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Reposted by Harriet Dashnow

CU Department of Biomedical Informatics @cubiomedinfo.bsky.social · 13d

🧬 Ever wonder how fast your DNA changes from one generation to the next? @hdashnow.bsky.social and her team explored how quickly the human genome mutates by analyzing DNA from four generations of a single family. Dive into this video from @nature.com ⤵️

How quickly do humans mutate? Four generations help answer the question

YouTube video by nature video

youtu.be

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Reposted by Harriet Dashnow

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Mar 26

A new article from Laurel Hiatt and @hdashnow.bsky.social describing STRchive is now available at Genome Medicine. genomemedicine.biomedcentral.com/articles/10....
Check out the database resource, as STRchive "streamlines TR variant interpretation at disease-associated loci."
strchive.org

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

genomemedicine.biomedcentral.com

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Harriet Dashnow @hdashnow.bsky.social · Mar 26

A huge congratulations to Laurel Hiatt on their first first-author publication from their PhD!! And thank you to all our wonderful coauthors for making this happen.

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Harriet Dashnow @hdashnow.bsky.social · Mar 26

The strchive.org paper is out!!
The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases.
🖥️ 🧬
link.springer.com/article/10.1...

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...

link.springer.com

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Harriet Dashnow @hdashnow.bsky.social · Dec 12

Credit to Laurel Hiatt for driving this, @vincerubinetti.bsky.social for beautiful new website design, and Akshay Avvaru for data vis.
Thanks to the continued support of Ben Weisburd @egor-dolzhenko.bsky.social @heidirehm.bsky.social @aaronquinlan.bsky.social.
It's a pleasure working with you all!

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Harriet Dashnow @hdashnow.bsky.social · Dec 12

I am excited to present STRchive.org v2!

A resource for tandem repeats associated with Mendelian disease. We have resigned the website, added new loci, streamlined our data for easier reuse, added more detailed citations, presented population frequency data and more!

STRchive

An archive of STRs associated with human diseases

STRchive.org

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Reposted by Harriet Dashnow

Tamar Gur MD PhD @tamargurmdphd.bsky.social · Nov 14

I’m launching a small but mighty starter pack for Academic Research Moms- those of us navigating the travails of parenthood and academic careers- and those who support them! Aka 💪 ARMy bsky.app/profile/did:...

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Harriet Dashnow @hdashnow.bsky.social · Nov 15

Thanks for doing this, @tamargurmdphd.bsky.social ! Following

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Harriet Dashnow @hdashnow.bsky.social · Nov 7

Enjoying all the tandem repeat fun at #ASHG24?
The Dashnow lab is hiring software developer/data analyst roles. Apply by Nov 13 for best consideration
dashnowlab.org 🖥️ 🧬

Dashnow Lab

This is the website for the Dashnow Lab. We do computational genomics in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus.

dashnowlab.org

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Harriet Dashnow @hdashnow.bsky.social · Nov 4

Very cool new work by @htanudisastro.bsky.social on the contribution of tandem repeat variants to gene expression in single cells! Check it out.

Hope Tanudisastro @htanudisastro.bsky.social · Nov 4

📢 New preprint alert: Excited to share our deep dive into the role of tandem repeats (TRs) in single-cell gene expression across the immune system, using WGS and scRNA-seq data from 1,790 individuals and over 5 million blood cells! 🧬
🧵👇 #repeats #SingleCell 1/9

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Harriet Dashnow @hdashnow.bsky.social · Apr 11

I am currently recruiting a computational postdoc in my lab at CU dashnowlab.org
The candidate would develop and use computational genomics methods to understand the genetic underpinnings of rare diseases and increase diagnoses.
Pay starts at $70k for recent PhD grads

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Reposted by Harriet Dashnow

Hope Tanudisastro @htanudisastro.bsky.social · Feb 16

Our review article, with Ira Deveson, @hdashnow.bsky.social, @dgmacarthur.bsky.social, on sequencing & characterising short tandem repeats is out in @NatRevGen! We delve into short read & long read STR genotyping tools and applications in rare disease & population genetics 🧬go.nature.com/48pWZix

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

Algorithmically, I'd say some error correction may be needed, especially for long alleles and high GC repeats. It uses local SNVs, so that might be more challenging and result in read phasing errors.
This is a key obstacle: github.com/PacificBiosc... (see paragraph 3)

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

Unfortunately, no. It's tuned to HiFi read specs.

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

Huge congratulations to Egor Dolzhenko, Adam English, and everyone else involved. @aaronquinlan.bsky.social @meberle.bsky.social @sedlazeck.bsky.social @pacbio.bsky.social

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

TRGT also reports methylation. Here’s a nice analysis of the FMR1 Fragile X locus.

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

TRGT reports full sequence alleles, including repeat interruptions and motif diversity. We found some fascinating motif heterogeneity at the RFC1 CANVAS locus in HPRC.

a, An HMM representing the population structure of the RFC1 TR derived from a priori known motifs. b, A TRVZ plot depicting both alleles of the RFC1 repeat in the HG04228 sample. c, A heat map depicting the span of each motif (columns) on each allele (rows); each cluster of alleles is associated with the color of its dominant motif. d, An example allele from each cluster. e, Lengths of alleles belonging to each cluster.

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Harriet Dashnow @hdashnow.bsky.social · Jan 2

Our paper was published today in Nature Biotech!
www.nature.com/articles/s41...
Tandem Repeat Genotyping Tool (TRGT) is a new method for genotyping tandem repeats in PacBio HiFi long reads. We used some nice algorithmic strategies to improve genotyping accuracy.
🖥️ 🧬

Characterization and visualization of tandem repeats at genome scale - Nature Biotechnology

A set of tools maps tandem repeats across complete genomes.

www.nature.com

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Reposted by Harriet Dashnow

Chenxin Li, PhD @chenxinli2.bsky.social · Nov 20

My "Friends don't let friends make bad graphs" repository has reached 1000+ stars on GitHub! I can't believe it! Thanks everyone for the interest and support. Gonna add this to my CV. 😂😂😂

github.com/cxli233/Frie...

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Harriet Dashnow @hdashnow.bsky.social · Nov 2

I'm looking for talented postdocs and staff scientists/software developers to join my lab at
medschool.cuanschutz.edu/dbmi
If you're fascinated by #RareDisease genomics, #STRs and computational methods, please get in touch! I'm at #ASHG2023 this week, and happy to chat. #hiring