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University of Washington   |   Department of Pediatrics   |   Department of Laboratory Medicine & Pathology

Around 50% of individuals with a suspected genetic disorder remain undiagnosed after a complete clinical evaluation, which often takes years to complete. We believe this burden on patients and families is simply too high. In the Miller Lab, our goals are twofold: to improve the efficiency and effectiveness of genetic testing, and to better understand human genetic disease through the identification and characterization of novel disease-causing variation.


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OUR TEAM

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Danny Miller, MD, PhD

Principal Investigator

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Miranda Galey, MS

Lab Manager

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Pax Reed

Research Scientist

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NEWS & VIEWS

We're sequencing 1000 Genomes samples

We're excited to collaborate with ONT to sequence 500 of the 1000 Genomes samples. If you're interested in working on this project or joining the 1000G ONT Sequencing Consortium, please reach out. This will be a fun dataset to explore! More details on the 1000G ONT consortium site.

Hello, World

Hi folks, we're opening our lab in July 2022 in the Departments of Pediatrics and Laboratory Medicine & Pathology at the University of Washington. We use long-read sequencing on the Oxford Nanopore platform to find the genetic basis for unsolved genetic disorders. If you have interesting unsolved cases, drop us a note. We love collaborating on tricky problems!

Backstory about the T2T project

Danny's contribution to the Telomere-to-Telomere project was highlighted here by the Brotman Baty Institute.

Smith Workshop

We're sequencing cases that will be presented during the Unsolved session at the 2022 David W. Smith Workshop this August. If you're attending the meeting and have an unsolved genetics case, let us know!

Want to work with us?

We have open postdoc, technician, and grad student positions. Send us a message if you're interested in joining our lab, and check out more details in the Positions section below.

Woot!

Danny's targeted long-read sequencing paper was highlighted in AJMG, GenomeWeb, and ClinicalOMICS!


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RESEARCH

Unsolved genetic disorders

We are interested in understanding why 50% of individuals with a suspected genetic disorder remain unsolved after a complete clinical evaluation. Using long-read DNA and RNA seqeuencing we have identified disease-causing variants that are difficult or impossible to resolve using standard clinical testing. We are always happy to collaborate, so reach out if you have a challenging unsolved case.

Clinical applications of long-read sequencing

Standard clinical genetic testing can take years to complete and is diagnostic only 50% of the time. It's a challenging process often referred to as the diagnostic odyssey. We are working to change this paradigm by using long-read sequencing as a single test in the clinical setting. Our efforts extend beyond the genetics clinic into spaces such as cancer biology and infectious disease.

Structural variation

A big challenge when analyzing long-read sequencing data is interperting all of the structural variants that are found. In collaboration with Oxford Nanopore, we are seqeuencing a large number of 1000G Project samples to understand what normal human structural variation looks like and to build a database of controls for everyone to use. Check out the 1000G ONT Consortium site for more information.
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Methylation

Because long-read seqeuncing data contain signal for both the DNA sequence and methylation status, we can identify differences in methylation in unsolved cases and healthy controls. We are building tools to identify differences in methylation genome-wide and understand what methylation looks like in a large number of healthy controls.

Genome assembly and analysis

This is how we got into Nanopore sequencing! We are always interested in sequencing and assembling genomes from all critters big and small. We're part of a large group working on sequencing all of the species in the Drosophila species group, and we're interested in all types of genome assembly projects.

Long-read RNA sequencing

Sequencing of native RNA is just cool. We do RNA seqeuncing of our unsolved clinical cases and are interested in using long reads to identify tissue-specific isoforms and expression. Also, what are all those RNA modifications doing? Sequencing of native RNA from different tissues is going to be interesting.




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SEQUENCING SERVICES

We provide long-read sequencing on the Oxford Nanopore Technologies (ONT) platform to researchers at UW, SCH, SCRI, FHRC, external institutions, and private companies. Services include whole-genome sequencing, targeted sequencing, RNA sequencing, variant calling and phasing, and methylation calling. If you are interested in long-read sequencing services, please contact us to discuss options and costs.



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PUBLICATIONS

2022
2021

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POSITIONS

We're a new lab, so we have several positions to fill. Although our lab is heavily computational, benchwork is also necessary. In the Miller Lab, you'll be joining a friendly, hardworking group of people with diverse backgrounds. Danny (a runner, and a former programmer and financial analyst) is a Pediatrician and Medical Geneticist with extensive experience analyzing long-read ONT data. If you're looking for a fun, collaborative, and productive work environment, we'd love to hear from you! Please email Danny at dm1@uw.edu with any inquiries.


Postdoctoral Researchers

We're currently recruiting for postdoc positions. Ideal candidates should have programming knowledge as well as wet lab experience and an interest in long-read sequencing.


Graduate students

Graduate students who want to learn more about long-read DNA or RNA sequencing, structural variation, genome assembly, or developing long-read-sequencing-based clinical tests are encouraged to rotate in our lab.


Undergraduates

We welcome undergraduate students in our lab. Please reach out if you're interested!



CONTACT INFORMATION

TWITTER

@danrdanny