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Simplified genome
Application Note

Simplified genome wide detection of genetic variants with NEXTFLEX Rapid XP V2 library prep kit.

Whole Genome Sequencing (WGS) is a powerful tool that can detect a broad spectrum of genetic variations, from SNP to large structural variants, across the entire genome of an individual. With decreasing sequencing costs, WGS is becoming a viable option for population-wide screening for specific disease risk, including expanded carrier testing, pharmacogenomic variants, and polygenic risk scores, for example. Additionally, WGS is also gaining interest as a complementary research tool in the context of newborn screening, a cornerstone of pediatric healthcare.

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Introduction

Library prep can be intimidating for labs without extensive NGS experience. The NEXTFLEX™ Rapid XP V2 NEXTFLEX Rapid XP V2 DNA-Seq Kit NEXTFLEX Rapid XP V2 DNA-Seq Kit  Library prep kit incorporates a streamlined protocol to simplify library prep while delivering robust results. Pooling with the NEXTFLEX UDI barcodes NEXTFLEX UDI Barcodes (10NT, 1-24) NEXTFLEX UDI Barcodes (10NT, 1-24)  enables extreme multiplexing to reduce sequencing costs. Additionally, a complete automated workflow is available for labs seeking to increase throughput and minimize human error. Using cell line-derived reference standards with known mutations, we conducted a proof-of-concept study to evaluate the suitability of the NEXTFLEX Rapid XP V2 library prep kit for detecting germline mutations. These standards offer a controlled means to assess the performance of our WGS workflow, confirming its ability to identify genetic variants in sample material. This study also highlights the potential of the NEXTFLEX Rapid XP V2 kit for comprehensive genomic analysis in research applications.

Methods

Briefly, 25 ng of Mimix™ Male Genomic DNA (HD865) reference standard was used as input for whole genome library preparation. 8 replicates were made. Libraries were made using the NEXTFLEX Rapid XP V2 DNA-seq kit NEXTFLEX Rapid XP V2 DNA-Seq Kit for Metagenomics NEXTFLEX Rapid XP V2 DNA-Seq Kit for Metagenomics  and the NEXTFLEX Unique Dual Index Barcodes NEXTFLEX Unique Dual Index Barcodes (8NT index, 1-96) NEXTFLEX Unique Dual Index Barcodes (8NT index, 1-96)  according to manufacturer’s instructions. The technicians that prepared libraries are experienced in molecular biology but had never used this library prep kit before. Once libraries were prepared, they were quantified using the Thermo Scientific® Qubit® assay, pooled and run on a S2 flow cell on Illumina® NovaSeq® 6000 platform at 2x150 bp read length. Analysis was performed using a custom script, using the VCF file provided for the Mimix reference standards and GRch38 build as reference.

mimix data gc bias

Figure 1: Normalized coverage across varying %GC content for the 8 replicates analysed. The minimal GC bias observed indicates a high degree of coverage uniformity in the data generated.

The Mimix Male Genomic DNA reference standard contains 2,663 variants with AF<10% distributed across multiple regions, including 3’UTR, introns etc. Of those, 269 are missense variants, and they are distributed across 149 genes, all of them relevant in the context of newborn screening. Missense variants are particularly significant in genome-wide screening as they result in amino acid substitutions, directly impacting protein function. For this reason, we focus our attention to them in this test. These group of variants comprises mutations classified as benign, uncertain significance and pathogenic.

Results

On average 626 M reads per sample were generated after sequencing. 98.3% aligned to human genome, corresponding to an average genome coverage of 56x. Coverage uniformity is important to ensure reliable and efficient identification of genetic variation across the genome. To assess the uniformity of coverage distribution in the data, we looked at the GC bias across the 8 replicates (Figure 1).

Concordance between expected genotype from Mimix and observed genotype was 100% for the 269 variants studied. The table below lists some of those variants indicating their ClinVar number, the reference and alternative allele, and the average coverage obtained across the 8 replicates for reach of the alleles.

Table 1: Detail of the 15 first variants analysed, all of them concordant with the expected genotype. A full list of the 269 variants can be provided upon request. 
 

