[China Pharmaceutical Network Technology News] Recently, the fastest genome sequencing Guinness World Record was born in the "World Genome Capital - San Diego, USA". The researchers successfully performed genetic diagnosis for newborns with severe birth defects within 26 hours. However, there are some shortcomings in this record, and it is still a long way to go to the clinic. 
Although the cost of whole-genome sequencing has gradually approached the cost of conventional medical testing, it is still too slow to guide and help manage many serious diseases. As more and more evidence demonstrates the utility of whole-genome sequencing in acute care, rapid genome-wide rapidity is necessary for disease diagnosis, such as genetic diagnosis of severe neonates and chemotherapy genotype guidance for cancer recurrence. In this case, delays in clinical decision-making or relying on experience and relying on phenotypes often result in a large morbidity or mortality. Fortunately, recently, the fastest genome sequencing Guinness World Record was born in the "World Genome Capital - San Diego, USA". However, there are some shortcomings in this record, and it is still a long way to go to the clinic.
126 hours! The fastest genetic diagnosis Guinness World Record was born (WGS-26)
Stephen Kingsmore, MD
Stephen Kingsmore, MD, President and CEO of the RadyChildren's Hospital Genome Medicine Institute in San Diego, USA, completed the world's fastest genetic diagnosis to date - 26 hours. He successfully suffered from severe births within 26 hours. Defective newborns undergo genetic diagnosis and become the fastest genetically diagnosed Guinness World Record holder. Related diagnostic procedures and results were published in the journal GenomeMedicine.
Prior to this, the researchers introduced a rapid genome-wide detection method, STATseq, with a sensitivity of more than 96%, which can complete the temporary diagnosis of genetic diseases within 50 hours. Today, researchers have improved sequencing run times, alignment sequences, and variable calls, using EdicoGenome's bioinformatics data processing platform and Illumina's high-throughput sequencing instrument to successfully complete with a sensitivity of 99.5% in 26 hours. Molecular diagnosis.
Dr. Kingsmore said, “The diagnosis of a severely ill newborn is a race against time, which is why there is an urgent need for doctors to quickly provide answers and guide treatment techniques.†In the United States, I am sent to a newborn ICU. As many as one-third of children have hereditary diseases, and more than 20% of newborns die from hereditary diseases. Currently, more than 500 diseases have viable treatments, and for 70 of them, treatment in the neonatal period can help prevent disability and prevent its progression to fatal diseases. The current cost reduction of whole genome sequencing has made possible clinical testing of these and other diseases. In addition, the new bioinformatics chip has reduced the time required for genomics data analysis and promoted the application of genomics in acute medicine.
“Analysis of gene sequencing big data is often a time-consuming process, which has become a major obstacle to the clinical or forward development of genomics, especially for newborns with serious birth defects. Time is life. Dr. Pietervan Rooyen, CEO of EdicoGenome, said.
The Truth Behind 2WGS-26 - Limitations
WGS-26 has created a Guinness World Record. Not everything is perfect. It still has some limitations. Whole-genome sequencing is becoming more and more powerful, but the limitations for the diagnosis and analysis of hereditary diseases are becoming more and more prominent.
Applied to an independent clinical trial, genome-wide sequencing is still too insensitive to variant analysis, especially phenotypic genes that are highly homologous to pseudogenes require custom software to eliminate mapping of ambiguous genes or pseudogene variations. The biggest limitation of rapid whole-genome sequencing and exon sequencing in medical treatment is the interpretation of unidentified variants. For these reasons, the diagnosis of genetic diseases will require subsequent multiple types of testing, including functional testing and validation testing.
Another limitation of WGS-26 is its research methodology and validation testing of disease-causing genotypes, which often require diagnostic reports and require at least two days. When the test protocol is consistent with the guidance of CLIA and CAP on LDTs ​​(Laboratory Development Tests), the requirements for verification tests will be finalized by a recognized laboratory supervisor through a single case. However, in the next few years, high-quality complex LDTs ​​(such as whole-genome sequencing in healthcare) will require FDA approval.
A third limitation of whole genome sequencing is the lack of comprehensive negative predictive values. In addition to imperfect sensitivity analysis, the sensitivity of diagnosis is limited by the lack of knowledge of pathogenic variation. In particular, the proportion of pathogenic introns and regulatory variants in clinical databases is insufficient, and compared with unidentified exon variants, they cannot be roughly analyzed by existing pathogenicity prediction tools.
The unresolved issue of WGS26 in medical care is the multiplexing and price of the samples. WGS-26 tests a sample (dual measuring tube) with a reagent cost of $6,500, which is eight times the cost of HiseqXWGS. The prices of computer and automated analysis vary widely, averaging about $100 per genome, and the price explained and reported is about $70-700, depending on the variant. Therefore, cost is a major obstacle to the widespread adoption of WGS-26.
3 The next Guinness World Record – WGS-24 will be achieved in 2020?
In 2001, scientists from six countries spent 11 years and spent $3 billion to jointly publish a sketch of the first human genome work. As technology advances, we have achieved gene sequencing at a cost of $1,000 and the detection time has been greatly reduced. In recent years, sequencing applications have continued to emerge based on the Intel technology and Alibaba Cloud online services model. Intel’s senior vice president, general manager of the data center and interconnected systems division, Bai Anna, said that in this model, the completion of the genetic sequence The main process of precision medicine, such as testing, data analysis, disease diagnosis, and the development of personalized treatment programs, may not take 24 hours, and hopes to complete the sequencing of a person's entire genome within 24 hours by 2020.
