Independent Testing Proves Dragen Provides a Vastly More Comprehensive Genome
Illumina's DRAGEN Secondary Analysis software has received third-party validation from Baylor College of Medicine, with results published in Nature Biotechnology. The study confirms DRAGEN's superior performance in genome analysis, featuring proprietary algorithms developed in-house. The software includes over a dozen specialized variant callers for challenging genome sections and incorporates a pangenome reference to address Eurocentric bias in genetic data.
The validation demonstrated DRAGEN's exceptional accuracy, with competing tools showing up to 470% more errors. Notably, DRAGEN can process whole human genome analysis in just 30 minutes, compared to several days with other tools. The software's comprehensive approach integrates multiple components efficiently, making it particularly valuable for both individual samples and large-scale population studies.
Il software di analisi secondaria DRAGEN di Illumina ha ricevuto una validazione da parte di terzi dal Baylor College of Medicine, con risultati pubblicati su Nature Biotechnology. Lo studio conferma la superiorità delle prestazioni di DRAGEN nell'analisi genomica, grazie a algoritmi proprietari sviluppati internamente. Il software include oltre una dozzina di chiamatori di varianti specializzati per sezioni genomiche complesse e incorpora un riferimento pangenomico per affrontare il bias eurocentrico nei dati genetici.
La validazione ha dimostrato l'eccezionale accuratezza di DRAGEN, con strumenti concorrenti che mostrano fino al 470% di errori in più. In particolare, DRAGEN è in grado di elaborare l'analisi dell'intero genoma umano in soli 30 minuti, rispetto a diversi giorni richiesti da altri strumenti. L'approccio completo del software integra vari componenti in modo efficiente, rendendolo particolarmente prezioso sia per campioni singoli che per studi di popolazione su larga scala.
El software de Análisis Secundario DRAGEN de Illumina ha recibido validación de terceros por parte del Baylor College of Medicine, con resultados publicados en Nature Biotechnology. El estudio confirma el rendimiento superior de DRAGEN en el análisis genómico, con algoritmos propietarios desarrollados internamente. El software incluye más de una docena de detectores de variantes especializados para secciones genómicas desafiantes e incorpora una referencia pan-genómica para abordar sesgos eurocéntricos en los datos genéticos.
La validación demostró la excepcional precisión de DRAGEN, con herramientas competidoras mostrando hasta un 470% más de errores. Notablemente, DRAGEN puede procesar el análisis del genoma humano completo en solo 30 minutos, en comparación con varios días que requieren otras herramientas. El enfoque integral del software integra múltiples componentes de manera eficiente, haciéndolo especialmente valioso tanto para muestras individuales como para estudios poblacionales a gran escala.
일루미나의 DRAGEN 이차 분석 소프트웨어는 베일러 의대의 제3자 검증을 받았으며, 결과는 네이처 생명공학에 발표되었습니다. 이 연구는 DRAGEN의 우수한 유전체 분석 성능을 확인하며, 내부에서 개발된 독점 알고리즘을 특징으로 합니다. 이 소프트웨어는 도전적인 유전체 영역에 대해 12개 이상의 전문 변이 호출기를 포함하고 있으며, 유전 데이터의 유럽 중심 편향을 해소하기 위해 팬유전체 참조를 통합하고 있습니다.
이 검증은 DRAGEN의 뛰어난 정확성을 보여주었으며, 경쟁 도구들은 최대 470% 더 많은 오류를 나타냈습니다. 특히 DRAGEN은 다른 도구들이 며칠 걸리는 것에 비해 전체 인간 유전체 분석을 단 30분 만에 처리할 수 있습니다. 소프트웨어의 종합적인 접근 방식은 여러 구성 요소를 효율적으로 통합하여 단일 샘플과 대규모 인구 연구 모두에 특히 유용하게 만듭니다.
Le logiciel d'analyse secondaire DRAGEN d'Illumina a reçu une validation de tierce partie de la part du Baylor College of Medicine, avec des résultats publiés dans Nature Biotechnology. L'étude confirme la performance supérieure de DRAGEN dans l'analyse génomique, présentant des algorithmes propriétaires développés en interne. Le logiciel inclut plus d'une douzaine de détecteurs de variantes spécialisés pour des sections génomiques difficiles et intègre un référentiel de pangénom pour traiter le biais eurocentrique dans les données génétiques.
La validation a démontré l'extraordinaire précision de DRAGEN, les outils concurrents affichant jusqu'à 470 % d'erreurs supplémentaires. Notamment, DRAGEN peut traiter l'analyse complète du génome humain en seulement 30 minutes, contre plusieurs jours pour d'autres outils. L'approche complète du logiciel intègre efficacement plusieurs composants, le rendant particulièrement précieux tant pour les échantillons individuels que pour les études de population à grande échelle.
