November 29, 2022  |  Human genetics research

Transposable element-mediated rearrangements are prevalent in human genomes

Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.

November 2, 2022  |  Pharmacogenomics

Design and performance of a long-read sequencing panel for pharmacogenomics

Pharmacogenomics (PGx)-guided drug treatment is one of the cornerstones of personalized medicine. However, the genes involved in drug response are highly complex and known to carry many (rare) variants. Current technologies (short-read sequencing and SNP panels) are limited in their ability to resolve these genes and characterize all variants. Moreover, these technologies cannot always phase variants to their allele of origin. Recent advance in long-read sequencing technologies have shown promise in resolving these problems. Here we present a long-read sequencing panel-based approach for PGx using PacBio HiFi sequencing.

July 30, 2015  |  

Clinical NGS 

PacBio CSO Jonas Korlach discusses the implications for SMRT Sequencing in clinical research.

July 9, 2015  |  

SMALR Bacterial Epigenetics

Researchers have reported an important advance for using SMRT sequencing for epigenetic studies with a new approach capable of probing epigenetic heterogeneity in a population of seemingly identical bacteria.

June 29, 2015  |  

Human Genome Sequenced without Cloning Steps

A collaboration of scientists led by researchers from Icahn School of Medicine at Mt. Sinai has created a comprehensive analysis of a diploid human genome using two complementary single DNA molecule methods for sequencing and genome mapping, and without the need for any DNA amplification techniques.

April 20, 2015  |  

Tapping the Yeast Genome

Cover Story – Researchers are bringing advanced technologies like SMRT Sequencing to improve the ancient art of beer brewing.

March 3, 2015  |  

PacBio at AGBT

Pacific Biosciences held a star-studded workshop to show off the feats that can be accomplished with its SMRT (Single Molecule, Real-Time) sequencers, the instruments of choice for recovering long-range structural information on the genome.

March 1, 2015  |  

When Whole Genome Sequencing Doesn’t Give Us the Whole Genome

As its throughput and average read length have continued to increase, customers have been using the technology for larger and larger genomes. Now, a number of customers are using the technology to de novo sequence whole human genomes, according to presentations at last week’s AGBT meeting.

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