If WGS-24 is really implemented, can it solve the current limitations of WGS-26? Can it overcome the obstacles faced in hereditary diseases? These questions may not be answered easily.
Although the cost of whole-genome sequencing has gradually approached the cost of conventional medical testing, it is still too slow to guide and help manage many serious diseases. As more and more evidence demonstrates the utility of whole-genome sequencing in acute care, rapid genome-wide rapidity is necessary for disease diagnosis, such as genetic diagnosis of severe neonates and chemotherapy genotype guidance for cancer recurrence. In this case, delays in clinical decision-making or relying on experience and relying on phenotypes often result in a large morbidity or mortality. Fortunately, recently, the fastest genome sequencing Guinness World Record was born in the "World Genome Capital - San Diego, USA". However, there are some shortcomings in this record, and it is still a long way to go to the clinic.
126 hours! The fastest genetic diagnosis Guinness World Record was born (WGS-26)
Stephen Kingsmore, MD
Stephen Kingsmore, MD, President and CEO of the RadyChildren's Hospital Genome Medicine Institute in San Diego, USA, completed the world's fastest genetic diagnosis to date - 26 hours. He successfully suffered from severe births within 26 hours. Defective newborns undergo genetic diagnosis and become the fastest genetically diagnosed Guinness World Record holder. Related diagnostic procedures and results were published in the journal GenomeMedicine.
Prior to this, the researchers introduced a rapid genome-wide detection method, STATseq, with a sensitivity of more than 96%, which can complete the temporary diagnosis of genetic diseases within 50 hours. Today, researchers have improved sequencing run times, alignment sequences, and variable calls, using EdicoGenome's bioinformatics data processing platform and Illumina's high-throughput sequencing instrument to successfully complete with a sensitivity of 99.5% in 26 hours. Molecular diagnosis.
Dr. Kingsmore said, “The diagnosis of a severely ill newborn is a race against time, which is why there is an urgent need for doctors to quickly provide answers and guide treatment techniques.†In the United States, I am sent to a newborn ICU. As many as one-third of children have hereditary diseases, and more than 20% of newborns die from hereditary diseases. Currently, more than 500 diseases have viable treatments, and for 70 of them, treatment in the neonatal period can help prevent disability and prevent its progression to fatal diseases. The current cost reduction of whole genome sequencing has made possible clinical testing of these and other diseases. In addition, the new bioinformatics chip has reduced the time required for genomics data analysis and promoted the application of genomics in acute medicine.
“Analysis of gene sequencing big data is often a time-consuming process, which has become a major obstacle to the clinical or forward development of genomics, especially for newborns with serious birth defects. Time is life. Dr. Pietervan Rooyen, CEO of EdicoGenome, said.
The Truth Behind 2WGS-26 - Limitations
WGS-26 has created a Guinness World Record. Not everything is perfect. It still has some limitations. Whole-genome sequencing is becoming more and more powerful, but the limitations for the diagnosis and analysis of hereditary diseases are becoming more and more prominent.
Applied to an independent clinical trial, genome-wide sequencing is still too insensitive to variant analysis, especially phenotypic genes that are highly homologous to pseudogenes require custom software to eliminate mapping of ambiguous genes or pseudogene variations. The biggest limitation of rapid whole-genome sequencing and exon sequencing in medical treatment is the interpretation of unidentified variants. For these reasons, the diagnosis of genetic diseases will require subsequent multiple types of testing, including functional testing and validation testing.
Another limitation of WGS-26 is its research methodology and validation testing of disease-causing genotypes, which often require diagnostic reports and require at least two days. When the test protocol is consistent with the guidance of CLIA and CAP on LDTs ​​(Laboratory Development Tests), the requirements for verification tests will be finalized by a recognized laboratory supervisor through a single case. However, in the next few years, high-quality complex LDTs ​​(such as whole-genome sequencing in healthcare) will require FDA approval.
A third limitation of whole genome sequencing is the lack of comprehensive negative predictive values. In addition to imperfect sensitivity analysis, the sensitivity of diagnosis is limited by the lack of knowledge of pathogenic variation. In particular, the proportion of pathogenic introns and regulatory variants in clinical databases is insufficient, and compared with unidentified exon variants, they cannot be roughly analyzed by existing pathogenicity prediction tools.
The unresolved issue of WGS26 in medical care is the multiplexing and price of the samples. WGS-26 tests a sample (dual measuring tube) with a reagent cost of $6,500, which is eight times the cost of HiseqXWGS. The prices of computer and automated analysis vary widely, averaging about $100 per genome, and the price explained and reported is about $70-700, depending on the variant. Therefore, cost is a major obstacle to the widespread adoption of WGS-26.
3 The next Guinness World Record – WGS-24 will be achieved in 2020?
In 2001, scientists from six countries spent 11 years and spent $3 billion to jointly publish a sketch of the first human genome work. As technology advances, we have achieved gene sequencing at a cost of $1,000 and the detection time has been greatly reduced. In recent years, sequencing applications have continued to emerge based on the Intel technology and Alibaba Cloud online services model. Intel’s senior vice president, general manager of the data center and interconnected systems division, Bai Anna, said that in this model, the completion of the genetic sequence The main process of precision medicine, such as testing, data analysis, disease diagnosis, and the development of personalized treatment programs, may not take 24 hours, and hopes to complete the sequencing of a person's entire genome within 24 hours by 2020.
If WGS-24 is really implemented, can it solve the current limitations of WGS-26? Can it overcome the obstacles faced in hereditary diseases? These questions may not be answered easily.
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