August 19, 2021  |  Sequencing methods

Application Brief: Long-read RNA sequencing – Best Practices

With Single Molecule, Real-Time (SMRT) Sequencing and the Sequel Systems, you can easily and affordably sequence complete transcript isoforms in genes of interest or across the entire transcriptome. The Iso-Seq method allows users to generate full-length cDNA sequences up to 10 kb in length — with no assembly required — to confidently characterize full-length transcript isoforms.

August 19, 2021  |  Sequencing methods

Application Brief: Single-cell RNA sequencing with HiFi reads – Best Practices

With PacBio single-cell RNA sequencing using the Iso-Seq method, you can now distinguish between alternative transcript isoforms at the single-cell level. The highly accurate long reads (HiFi reads) can span the entire 5′ to 3′ end of a transcript, allowing a high-resolution view of isoform diversity and revealing cell-to-cell heterogeneity without the need for assembly.

August 19, 2021  |  Human genetics research

Application Brochure: Scalable human whole genome HiFi sequencing for rare and inherited disease research

PacBio highly accurate long reads – HiFi reads – offer a single-platform solution for rare and inherited disease research, elucidating suspected genetic causes of disease in up to ~50% of cases that have not previously been explained using short-read exome or whole genome sequencing. PacBio offers an efficient workflow, developed in collaboration with Children’s Mercy Kansas City, which provides a scalable solution for sequencing 100s to 1000s of whole human genomes per year on the Sequel II and Sequel IIe Systems.

August 19, 2021  |  Infectious disease research

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II or IIe Systems you can comprehensively detect variants in 100s to 1000s of genomes in a year. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

June 1, 2021  |  

Structural variant detection with low-coverage Pacbio sequencing

Despite amazing progress over the past quarter century in the technology to detect genetic variants, intermediate-sized structural variants (50 bp to 50 kb) have remained difficult to identify. Such variants are too small to detect with array comparative genomic hybridization, but too large to reliably discover with short-read DNA sequencing. Recent de novo assemblies of human genomes have demonstrated the power of PacBio Single Molecule, Real-Time (SMRT) Sequencing to fill this technology gap and sensitively identify structural variants in the human genome. While de novo assembly is the ideal method to identify variants in a genome, it requires high depth of coverage. A structural variant discovery approach that utilizes lower coverage would facilitate evaluation of large patient and population cohorts. Here we introduce such an approach and apply it to 10-fold coverage of several human genomes generated on the PacBio Sequel System. To identify structural variants in low-fold coverage whole genome sequencing data, we apply a reference-based, re-sequencing workflow. First, reads are mapped to the human reference genome with a local aligner. The local alignments often end at structural variant loci. To connect co-linear local alignments across structural variants, we apply a novel algorithm that merges alignments into “chains” and refines the alignment edges. Then, the chained alignments are scanned for windows with an excess of insertions or deletions to identify candidate structural variant loci. Finally, the read support at each putative variant locus is evaluated to produce a variant call. Single nucleotide information is incorporated to phase and evaluate the zygosity of each structural variant. In 10-fold coverage human genome sequence, we identify the vast majority of the structural variants found by de novo assembly, thus demonstrating the power of low-fold coverage SMRT Sequencing to affordably and effectively detect structural variants.

June 1, 2021  |  

Detecting pathogenic structural variants with low-coverage PacBio sequencing.

Though a role for structural variants in human disease has long been recognized, it has remained difficult to identify intermediate-sized variants (50 bp to 5 kb), which are too small to detect with array comparative genomic hybridization, but too large to reliably discover with short-read DNA sequencing. Recent studies have demonstrated that PacBio Single Molecule, Real-Time (SMRT) sequencing fills this technology gap. SMRT sequencing detects tens of thousands of structural variants in the human genome, approximately five times the sensitivity of short-read DNA sequencing.

June 1, 2021  |  

Improving the reference with a diversity panel of sequence-resolved structural variation

