Which method is better for prenatal clinical application at this stage: CNV-seq and CMA?

The application of CNV-seq technology in prenatal diagnosis has been recognized by domestic experts, which provides a guide for clinical and laboratory use of new technologies. As the gold standard of CNV detection, CMA technology has been applied in clinic for many years and has formed a relatively mature system. At present, many clinicians are faced with a difficult problem. Faced with different technologies, how should they choose in clinical application?

Positive view: CNV-seq may be more suitable as a first-line prenatal diagnosis technology.

CNV- sequence has the advantage of uniform coverage of the whole genome, and can detect CNV larger than 100Kb, while CMA may not detect part of CNV due to limited probe coverage.

CNV-seq has the advantage of Qualcomm quantity, and can detect more than 80 samples at a time. CMA is a chip for one sample or a chip for 6-8 samples.

The operation of CNV-seq is simple, without PCR database, the amplification preference can be reduced, and the sample size is low, and all DNA samples as low as 10ng can be detected.

CNV-seq has better detection efficiency in small-scale chimeras, and can detect about 10% of chimeras, while CMA is not accurate for less than 30% of chimeras.

CNV-seq platform has good compatibility and can be used on computers at the same time as NIPT.

Aneuploidy was also detected by CNV sequence combined with short tandem repeats.

CNV-seq technology has strong expansibility and conforms to the development of the times.

Contrastive point of view: CMA is still recommended for prenatal application at this stage.

Technological innovation is the trend. We don't deny that whole genome sequencing will greatly promote the development of detection technology and find more variations. However, at this stage, microdeletions and microreplications caused by pathogenic CNV can basically be detected by CMA, and authoritative organizations at home and abroad have issued guidelines for clinical application of CMA before and after delivery, detailing the application details of CMA technology. In terms of overall efficiency, CMA is not lost to CNV-seq, so CMA is still one of the excellent methods for prenatal diagnosis of genetics.

There are still many details to be clarified before the clinical application of CNV-seq, and large-scale prenatal promotion still needs large sample size to verify the efficacy. Some key indexes such as sequencing depth, PPV/NPV of pathogenic small CNV need to be clarified.

Although the detection range of CNV sequences has expanded, it has also brought more unexpected discoveries. It is not a good thing for clinicians and their families to provide too many variations beyond the current medical knowledge.

At present, CMA is still the gold standard for CNV detection, and its SNP probe can not only verify CNV signal again, but also provide UPD/AOH signal to avoid missed detection of some important diseases. In an experienced laboratory, 10% chimera can be found by SNP signal.

Through technological innovation, such as the development of exon chip, CMA still has good application value.

We believe that at this stage, the efficiency of the two technologies is similar. Prenatal application should pay more attention to the accurate interpretation of test results and genetic counseling.

Speaker 1:

1. For chimeras, through consulting the data of our center, it is found that CMA is actually superior to CNV-seq in all aspects, and chimeras larger than 10% can be routinely detected.

2.CMA is not a problem when detecting flux. For a maternity clinic with 80 cases of amniotic fluid a month, although one chip can take 8 samples at a time, it can make 10 chips at the same time.

3. In the aspect of efficacy verification, CMA and CNV-seq of amniotic fluid samples were compared in parallel in our hospital. Because CMA adopts high-density SNP chip, the detection rate is 0.25 times higher than CNV-seq of big data in the case of100-400 K.

4. We believe that what we are pursuing is that SNV+CNV can produce effects at the same time, that is, the integration of WES and CNV-seq can get higher income with less money and improve a higher service platform for patients.

5. From the technical point of view, the two are equivalent, but at present, the clinical detection of amniotic fluid CMA is more stable, and CNV-seq can do it, but we have not stopped CMA detection, just in case, after all, it is a prenatal sample, so we need to be cautious.

Speaker 2:

1, the more loci detected, the better. Some mutation sites are unclear, patients have no clinical phenotype, and the penetrance rate is low, which brings difficulties to clinicians' genetic counseling.

2. Not all mutations will lead to very unfavorable results, and not all children are suitable for WES or WGS. More than ten years of clinical experience tells us that even if there is pathogenic variation, the impact of targeted clinical management, quality of life and longevity can be controlled.

