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Tuesday, April 21, 2020

The tech for the next decade: promises and challenges in genome biology.

The 19th Annual Advances in Genome Biology and Technology (AGBT) meeting came back to Marco Island, Florida, and was held in the renovated venue from 27 February to 2 March 2019. The meeting showed a variety of new technology, both in wet lab and in bioinformatics. This year’s themes included single-cell technology and applications, spatially resolved gene expression measurements, new sequencing platforms, genome assembly and variation, and long and linked reads.

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Monday, March 30, 2020

AGBT Presentation: Single cell isoform sequencing (scIso-Seq) identifies novel full-length mRNAs and cell type-specific expression

In this AGBT presentation from AGBT 2019, Jason Underwood, shares information about single-cell isoform sequencing (scIso-Seq), focusing on a collaborative project with the labs of Evan Eichler and Alex Pollen. For this effort, scientists used Drop-seq sample prep and then loaded cDNA products onto the Sequel System. Results from a barnyard experiment using mouse and human cells as well as from cerebral organoids demonstrated that this approach could deliver cell type-specific gene expression data. Underwood also presents data from the Sequel II System comparing chimp and human organoids, resulting in information about 14,000 unique genes with important insights for post-transcriptional…

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Monday, March 30, 2020

AGBT Presentation: The Sequel II System – The next evolution of SMRT Sequencing

In this AGBT presentation, Marty Badgett shares a look at the latest results from circular consensus sequencing (CCS) mode for highly accurate reads and data from our soon-to-be-released Sequel II System. As he demonstrates, CCS reads cover the same molecule many times, delivering high consensus accuracy despite noisy raw reads; on average, reaching 10 passes achieves Q30 accuracy. Badgett offers several examples where this is useful, such as pharmacogenomic gene analysis and resolving metagenomic communities. He also provides an update on the Iso-Seq method, which can now segregate transcripts into haplotype-specific alleles using a new tool called Iso-Phase.

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Monday, March 30, 2020

AGBT Presentation: HiFi long reads for comprehensive genomic analysis

In this AGBT presentation, Mike Hunkapiller shares insights on using highly accurate long (HiFi) reads generated in circular consensus sequencing (CCS) mode for comprehensive genomic analysis and provides examples such as the sequencing of a Genome in a Bottle reference sample, which concluded with Q48 accuracy, 18 Mb contigs, and clearly phased haplotypes.

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Monday, March 30, 2020

Customer Experience: At CSHL, new achievements with long-read sequencing

Michael Schatz from Cold Spring Harbor Laboratory talks about using SMRT Sequencing to generate the world’s best crop genome assembly, discovering thousands of gene elements that had never been seen before. He also reports on how long reads made it possible to interrogate a highly complex breast cancer cell line that was too challenging to sequence with previous platforms.

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Monday, March 30, 2020

AGBT PacBio Workshop: Introduction – 15 years of human genomes

PacBio CEO Mike Hunkapiller looks at the past, present, and future of human genome sequencing, reflecting on the 15-year anniversary of the announcements of the first human genomes, noting these efforts required considerable effort and produced draft assemblies with contig N50s in the 20-24 kb range. He unveils the PacBio® diploid assembly of Craig Venter’s genome.

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Monday, March 30, 2020

AGBT 2015 Highlights: Customer interviews day 1

PacBio customers discuss their applications of PacBio SMRT Sequencing and long reads, including Lemuel Racacho (Children’s Hospital of Eastern Ontario Research Institute), Matthew Blow (JGI), Yuta Suzuki (U. of Tokyo), Daniel Geraghty (Fred Hutchinson Cancer Center), and Mike Schatz (CSHL)

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Monday, March 30, 2020

AGBT Virtual Poster: Balancing act of transcript isoforms

Anne Deslattes Mays from Georgetown University presents her AGBT poster on the balancing act of discovering transcriptome isoforms. Using SMRT Sequencing to study differentiated and undifferentiated cells from human bone marrow, she analyzed full-length isoforms and confirmed unexpected findings with mass spec. She says access to unfragmented long reads allows scientists to move from transcripts to proteins.

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Monday, March 30, 2020

AGBT Conference: Functional genomics – gene annotation and methylome analysis in bacteria

In his AGBT talk, Matthew Blow from the Joint Genome Institute describes high-throughput pipelines to annotate gene function and explore methylation in microbes. He uses transposon sequencing to annotate thousands of genes in bacteria and archaea. Later, he presents a study using SMRT Sequencing to generate complete methylomes for 232 prokaryotes, showing that orphan methylases appear to have a regulatory role.

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Monday, March 30, 2020

AGBT Virtual Poster: Clinical sequencing using Pacific Biosciences RS II for HLA typing and monitoring of drug resistance in chronic myeloid leukemia (CML)

Ulf Gyllensten from Uppsala University describes his AGBT poster showing the use of SMRT Sequencing for HLA allele typing. He says long reads are essential for sequencing the HLA genes because they link exons in a single read and do not introduce bias, as short-read sequencers can. Looking at fusion transcripts from CML patients generated information that couldn’t be achieved with any other technology, he adds.

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