Gene dbSNP ID ClinVar Alt(%) Ref Alt Ref coverage Alt coverage
HPS1 rs58548334 175335 69.20% A G 21.8 47.9
RBM20 rs942077 53184 68.00% G C 25.8 53.5
BAG3 rs3858340 53943 48.80% C T 24.6 46.1
ECHS1 rs1049951 370659 100.00% G A 0.0 26.9
ECHS1 rs10466126 1245298 100.00% A G 0.0 31.3
DCLRE1C rs12768894 253714 61.80% T C 19.1 20.1
CDH23 rs779974496 1481561 45.50% C T 26.8 23.0
CDH23 rs1449510921 1319554 48.80% G A 22.9 25.9
CDH23 rs1227065 55102 100.00% A G 0.0 49.8
CDH23 rs1227051 55120 100.00% G A 0.0 53.3
CDH23 rs41281330 55122 45.80% G A 27.1 21.5
CDH23 rs11592462 55162 40.00% C G 28.4 26.1
BMPR1A rs11528010 50221 72.20% C A 27.1 21.0
DBT rs12021720 134332 100.00% T C 0.0 51.1
ATM rs1801516 133907 31.80% G A 30.3 30.4
The variants reported were inspected using IGV across the 8 replicates
Visualization of rs1801516

Figure 2: Visualization of rs1801516, located on the exon 37 of ATM (chr 11) and leading to the change p.Asp1853Asn

Conclusion

WGS is increasingly recognized as a pivotal tool for comprehensive screening across diverse applications. Our evaluation using Mimix reference standards demonstrates that NEXTFLEX Rapid XP V2 library preparation kit delivers uniform data coverage and enhanced variant detection accuracy, even when implemented by first-time users. These results demonstrate that laboratories can confidently adopt this robust solution regardless of their prior NGS experience, supporting reliable and consistent genomic analysis with minimal technical barriers.

Featured products

Robust library prep kit that generates high-complexity libraries for NGS on Illumina and Element platforms.

NEXTFLEX Rapid XP V2 DNA-Seq Kit

&lt;p&gt;The NEXTFLEX™ Rapid XP V2 DNA-Seq Kit is a fragmentation-based whole genome sequencing (WGS) library preparation workflow, taking samples from DNA to sequencing-ready libraries in as little as 2.5 hours. Proprietary NEXTFLEX normalization beads equalize library concentrations during the library prep process, so no separate quantitation or manual pooling is required.&lt;/p&gt;&lt;p&gt;The protocol supports inputs from 100 pg to 1 µg and offers a PCR-free option for ≥ 250 ng, preserving library complexity and minimizing GC bias. Resulting libraries show uniform coverage and low duplicate rates on Illumina® and Element Biosciences™ AVITI platforms, enabling confident variant detection in whole genome, metagenomic, and other research applications.&lt;/p&gt;&lt;p&gt;Automation-ready reagents, high indexing capacity (up to 1,536 UDIs), and streamlined clean-ups deliver fast, reproducible DNA-seq results at any scale.&lt;/p&gt;
  • Single-tube enzymatic fragmentation, end-repair & A-tailing - DNA to sequencing-ready libraries in as little as 2.5 hours
  • PCR-free option for ≥ 250 ng input plus a broad 100 pg - 1 µg range for low- and high-input samples with PCR amplification
  • Built-in NEXTFLEX normalization beads - skip post-library quantitation and manual pooling
  • Ultra-low adapter-dimer formation & uniform GC coverage for confident variant detection
  • Up to 1,536 UDIs available for large, multiplexed studies
  • 96 UDI-UMI barcode set enables molecular error-correction for rare variant calling
  • Automation-ready workflow validated on Revvity Automation NGS workstations
  • Quality assured through rigorous testing of every lot

The NEXTFLEX Rapid XP V2 DNA-Seq Kit unites speed, data quality, and scalability: enzymatic fragmentation streamlines the workflow, proprietary normalization beads remove an entire QC step, and an optional PCR-free path preserves library complexity. Whether processing a handful of samples or a 96-well plate on a liquid-handler, you get consistent, unbiased libraries ready for Illumina and Element AVITI sequencing.

Learn more
Adapters for NGS sequencing and multiplexing compatible with Illumina and Element systems.

