫠
Really good questions. Used blat/blast to annotate. We do not see variation in the VNTR as it's the same size in all affected individuals and their parents. We don't have a way to check in the controls but I assume it is the same size. We did not look at methylation in the SVAE.
December 23, 2024 at 1:45 PM
Really good questions. Used blat/blast to annotate. We do not see variation in the VNTR as it's the same size in all affected individuals and their parents. We don't have a way to check in the controls but I assume it is the same size. We did not look at methylation in the SVAE.
We were able to easily see the insertion using using LRS. And while you can see it with SRS (split reads, target site dup), it was not detected by prior clinical or research efforts. Another argument for why LRS will be used as a first test in the inpatient and outpatient setting in the near future.
December 23, 2024 at 2:49 AM
We were able to easily see the insertion using using LRS. And while you can see it with SRS (split reads, target site dup), it was not detected by prior clinical or research efforts. Another argument for why LRS will be used as a first test in the inpatient and outpatient setting in the near future.
The amazing thing? Based on analysis of ~80,000 individuals the allele frequency of this insertion would make it the most common pathogenic variant associated with this devastating condition--more common than known pathogenic SNVs or indels.
December 23, 2024 at 2:49 AM
The amazing thing? Based on analysis of ~80,000 individuals the allele frequency of this insertion would make it the most common pathogenic variant associated with this devastating condition--more common than known pathogenic SNVs or indels.
Excellent suggestion--except I can't take part in it. I was fortunate to receive a DP5, which was key to getting a job, having a fast start to my lab, etc. But it excludes me from the early career reviewer program. I am not sure what the reasoning is for this limitation.
November 24, 2024 at 8:44 PM
Excellent suggestion--except I can't take part in it. I was fortunate to receive a DP5, which was key to getting a job, having a fast start to my lab, etc. But it excludes me from the early career reviewer program. I am not sure what the reasoning is for this limitation.