Next-generation sequencing refers to a class of instruments that determine the nucleic acid sequences of individual DNA molecules. All DNA molecules are sequenced separately and simultaneously, and the resulting data contains individual nucleotide strings for up to billions of DNA molecules. For this reason, these technologies are sometimes also called “Massively Parallel Sequencing.” There are several technologies/platforms which produce NGS results in different ways, but the data is always reported at an individual nucleotide and DNA molecule resolution.
Generally speaking, genotyping is the determination of genetic differences between a sample’s DNA and other samples or a reference sequence. These differences are often identified as single-nucleotide polymorphisms (SNPs) and other markers.
SNPs are variants of DNA sequences which are defined by analyzing their position against other individuals at the same DNA sequence. SNPs are the most common genetic marker used to analyze NGS data and provide powerful insights and applications to a wide range of industries and research areas. Alleles often refer to genetic variants but across a region of DNA, and may be comprised of several SNPs or other genetic markers.
These terms are often used interchangeably. Generally speaking, an SNP is always a marker but a marker is not always an SNP. A marker may also be an insertion or deletion (InDel) or other genetic variants, and can also refer to a region or locus within a genome.
Sanger sequencing uses lower-throughput technology than NGS and is not as suitable for detecting sequence variants for further analysis. NGS produces more data, with greater accuracy, and enables improved processing of large sample volumes or complex genomes. Additionally, these improvements allow for more flexibility and confidence in post-sequencing analyses like copy number assessments and rare allele detection.
NGS genotyping applications deliver the optimum combination of accuracy, flexibility, and scalability. qPCR typically targets only 1 - 3 regions per reaction, while NGS can target hundreds of thousands of regions simultaneously. Genotyping arrays are relatively inflexible in their selection of targets, and developing custom products is laborious and time-consuming, while NGS offers many flexible and easily customizable solutions for targeting loci of interest. Additionally, by sequencing hundreds of nucleotides, NGS inherently allows for greater allele discovery with minimal ascertainment bias, while arrays and qPCR focus only on single nucleotides at previously-known targets.
The majority of samples we process are sequenced using short-read Illumina® technologies, mainly PE150, and we also incorporate long-read PacBio® and Nanopore sequencing where relevant.
Exome sequencing refers to the targeting and selective sequencing of coding regions, or exons, of genes within an organism’s genome. Custom exome sequencing is when a user-defined subset of the total exome content is targeted for sequencing. Exome sequencing is distinct from RNA-seq in that it targets the DNA of all genes instead of the RNA transcripts produced from the genome.
Any species may be sequenced and analyzed using next-generation sequencing. We have sequenced and analyzed hundreds of species to date, including many non-model organisms with challenging or poorly understood genomes.
We are here to help. The best solution to fit your goals and requirements can be identified by discussing options with our team. Please complete the Contact Us form to get in touch, and you can also find additional information on our technology and application pages.
Our data deliveries and formatting vary by platform/application and follow the industry standards for the NGS community. Sequencing data, either filtered or unfiltered, are typically provided as .fastq files. Alignments against references are provided as .bam files. SNP calls and/or variants are provided as VCF files. We also offer customized data formats and reporting to meet your team’s specific requirements.
Yes – we have a full bioinformatic support team providing additional data analysis for both routine and custom requirements.
No – we are here to help and would be glad to discuss possible solutions with you. Whether you are starting out with a conceptual goal or require a specific reporting format, our team can provide the answer.
Yes – we have options for sample storage at varying lengths. Please inquire about this when speaking with one of our representatives.
Yes – the overwhelming majority of our clients are able to publish their results, and we provide supporting materials to ease your writing burden. Occasionally, proprietary materials are used to generate research data which may impact publication, but this is rare. If you have any concerns, please let us know and we will be happy to help.
The answer will depend on the level to which you have already implemented genomics, but generally speaking, our Flex-Seq® Ex-L platform is the best solution for ongoing, routine genotyping. We also offer full support for the introduction of genomics to any breeding program. Contact us and one of our representatives will be happy to provide additional information.
Genomic selection is a molecular breeding strategy that utilizes both genetic and phenotypic data to identify the best individuals for selection within a breeding program. Once implemented, GS can reduce or eliminate the need for routine phenotyping at each breeding selection stage.
The core principle of GS is that most traits will have dozens of genes or alleles interacting together to create the desired phenotype, and it can be equally useful to identify a marker near the causal allele as finding the causal allele itself. For that reason, GS uses markers distributed throughout the genome to estimate breeding values without the need for extensive and research-heavy efforts to arrive at single functional markers, which often do not accurately predict more complex traits like growth rate and yield. In this way, GS represents one of the fastest paths to realizing commercial gains through the use of genotyping.
Marker-Assisted Selection relies on identifying a single marker (or small set of markers) associated with a desired phenotype to improve breeding selections. Individuals can be genotyped for this marker and selections can be made based on the presence or absence of the desired variant. MAS works best for simple traits caused by single genes, whereas complex traits are difficult to characterize with single markers. MAS can work well when developed for specific breeding programs but requires extended research to arrive at optimized markers. Additionally, MAS may not be as effective in different breeding programs, with different genomic backgrounds, where the same allele is not found.