Although the accuracy of the human reference genome is critical for basic and clinical research, structural variants (SVs) have been difficult to assess because data capable of resolving them have been limited. To address potential bias, we sequenced a diversity panel of nine human genomes to high depth using long-read, single-molecule, real-time sequencing data. Systematically identifying and merging SVs =50 bp in length for these nine and one public genome yielded 83,909 sequence-resolved insertions, deletions, and inversions. Among these, 2,839 (2.0 Mbp) are shared among all discovery genomes with an additional 13,349 (6.9 Mbp) present in the majority of humans, indicating minor alleles or errors in the reference, which is partially explained by an enrichment for GC-content and repetitive DNA. Genotyping 83% of these in 290 additional genomes confirms that at least one allele of the most common SVs in unique euchromatin are now sequence-resolved. We observe a 9-fold increase within 5 Mbp of chromosome telomeric ends and correlation with de novo single-nucleotide variant mutations showing that such variation is nonrandomly distributed defining potential hotspots of mutation. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. To illustrate the utility of sequence-resolved SVs in resequencing experiments, we mapped 30 diverse high-coverage Illumina-sequenced samples to GRCh38 with and without contigs containing SV insertions as alternate sequences, and we found these additional sequences recover 6.4% of unmapped reads. For reads mapped within the SV insertion, 25.7% have a better mapping quality, and 18.7% improved by 1,000-fold or more. We reveal 72,964 occurrences of 15,814 unique variants that were not discoverable with the reference sequence alone, and we note that 7% of the insertions contain an SV in at least one sample indicating that there are additional alleles in the population that remain to be discovered. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity. We present a summary of our findings and discuss ideas for revealing variation that was once difficult to ascertain.

June 1, 2021  |  

TLA & long-read sequencing: Efficient targeted sequencing and phasing of the CFTR gene

Background: The sequencing and haplotype phasing of entire gene sequences improves the understanding of the genetic basis of disease and drug response. One example is cystic fibrosis (CF). Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have revolutionized CF treatment, but only in a minority of CF subjects. Observed heterogeneity in CFTR modulator efficacy is related to the range of CFTR mutations; revertant mutations can modify the response to CFTR modulators, and other intronic variations in the ~200 kb CFTR gene have been linked to disease severity. Heterogeneity in the CFTR gene may also be linked to differential responses to CFTR modulators. The Targeted Locus Amplification (TLA) technology from Cergentis can be used to selectively amplify, sequence and phase the entire CFTR gene. With PacBio long-read SMRT Sequencing, TLA amplicons are sequenced intact and long-range phasing information of all fragments in entire amplicons is retrieved. Experimental Design and Methods: The TLA process produces amplicons consisting of 5-10 proximity ligated DNA fragments. TLA was performed on cell line and genomic DNA from Coriell GM12878, which has few heterozygous SNVs in CFTR, and the IB3 cell line, with known haplotypes but heterozygous for the delta508 mutation. All sample types were prepared with high and low density TLA primer sets, targeting coverage of >100 kb of the CFTR gene. Conclusion: We have demonstrated the power and utility of TLA with long-read SMRT Sequencing as a valuable research tool in sequencing and phasing across very long regions of the human genome. This process can be done in an efficient manner, multiplexing multiple genes and samples per SMRT Cell in a process amenable to high-throughput sequencing.

June 1, 2021  |  

Amplification-free protocol for targeted enrichment of repeat expansion genomic regions and SMRT Sequencing

Many genetic disorders are associated with repeat sequence expansions. Obtaining accurate DNA sequence information from these regions will facilitate researchers to further establish the relationship between these genetic disorders and underlying disease mechanisms. Moreover, repeat interruptions have also been shown to act as phenotypic modifiers in some disorders. Targeted sequencing is an economical way to obtain sequence information from one or more defined regions in a genome. However, most targeted enrichment and sequencing methods require some form of DNA amplification. Amplifying large regions with extreme GC content as seen in repeat expansion disorders is challenging and prone to introducing sequence artifacts. DNA amplification also removes any epigenetic signatures present in native DNA. This technique also preserves native DNA molecules for the possibility of direct characterization of epigenetic signatures.

June 1, 2021  |  

A complete solution for full-length transcript sequencing using the PacBio Sequel II System

Long read mRNA sequencing methods such as PacBio’s Iso-Seq method offers high-throughput transcriptome profiling in prokaryotic and eukaryotic cells. By avoiding the transcript assembly problem and instead sequencing full-length cDNA, Iso-Seq has emerged as the most reliable technology for annotating isoforms and, in turn, improving proteome predictions in a wide variety of organisms. Improvements in library preparation, sequencing throughput, and bioinformatics has enabled the Iso-Seq method to be complete solution for transcript characterization. The Iso-Seq Express kit is a one-day library prep requiring 60-300 ng of total RNA. The PacBio Sequel II system produces 4-5 million full-length reads, sufficient to profile a whole human transcriptome. Finally, the SQANTI2 software is a powerful tool for categorizing the complex isoforms against reference annotations, while also incorporating orthogonal information such as CAGE peak data, public RNA-seq junction data, and ORF predictions.

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