Scientists Use Multiple Technologies to Produce High-Quality Chinese Genome Assembly

A newly reported genome assembly of a Chinese individual, generated by scientists in China and the US, used long-read PacBio sequencing, short-read Illumina data, and BioNano Genomics physical maps to achieve remarkably high accuracy and contiguity. Along the way, the team deployed our BluePippin automated DNA size selection platform for both the genome and transcriptome analysis.

From lead author Lingling Shi and many collaborators, the Nature Communications publication reports that long-read data contributed to a more complete picture of the DNA and RNA, allowing the team to find a significant amount of sequence and gene content that had never been observed before. Scientists produced 12.8 Mb of sequence data that did not map to the current human reference genome, and identified many likely functional structural variants that may be specific to the Asian population. The genome assembly also addresses 274 gaps — nearly 30% of existing gaps — in the reference genome, many of which were characterized by simple repeats.

In the transcriptome analysis, the scientists built four libraries with different insert sizes: 1–2 Kb, 2–3 Kb, 3–5 Kb, and greater than 5 Kb. The sequence results were used to predict more than 58,000 isoforms at 30,000 loci, including nearly 60 isoforms “that do not overlap with any GENCODE transcript,” they report. The team used BluePippin for this sizing step (our support department would point out that SageELF would have accomplished this with less hands-on time); check out the supplemental info for details.

This paper continues a promising trend that we’ve noticed in human genome sequencing: the use of multiple orthogonal technologies to produce many dimensions of data for a more comprehensive view of the underlying biology. While it’s more technically challenging upfront, the combo approach really delivers in the analysis. We hope to see many more sequencing projects using this concept to reveal novel information about what makes us tick.

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