BIOTECHNOLOGY
get the most accurate and complete view of tomato and maize genomes and epigenomes, unlocking insights that are out of reach with short-reads. Te researchers reported that gaining these insights from a single datatype, rather than results from multiple tests, presented an unmatched opportunity for analysis as well as streamlining their workflows.
SYNTHETIC LONG-READS – A PUZZLE THAT DOESN’T FIT TOGETHER Over the past decade, attempts have been made to synthetically reconstruct longer- molecule sequences by pasting together multiple partial reads using short-read technologies. However, these ‘linked reads’ still carry the accuracy issues of their short-read origins. Since short-reads are too short to detect more than 70% of human genome structural variation, it is possible that when pieced together, these short sequences paint an incorrect and incomplete picture of gene expression. One close comparison of native long-read and synthetic linked long-read sequencing found that a tandem repeat insertion was resolved as homozygous (identical pairs of genes for a specific trait) by the native long-read method but was falsely resolved as heterozygous (different genes) by the synthetic long-read, since it had been pieced together without the complete sequence. Mistaking homozygous for heterozygous leads to incorrect experiment results and in a clinical setting can cause misdiagnosis, so it’s vital scientists get these readings correct.
PacBio’s Sequel systems deliver accurate long-read sequencing Tere are several reasons why native
long-reads have higher quality and accuracy compared to synthetic long-reads, the first being molecular integrity. When using long- read, whole strands of DNA molecules are extracted from cells and directly submitted to sequencing, without being broken and pieced back together. Tis maintains molecular integrity, so no sequences are missed out and you have an accurate and complete reading. Simpler sample preparation steps is
another reason. Long-read sequencing does not require any DNA amplification or other sequence-altering molecular biology procedures. Tese additional steps are prone to biases, introduction of errors and
Sequencing helps scientists advance their projects
fragmentation, so eliminating them further increases the accuracy of long-read over synthetic counterparts. Simpler workflows is the third reason.
Simpler extraction and preparation reduces the workload for the scientist. Unlike linked short-reads, native long-reads do not require bioinformatics to work out which fragments originate from the same molecule, complicated assembly steps, or correction of errors introduced during sample prep. Tis further reduces the chance of error and accelerates research for scientists in the lab.
A NEW STANDARD OF SEQUENCING Highly accurate long-read sequencing has already proved it can make transformative contributions to our understanding of biology and give us a much deeper insight into genomes than traditional short-read technology. Adding the ability to also screen the epigenome is the next step in the genomics research journey. Capturing both genetic and epigenetic variation across the full genome in a single experiment will speed up sample preparation without compromising on read lengths, accuracy, or completeness. Only with this advanced sequencing method can scientists confidently advance their genomics projects.
Neil Ward is general manager of PacBio.
www.pacb.com
www.scientistlive.com 31
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