Lightnews — Scholar-powered news

Reposted by Danny Miller, MD, PhD

EichlerLab @eichlerlab.bsky.social · 13d

Thank you Dr. Danny Miller @danrdanny.bsky.social for hosting, and fantastic job Dr. Mastrorosa @fkma.bsky.social!
@uwgenome.bsky.social

brotmanbaty.org/news/long-re...

2 1

Reposted by Danny Miller, MD, PhD

Scary Lannert @klannert.bsky.social · 21d

Literal case in point: we worked with @danrdanny.bsky.social (and transfusion medicine teams across two organizations) to use long-read WGS to solve the case of an untransfusable patient.

#hemesky #medsky

doi.org/10.1111/trf....

1 2

Reposted by Danny Miller, MD, PhD

Brotman Baty Institute @brotmanbaty.bsky.social · Apr 21

One never knows the power and persuasion of elementary school teachers. Jonas ("Gus") Gustafson's fifth grade instructor 'allowed me to establish a life-long knack and passion for STEM.’
@uwmedicine.bsky.social
@danrdanny.bsky.social
brotmanbaty.org/news/promisi...

1 3

Danny Miller, MD, PhD @danrdanny.bsky.social · Apr 11

Interested in SV calling from LRS data but overwhelmed by the 25,000 variants you're sorting through? Check out needLR! Gus just updated it today to include SV calls from 450 1000 Genomes samples (900 haplotypes), vcf output, and much more. github.com/jgust1/needLR

GitHub - jgust1/needLR: A structural variant filtering and prioritization tool for long-read sequencing data

A structural variant filtering and prioritization tool for long-read sequencing data - jgust1/needLR

github.com

3 9

Danny Miller, MD, PhD @danrdanny.bsky.social · Feb 21

Has anyone had luck submitting a paper without submitting all author names on the paper? I am tired of spending an hour or more adding people to a journal submission site just to have the paper editorially rejected the next day... I know some journals have forms you can upload, but some do not.

1 1 1

Danny Miller, MD, PhD @danrdanny.bsky.social · Feb 2

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.

1 1

Danny Miller, MD, PhD @danrdanny.bsky.social · Jan 31

I am very sad to share that Scott Hawley passed away this morning. Scott was my graduate advisor and no other person had such a positive impact on my life. I will miss him dearly.

HunterLab.bsky.social @hunterlab.bsky.social · Jan 31

Sadly, our colleague and friend Scott Hawley passed away this morning. He was an irreplaceable presence and force for good in the meiosis an Drosophila communities and will be sorely missed.

1 3 21

Danny Miller, MD, PhD @danrdanny.bsky.social · Jan 25

Such a beautiful place but so many contrasts that I will be processing for a long time. Did anything happen while I was gone? 🫠

1

Danny Miller, MD, PhD @danrdanny.bsky.social · Jan 25

I never knew what it meant to go on a life changing trip until now. I just spent an amazing week in Nairobi teaching genetics to some truly wonderful physicians and seeing kids with suspected genetic conditions. It felt all the more special to have been there on Martin Luther King Jr. Day.

1 2 8

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 23

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.

1 2

Reposted by Danny Miller, MD, PhD

Veera Rajagopal @doctorveera.bsky.social · Dec 23

A homozygous SVA retrotransposon insertion is discovered to be likely the most common mutation in ASPA (encodes aspartoacylase) underlying Canavan disease. 1/

Gonzalez, Bell, et al. medRxiv
www.medrxiv.org/content/10.1...

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease

Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...

www.medrxiv.org

1 7 21

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 23

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.

1

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 23

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.

1

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 23

Been looking forward to sharing this for a long time! Great collaboration with folks from across the world in which we identified a SVA_E insertion missed by standard clinical testing in individuals with Canavan disease, an early onset neurodegenerative disease.

www.medrxiv.org/content/10.1...

A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease

Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...

www.medrxiv.org

2 17 38

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 11

Fine, this job isn’t all that terrible…

11

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 8

Added!

1

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 8

Day 4 and 5 of computational genomics at CSH: students giving their project pitches and the view from my grant writing nest.

2 8

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 7

Your feel-good video for today. Dick Van Dyke at 99. www.youtube.com/watch?v=o4Ol...

Coldplay - ALL MY LOVE (Official Video) (Directors' Cut)

YouTube video by Coldplay

www.youtube.com

3

Danny Miller, MD, PhD @danrdanny.bsky.social · Dec 5

Day 2 of Computational Genomics at Cold Spring Harbor during the intro to UNIX session. 24 great students, 5 amazing TAs, fantastic lectures, and a few instructors who mostly complain about the coffee.

1 9

Reposted by Danny Miller, MD, PhD

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Dec 3

Biology of Genomes 2025 is coming up:
- meeting dates: May 6 - 10, 2025
- abstract deadline: Feb 14, 2025
We hope to see you there for another great meeting with a fantastic speaker lineup!

meetings.cshl.edu/meetings.asp...

Biology of Genomes

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

1 34 67

Reposted by Danny Miller, MD, PhD

Eric Topol @erictopol.bsky.social · Nov 24

A vertical takeoff of life science with #AI LLLMs.
Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks!
Unprecedented progress, reviewed in the new Ground Truths
erictopol.substack.com/p/learning-t...

Covers of Science and Nature journals in the past 2 weeks denoting remarkable progress of life science with A.I. tools

15 86 350

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 24

Amazing story

Jeremy Berg @jeremymberg.bsky.social · Nov 24

A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.

homer simpson from the simpsons is holding a cup in front of a picture

ALT: homer simpson from the simpsons is holding a cup in front of a picture

media.tenor.com

1 2

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 24

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.

1 1

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 24

Good read about how the NIH functions. After 2 years as a new investigator I only now feel like I am starting to understand the process. This is one of the challenges for new investigators: why is the learning curve so steep?

Sasha Gusev @sashagusevposts.bsky.social · Nov 24

I wrote about the National Institutes of Health and the various serious and unserious proposals for NIH reform that have been floating around. It is important to understand how this agency actually functions and point criticism at the right problems. A short 🧵:

Distinguishing real from invented problems with the NIH

How does the NIH work and where does it work well?

open.substack.com

1 3 8

Danny Miller, MD, PhD @danrdanny.bsky.social · Nov 24

Added!

1