3. There are more than 8,000 monogenic diseases. At present, cognition is limited, which leads to limited clinical experience. The mutation frequency based on population may vary greatly, so it is very challenging to give genetic counseling to patients.

Speaker 3:

1, we admit that the newer the technology, the better, and the old technology will definitely be eliminated. The use of technology is targeted. I recognize the advantages of CNV-seq, and admit that UPD is not as good as CMA, so there is no need to avoid it objectively.

2. The more information you detect, the more choices you give your family. The premise is that genetic counseling should be professional, not testing anything, but focusing on genetic counseling.

Speaker 4:

CNV-seq*** was released before the United States, which may be the result of technology, data and business promotion. The two technologies are tools of different methodologies, and which one to use mainly depends on how to choose. From the clinical point of view, if prenatal diagnosis is to be made, CNV, UPD, LOH and CMA are recommended; If you can tolerate the above-mentioned missed detection, you can choose CNV sequence.

Comments:

The debate about the comparison between CNV sequence and CMA is good and necessary. CMA is a mature platform with more than ten years of clinical application history, but it is a "closed" platform; CNV sequence is a new technology based on NGS, and it is an "open" platform. It is conceivable that this technology will continue to improve in the future. The purpose of this debate is to compare CNV- sequence, a clinical CNV detection project, with CMA platform commonly used in clinic. Any viewpoint is time-sensitive, and its true meaning needs to be analyzed through superficial phenomena:

1. Whole genome unified coverage:

CNV-seq is a technology based on the second generation sequencing to detect CNV, so the uniform coverage of the whole genome is the feature of this technology platform, which is an advantage for the detection of SNV, but this feature is not necessarily the advantage of CNV detection. We know that the relationship between genome and disease is heterogeneous, some regions of genome are closely related to genetic diseases, and some regions can be known polymorphism. At present, the design of CMA chip deliberately avoids the polymorphic region, repetitive region and pseudogene region of CNV in genome, but for pathogenic genes, especially those that often take CNV as pathogenic variation, the probe density is deliberately increased to detect smaller CNV. Therefore, the heterogeneity of CMA probe distribution is an advantage rather than a disadvantage. On the contrary, many CNVs with no clinical significance can be detected even by covering CNV sequences, which increases the burden of analysis and the possibility of false positives. Of course, the problem of false positives can be controlled by CNV filtering.

2. Detection sensitivity

It is possible and credible to detect CNV of 10kb or even smaller with CMA. At present, the detection sensitivity of CNV-seq is about 100K K. As for the accuracy of CNV, we don't need to verify most CNV detected by CMA due to the accumulation of empirical data, but at present, our credibility of CNV-seq is not certain enough. In addition, CMA can detect UPD, AOH and polyploid due to SNP probe. At present, CNV-seq has no ability to detect these important mutations, and it needs to be combined with STR probe experiments to make up for them.

3. Operating flux

CNV-seq should have a higher detection flux, but at present, the flux of CMA can reach 200 samples/person/week, but CNV-seq can't reach this flux and needs more personnel input, so the Qualcomm amount of CNV-seq needs to be realized in the routine operation of the laboratory.

4. Chimera detection

Both CMA and CNV-seq can detect low-proportion chimeras (such as 10%). In fact, CMA can detect low-level chimeras, but general laboratories will not choose to report low-level chimeras.

5. All five. CNV seq and CMA are facing the challenge of genetic counseling.

At present, no matter which technology is adopted, the development of technology is beyond the development of clinical medicine. In the face of CNV with unknown clinical significance and CNV with unknown penetrance detected by prenatal diagnosis, genetic counseling is difficult no matter which technical platform is used.

The second generation sequencing technology (NGS) will be the development direction of CNV detection in the future because of its flexibility and high sensitivity. Considering the correlation between coverage depth and cost, the products developed by NGS are used for clinical prenatal diagnosis to replace CMA technology, which requires more verification and improvement of relevant analysis processes, and we need to have a more comprehensive understanding of CNV produced by the whole genome.

I am Yining, who has been engaged in Internet and prenatal genetic testing for many years. Anyone who is interested in joining our team can drop me: yining00 10.