Die DRAGEN-Analyse-Software von Illumina hat eine Drittvalidierung durch das Baylor College of Medicine erhalten, mit Ergebnissen, die in Nature Biotechnology veröffentlicht wurden. Die Studie bestätigt die überlegene Leistung von DRAGEN bei der Genomanalyse, die proprietäre Algorithmen umfasst, die intern entwickelt wurden. Die Software beinhaltet über ein Dutzend spezialisierte Variantencaller für herausfordernde Genombereiche und integriert ein Pangenom-Referenz, um dem eurozentrischen Bias in genetischen Daten entgegenzuwirken.
Die Validierung zeigte die außergewöhnliche Genauigkeit von DRAGEN, wobei konkurrierende Tools bis zu 470 % mehr Fehler aufwiesen. Bemerkenswert ist, dass DRAGEN die Analyse des gesamten menschlichen Genoms in nur 30 Minuten verarbeiten kann, während andere Tools mehrere Tage benötigen. Der umfassende Ansatz der Software integriert mehrere Komponenten effizient und macht sie besonders wertvoll für sowohl Einzelproben als auch großangelegte Bevölkerungsstudien.
- Superior accuracy demonstrated with competitors showing 144-470% more errors
- Rapid processing capability - 30 minutes for whole genome analysis versus days for competitors
- Comprehensive in-house developed algorithms validated by third-party testing
- Integration with major research programs including UK Biobank and NIH All of Us
- None.
Insights
This independent validation of DRAGEN software represents a significant technological breakthrough in genome sequencing analysis. The software's ability to process whole-genome sequences in just 30 minutes compared to several days for competitors marks a substantial efficiency gain. The validation by Baylor College of Medicine, published in Nature Biotechnology, demonstrates DRAGEN's superior accuracy with up to
The software's pangenome reference feature addresses a critical bias in genetic research by incorporating diverse ethnic genetic data, potentially revolutionizing personalized medicine. The specialized variant callers for complex genes linked to diseases like Parkinson's and cardiovascular conditions significantly enhance the software's clinical utility. This comprehensive validation proves DRAGEN's capability to handle both individual samples and massive population studies efficiently.
The validation of DRAGEN's germline algorithms represents a major advancement in genetic analysis accuracy and accessibility. The software's ability to accurately analyze challenging genes like GBA (linked to Parkinson's disease) and LPA (associated with cardiovascular risk) has significant implications for clinical research and diagnostic capabilities. The reduction in false positives and negatives compared to other variant callers enhances the reliability of genetic testing results.
The introduction of the pangenome reference system addresses a important limitation in current genetic research by better representing global genetic diversity. This improvement could lead to more accurate diagnoses and better understanding of genetic conditions across different ethnicities, potentially expanding the scope of precision medicine applications.
The new study published in Nature Biotechnology validates all of the software's germline algorithms
Originally published on Illumina News Center
NORTHAMPTON, MA / ACCESSWIRE / December 10, 2024 / Illumina Vice President of Bioinformatics James Han has been in the industry for decades-so he's witnessed every stride the company has made in that time. "Illumina has worked tirelessly for the last 20 years to improve sequencing," he says. "We brought the cost of a genome from hundreds of thousands-maybe even millions-down to
For over six years, DRAGEN Secondary Analysis software from Illumina has stood out among its competitors for its speed and accuracy. But one comment its developers have heard from members of the scientific community has been that, because it's a commercial product that uses proprietary code, the inner workings of its algorithms-the secrets to its success-are invisible to the user.
Senior Director of Bioinformatics Severine Catreux has even encountered the assumption that the DRAGEN team relies on open-source components to achieve such high performance and rapid algorithmic evolution. "However, our approach is fully independent," she says. "We develop all methods in house, from initial concept through to complete implementation."
This perception needed to change. "Illumina believes in objective review of our methods," Han says. "So, we're being open with the scientific community about how the algorithms work."
A new peer-reviewed study in the October 2024 issue of Nature Biotechnology publishes the results of an unprecedented third-party validation by the Human Genome Sequencing Center at Baylor College of Medicine of every single one of DRAGEN's germline sequencing algorithms, rigorously comparing the software against other tools on the market and measuring it against industry-standard benchmarks.
