Shared SNP percentage >96% in exome library data and quantification correlation >97% in transcriptome library data – NovaSeq X Plus new data release

The NovaSeq X Plus platform provides extraordinary sequencing power not only for whole genome sequencing but also for whole exome sequencing and transcriptome sequencing. Following the previous release of human whole genome sequencing test on the NovaSeq X Plus, data from more library types are now available. Try a NovaSeq X Plus lane with Novogene！

1. Testing Result of Human Whole Exome Sequencing Library

To further evaluate the platform’s performance, a whole exome sequencing library with NA12878 was simultaneously sequenced on both the NovaSeq X Plus and NovaSeq 6000 platforms. The library was prepared using Agilent SureSelect Human All Exon V6.

1.1 Quality Control

Compared with the NovaSeq 6000, the NovaSeq X Plus platform performs better in Q30, with an average of 95.70%.

1.2 Mapping Statistics

The NovaSeq X Plus achieves even coverage across the entire exome, with coverage of 99.5% and capture efficiency of 67.6%.

Figure 1 Capture efficiency in NovaSeq X Plus and NovaSeq 6000

1.3 Variant Calling Accuracy

The NovaSeq X Plus and NovaSeq 6000 platforms have >96% similarity in SNP detection. The SNP and InDel precision and recall deviation between the two platforms is <0.5%.

Figure 2 Venn diagrams of shared SNPs between NovaSeq X Plus and NovaSeq 6000

2. Testing Result of mRNA Sequencing library

An mRNA sequencing library with UHRR was simultaneously sequenced on both the NovaSeq X Plus and NovaSeq 6000 to further evaluate the platform performance.

2.1 Quality Control and Mapping Statistics

The effective rate, Q30 score, and rRNA rate of NovaSeq X Plus are almost similar to that of NovaSeq 6000, with <1% deviation.

2.2 Quantification and Correlation

The quantification results indicate that the NovaSeq X Plus and NovaSeq 6000 platforms have high similarity in gene expression. The R² value between the two platforms is >0.97, which is comparable to the R² value between two lanes in the NovaSeq X Plus.

Figure 3 Quantification and correlation features of mRNA sequencing library in NovaSeq X Plus and NovaSeq 6000

3. Testing Result of LncRNA Sequencing Library

LncRNA sequencing library with UHRR was simultaneously sequenced on the NovaSeq X Plus and NovaSeq 6000 to further evaluate the platform performance.

3.1 Quality Control and Mapping Statistics

When compared to the NovaSeq 6000, the effective rate, Q30 and rRNA rate of the LncRNA sequencing library on the NovaSeq X Plus showed almost identical results, with <1% deviation.

3.2 Quantification and Correlation

The quantification results indicate that the gene expression similarity between the NovaSeq X Plus and the NovaSeq 6000 is high, with an R² value >0.96, which is similar to the R² value between two lanes on the NovaSeq X Plus platform.

Figure 4 Quantification and correlation features of lncRNA sequencing library in NovaSeq X Plus and NovaSeq 6000

In summary, the NovaSeq X Plus platform demonstrates improved data quality and high consistency with the NovaSeq 6000 in whole genome, whole exome, and transcriptome sequencing libraries. With its outstanding performance in data quality, turnaround time, and affordable price, the NovaSeq X Plus is an attractive option for studies related to population genomics, gene function and regulation.

About Novogene

Novogene is a pioneer in applying cutting-edge molecular biology technology and high-performance computing to research in the fields of life science and human health. Our vision is to continue as a global leader in the delivery of genomics services and solutions.
With one of the largest sequencing capacities in the world, we utilise our deep scientific knowledge, first-class customer service and unsurpassed data quality to help clients realise their research goals in the rapidly evolving world of genomics. Novogene is committed to become your trusted genomics partner.