Marker-Assisted Backcrossing is a genotyping strategy used to accelerate the movement of a specific region of the genome from one individual into the genetic background of a different individual. A common example is transferring a disease resistance gene from a wild species of crop into a well-established breeding cultivar. QTL analyses, or sites identified from MAS programs, can be used to identify markers associated with the desired trait in the wild species. After crossing the wild species with the cultivar, these markers are used to identify and select individuals that retain the desired trait. The progeny are then repeatedly backcrossed to the breeding cultivar, using genotyping to select only individuals with the desired marker at each stage for further backcrossing. After several generations, only the desired resistance gene is left within the breeding cultivar and most of the wild species genome has been removed.
Qualitative traits are traits typically controlled by a single gene or locus and do not exhibit continuous variation for their phenotype, e.g. traits that are easily scored as presence/absence or with relatively few categories. Quantitative traits are traits typically under multi-genic control and exhibit phenotypic values that are continuously distributed, such as yield or feed conversion efficiency.
Genomic selection is an application-focused breeding tool that does not require extensive research and effort to implement. Developing the predictive models needed for GS does not require complex crossing strategies or mapping populations, and can be done in just one breeding cycle. Additionally, GS is better suited for predicting complex, quantitative traits controlled by multiple genes or loci. For all of these reasons, GS can make meaningful impacts on your breeding program sooner and more easily.
Understanding the genetic diversity of your germplasm is an important first step for any molecular breeding program. Once your germplasm is genotyped and phenotyped, a predictive model for selecting future crosses can be developed and used with cost-effective NGS genotyping strategies to improve selection efficiency. After your genotyping and GS solutions are in place, phenotyping is no longer needed except when introducing new diversity into your program.
No – all of our genotyping solutions for breeding are legacy data compatible, ensuring continuity within your breeding program. A small percentage of markers are sometimes more challenging to genotype, but this is rare and will be discussed prior to any implementation.
Yes – we have extensive experience working with degraded samples from both plants and animals. If you are submitting a mixture of degraded and “fresh” DNA samples, it is important to identify each set to ensure proper sample processing.
Yes – any public or proprietary (with proper authorization) resources can be used to process your samples with us.
Yes - our bioinformatics team specializes in designing tools, products, and resources for use in systematics and evolutionary biology.
Yes – if you submitted DNA, we charge a small handling fee plus shipping costs and can return your DNA to you. For tissue samples submitted, we are unable to provide leftover material.
No – we do not provide libraries prepared at Rapid Genomics. If you submitted premade libraries, any leftover can be returned to you for a small handling fee plus shipping costs.
Yes – we understand that sampling sometimes spans across longer periods of time, and the importance of receiving data on an ongoing basis for continuous research is important. We offer bulk-contract discounts with options for batch submissions – please contact us to learn more.
We work on one of two arrangements with our customers: annual genotyping contracts and project-based initiatives. Annual contracts are best suited to routine breeding & testing applications, and project-based initiatives typically best fit research needs.
Yes – the data privacy and security of our clients are of the utmost importance. Your samples, data and related information will never be disclosed without your approval.
Prices are often defined on a per-sample basis but may be offered differently depending on scope. Costs are typically defined by your sample volume, commercial or research goals, and the organism. Please Contact Us to learn more.
We offer full-service solutions including DNA/RNA extraction (where relevant), marker panel, and assay design (where relevant), sample preparation, sequencing, data delivery, and data analysis.
Requesting a quote if easy – just Contact Us and one of our representatives will be in touch.
We work with clients all over the world and receive samples from international origins routinely. If you are submitting tissue samples, we can offer assistance with importation permits.
We accept payment via wire transfer or ACH. Credit card payments are also possible with a small fee. Instructions for making the payment will be provided on your invoice. Rapid Genomics is a paperless company and prefers not to receive paper checks. If paper checks are your only option, please mail them to:
Attn: Accounts Receivable
Rapid Genomics, LLC
747 SW 2nd Ave, Ste 314
Gainesville, FL USA 32601
Our sample submission requirements vary by service platform and sample type. You can find more information here.
We do have options for large volume commercial genotyping applications. Please contact us to inquire further.
We offer a client portal into our LIMS system, where sample progress can be easily tracked along with other key items and genotyping metrics.
We recommend expedited shipping via FedEx or DHL. UPS and government mailing systems are also possible, as well as additional couriers. Our sample submission requirements vary by service platform and sample type. You can find more information here.
All samples are processed in a commercially automated lab. This ensures consistent, high-quality results across all samples and time points, as well as faster turnaround times, compared to manual or semi-automated pipelines.
Yes – samples undergo several stages of QC before, during, and after sample processing, sequencing, and data analysis. These take place from both wet lab and data perspectives, and we use these metrics to ensure reliable data quality for our clients.