NEXTFLEX UDI Barcodes (10NT, 1-24)

&lt;p&gt;Multiplex up to 1,536 samples on a single flow cell with NEXTFLEX™ Unique Dual Index Barcodes (10NT UDIs). Each kit ships with up to 1,536 pre-validated i5/i7 index pairs that eliminate index hopping and are compatible with Illumina platforms such as the NovaSeq® and Element’s AVITI™ systems. Off-the-shelf plate sets (containing between 16 to 1,536 unique adapters) let you start small and scale to population-level projects without requiring custom ordering or re-balancing.&lt;/p&gt;
  • Up to 1,536 unique i5 / i7 pairs (10NT) ready to ship
  • Compatible with PCR-free and PCR-amplified workflows
  • ≥ 3-base Hamming distance across the entire set for robust error-correction and balanced base diversity on 2- & 4-color chemistries
  • Designed to minimize index hopping that can be present with patterned flow cells.
  • Compatible with Revvity library prep and TruSeq style, ligation-based workflows
  • Every lot is functionally validated and tested for index purity by sequencing in an ISO 9001 facility
  • Optional NEXTFLEX Universal Blockers boost on-target hybrid-capture efficiency when used with these UDIs.
Learn more
Adapters for NGS sequencing and multiplexing compatible with Illumina and Element systems.

NEXTFLEX Rapid XP V2 DNA-Seq Kit for Metagenomics

&lt;p&gt;The NEXTFLEX™ Rapid XP v2 DNA-Seq Kit for Metagenomics offers fast, fragmentation-based library prep for whole genome sequencing of microbial communities for sequencing on Illumina® and Element® platforms. Libraries are ready in ~ 2.5 hours, and proprietary normalization beads eliminate the need for quantitation or manual pooling. The protocol supports 100 pg to 1 µg input, with a PCR-free option at ≥ 250 ng. Purchase includes access to Cosmos-Hub®, providing validated pipelines for WGS metagenomics analysis, including taxonomic and functional outputs.&lt;/p&gt;

The NEXTFLEX Rapid XP v2 DNA-Seq Kit for Metagenomics combines fast, automation-ready library prep with built-in normalization and integrated downstream analysis. Designed for whole genome sequencing of microbial communities, purchase includes access to Cosmos-Hub® for streamlined WGS metagenomics interpretation.

  • Single-tube enzymatic fragmentation, end-repair and A-tailing. Libraries in as little as 2.5 hours
  • PCR-free option for ≥250 ng input; full 100 pg–1 µg input range with amplification
  • Integrated NEXTFLEX normalization beads, skip post-library quantitation and pooling
  • Validated Cosmos-Hub access for taxonomic and functional WGS metagenomics analysis
  • CHAMP and KEPLER pipelines support version-controlled, reproducible reporting
  • Up to 1,536 UDIs available for high-throughput multiplexing
  • Automation-validated on Revvity Sciclone™ and Zephyr™ NGS platforms
  • Compatible with Illumina and Element sequencing platforms
Learn more
Adapters for NGS sequencing and multiplexing compatible with Illumina and Element systems.

NEXTFLEX Unique Dual Index Barcodes (8NT index, 1-96)

&lt;p&gt;The NEXTFLEX™ Unique Dual Index Barcodes (UDI) are barcoded adapters that can be used with single read or paired-end read sequencing. Each index is separated by a ≥ 3-base edit distance, enabling error-correcting demultiplexing and sharply limiting index hopping on patterned flow cells. The barcodes are compatible with any TruSeq-style T-overhang workflows and are validated across all Illumina® instruments, as well as Element Bioscience® AVITI™ system. Up to 384 indices are available. Every lot is sequence-verified for index purity, safeguarding data integrity and keeping per-sample costs low.&lt;/p&gt;
  • UDI full length adapters for multiplexing up to 384 libraries for Illumina and Element sequencing platforms
  • Compatible with all PCR-free and amplified TruSeq-style T-overhang library preps as drop in replacement
  • Unique Dual Index design with ≥3 hamming distance reduces index hopping and sample mis-assignment on patterned flow cells
  • Each lot is sequence-verified for index purity (QC by sequencing)
  • Compatible with the NEXTFLEX Universal Blockers
Learn more

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