The most challenging genes require a custom solution
One of the study's lead authors, and head of the validation effort at Baylor, is associate professor of molecular and human genetics Fritz Sedlazeck. His research focuses on complex parts of the genome that are linked to rare diseases and cancer, and his group has never balked at the prospect of delving into even the largest and most challenging of these regions. He says, "I'm very curious and driven by the fact that we should study all types of variants that occur in our genomes, not just the small ones."
Back in the mid-2010s, he found that the secondary analysis software available at the time often misreported these regions, and he concluded that better accuracy would require specialized algorithms and targeted variant callers. Eventually he got in touch with the DRAGEN team at Illumina to provide feedback, though he stresses that he's not partial to any one company, saying, "I just want to get the science right."
The DRAGEN team prioritized a shortlist of genes of greatest interest to the scientific community because of their potential relevance to medical research, and in the past few years, they've rapidly developed tailored solutions for characterizing these genes-for instance, GBA, which is linked to Gaucher's disease and Parkinson disease; or LPA, the copy numbers of which are directly correlated with cardiovascular disease risk.
These high-priority genes are often present in multiple copies and/or located in highly homogenous regions of the genome. This repetitive genetic code can vary widely from person to person, and it constitutes a booby trap that confuses genomic sequencers during the demultiplexing step, which stitches the complete genome back together from the smaller fragments created during library preparation.
DRAGEN now includes over a dozen specialized variant callers, tailor-made to accurately read these most challenging sections of the genome. (For more detail on DRAGEN targeted callers, follow this link.) Sedlazeck explains that researchers from various institutions have done well developing individual variant callers, but few to none of them are designed to work together. This paper shows that with DRAGEN, "you have a really comprehensive genomics workflow built together, where each component efficiently communicates with the others. DRAGEN is one of the few cases-or the only case-where these components are connected, and benefit from the innovations across them."
Accurately reflecting the world's genetic diversity-and showing our work
Another recently developed feature-and major strength-of DRAGEN is its pangenome reference, sometimes called a multigenome reference or graph genome. This breakthrough aims to counter the Eurocentric bias present in most of the available reference data to date.
The reference genome most often used by researchers today, GRCh38, has its roots in the Human Genome Project of the 1990s. It has served researchers well for a long time, "but honestly, in my opinion it's nothing more than a kind of ruler," Sedlazeck says. Unique genetic sequences that appear in non-European ethnic groups are poorly represented or even absent in this data. "We compared every human genome to that ruler, and it doesn't cope well with different variants across different ancestries."
The pangenome reference in DRAGEN compares newly read genetic sequences against other known variations in that position, drawing from sample data that better captures the spectrum of people groups across the world. Sedlazeck says this feature, combined with the power of machine learning and Illumina's proprietary algorithms, is a significant milestone that improves variant calling at any scale-from single-nucleotide variants all the way up to large copy number variations. "With this paper, we hope to show that DRAGEN has matured a lot in identifying more complex variants. This is a significant jump forward to get the whole picture of what a genome looks like in a certain individual; hopefully this catches on, and more and more studies will make use of it."
In the spirit of scientific transparency, the paper in Nature Biotechnology references all the data and truth sets used, and all the command line parameters necessary for other computational biologists and geneticists to reproduce the same results. DRAGEN is built to handle everything from individual samples to population-size studies (such as the UK Biobank and the National Institutes of Health All of Us Research Program), encompassing hundreds of thousands of them.
The numbers don't lie: DRAGEN's speed and accuracy is in a class of its own
DRAGEN demonstrated higher accuracy and faster reads compared to eight other variant callers in this study-when tested on the same fully characterized benchmark data from the US National Institute of Standards, one third-party caller had
And it enables this laser-sharp analysis in just 30 minutes of computation time. "DRAGEN can go from raw reads to VCF files to variant reports in 30 minutes for the whole human genome," Sedlazeck says. "For many people, this takes, like, half a week." These comprehensive, scalable methods are necessary to detect medically relevant variants of all types, and to discover novel genetic markers and drug targets.
Catreux has been with Illumina ever since 2018, when the company acquired Edico Genome, the original developers of DRAGEN. She says that acquisition completely changed Illumina's software landscape: "I've seen the whole evolution of DRAGEN, starting from its infancy when nobody knew about it, to the point where we talk about it worldwide. We completely take ownership of how we help our customers with data processing, and we're having a real impact in improving human health."
She and Han are proud to share the latest fruits of their labor with the world-and they're excited to tackle the challenges that lie ahead, all the while listening to customers and using feedback from leading labs like Baylor. Sedlazeck says, "I think the genomics you can now accomplish with this framework is astonishing. And I'm really looking forward to seeing how scientists will use it."
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