The study of mRNA transcript isoforms has been challenging due to the short read lengths of other sequencing technologies. Long PacBio reads enable full-length transcript sequencing, as well as the identification of alternatively spliced forms of a gene. As a result, new genes and isoforms are accessible for study.
For example, Steve Quakeand Thomas Südhof,Professors at
specification of cell connections in the brain.
The Iso-Seq application can also be used for transcriptome-wide studies, improving the ability to annotate genes in reference genomes. Long sequence reads spanning full-length gene transcripts will eliminate the need for an RNA-seq assembly step, providing more complete gene models and more comprehensive annotation of transcribed genes.
The second new application is HLA haplotype phasing. The HLA loci are a group of genes critical to immune system function. In humans, the HLA genes are extraordinarily polymorphic. Several thousand alleles have been described and the number of new alleles continues to increase. HLA allele-specific genotyping is critical for autoimmune disease-association studies, drug hypersensitivity research and other applications. Accurate phasing of HLA polymorphisms has previously required several experiments at great expense. The long reads provided by PacBio sequencing are ideally suited for accurate allele-level genotyping with unambiguous allele phasing.
PacBio’s SMRT Analysis 2.2 generates consensus sequences that can be input into third-party software for HLA analysis. This data has successfully been used with the Conexio Genomics (
“PacBio’s analysis pipeline independently generates the consensus sequence of each allele in a heterozygous sample, including non-coding regions,” said
“The SMRT Analysis 2.2 upgrade streamlines two important applications that are uniquely enabled by our robust long-read sequencing technology,” said
The new SMRT Analysis software upgrade is available for download from Pacific Biosciences’ DevNet website. To access the software, data, and documentation, visit www.pacbiodevnet.com.
For more information on the new SMRT Analysis software and the PacBio RS II, please visit www.pacificbiosciences.com.
About the PacBio RS II and SMRT Sequencing
Pacific Biosciences’ Single Molecule, Real-Time (SMRT) Sequencing technology achieves the industry’s longest read lengths, highest consensus accuracyiii,iv and the least degree of bias.v These characteristics, combined with the ability to detect many types of DNA base modifications (e.g., methylation) as part of the sequencing process, make the PacBio RS II an essential tool for many scientists for studying genetic and genomic variation. The PacBio platform is being used as the sequencing solution to address a growing number of complex medical, agricultural and industrial problems.
About Pacific Biosciences
i Treutlein et al., “Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing.” PNAS, 10.1073/pnas.1403244111 (2014).
ii Sharon et al., “A single-molecule long-read survey of the human transcriptome,” Nature Biotechnology 31, 1009-1014 (2013).
iii Koren et al., “Reducing assembly complexity of microbial genomes with single-molecule sequencing.” Genome Biology, 14:R10.1 (2013).
iv Chin et al., “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.” Nature Methods, 10; 563-569 (2013).
v Ross et al. Characterizing and measuring bias in sequence data. Genome Biol 14: R51 (2013).
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