Dashnow Lab

Projects

1000 Genomes Project Long Read Sequencing Consortium
1000 Genomes Project Long Read Sequencing Consortium Re-sequencing >3,000 samples from the 1000 Genomes Project with long-read sequencing

The Dashnow Lab is leading the tandem repeat working group within the 1kGP-LRSC. The goal of the Consortium is to identify a broader spectrum of genomic variation than is possible using short-read sequencing, including SVs, repeat expansions and methylation patterns.

Consortium Paper (first 100)
Outliers
Long-read TR genotyper benchmark
resource
Discovering genetic determinants of de novo tandem repeat mutations
Discovering genetic determinants of de novo tandem repeat mutations Using long-read sequencing four-generation, 28-member family (CEPH 1463)

We employed multiple short and long-read sequencing technologies to generate phased assemblies and characterize both inherited and de novo variation.

Mutation Rates Paper
De novo TR Paper
TRGT-denovo Paper
Benchmark Paper
resource research de novo mutations tandem repeats
Understanding somatic mosaicism at tandem repeat loci
Understanding somatic mosaicism at tandem repeat loci
FMR1 brain mosaicism paper
Review
research mosaicism STRs
STRchive
STRchive Short Tandem Repeat Archive (pronouced "S-T-archive")

A database of STRs associated with disease in humans.

Paper
resource database
criTRia
criTRia A Classification System and Evidence Criteria for Tandem Repeat Locus-Disease Relationships

A framework for systematically classifying and curating the strength of evidence linking tandem repeat loci to disease.

research classification tandem repeats
ATaRVa
ATaRVa A technology-agnostic tandem repeat genotyper for long read sequencing data (led by the Sowpati Lab)
Paper
software
TRGT
TRGT Tandem Repeat Genotyping Tool (pronounced "target")

TRGT genotypes tandem repeats from PacBio HiFi long read data and visualizes them with TRVZ.

software publication
STRling
STRling A computational method to call short tandem repeat expansions at known and novel loci (pronounced "sterling").

STRling can detect novel expansions where there is no STR in the reference genome, or an alternate motif.

Paper
software publication
STRretch
STRretch A computational method to detecting short tandem repeat expansions from short-read sequencing data.

STRling can detect novel expansions where there is no STR in the reference genome, or an alternate motif.

Paper
software publication