Harriet Dashnow

YouTube video by nature video How quickly do humans mutate? Four generations help answer the question

🧬 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 ⤵️

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...

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

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.

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...

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...

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!

STRchive An archive of STRs associated with human diseases

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!

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:...

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

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.

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 🖥️ 🧬

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

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

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

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)

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

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

a, Distribution of FMR1 allele sizes in 100 HPRC samples. b,c, TRVZ plots of FMR1 repeat in the HG04184 (b) and HG00438 (c) samples, respectively, showing premutation alleles. d, TRVZ plot of FMR1 repeat in the HG01099 male sample displaying CpG methylation. e, Distribution of median methylation levels for HG01099 reads spanning FMR1 repeat. f, Distributions of median methylation levels for FMR1 reads across all male samples. g, TRVZ plot of FMR1 repeat in HG03831 female sample displaying CpG methylation. h, Distribution of median methylation levels for HG03831 reads spanning FMR1 repeat. i, Distributions of median methylation levels for FMR1 reads across all female samples. j, Premutation repeat allele from a prefrontal cortex sample from a female donor (short allele not shown). k, Premutation repeat allele from a prefrontal cortex sample from a male donor. l, Fully expanded repeat allele from a prefrontal cortex sample from a male donor. m, Methylation profile of prefrontal cortex sa

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

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.

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

Characterization and visualization of tandem repeats at genome scale - Nature Biotechnology A set of tools maps tandem repeats across complete genomes.

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.
🖥️ 🧬

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...

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

We're hiring a new faculty member in Clinical Informatics! Read more and apply at the link.

cu.taleo.net/careersectio...

Thanks! I also found this handy list: docs.google.com/spreadsheets...

I had NO idea this is a thing - great tip!!

Could you please add me to What's Science for 🖥️ 🧬? @danirabaiotti.bsky.social

Is this some emoji #hashtag magic?

It is today, and with my first post, that I discover there is no edit button. This is a perfect warning to all potential followers: there will be many typoos!

Just launched:

STRchive
(Short Tandem Repeat Archive)

A database of STRs associated with disease in humans.
harrietdashnow.com/STRchive/

This is inactive development. Looking for feedback and collaborators!