Recently, the list of the first batch of pilot units for clinical application of high-throughput sequencing technology, commissioned by the Department of Maternity and Childhood of the National Health and Family Planning Commission to the Chinese Medical Association, the Clinical Laboratory Center of the National Health and Family Planning Commission and the Expert Group for Prenatal Diagnosis Evaluation and Determination, was announced, and was granted to carry out pilot work in three specialties: diagnosis of genetic diseases, prenatal screening and diagnosis, and preimplantation embryo genetic diagnosis.
The Technical Specification for High-throughput Genetic Sequencing Prenatal Screening and Diagnosis (Trial) was researched and developed. 109 medical institutions nationwide were approved to carry out the pilot work of non-invasive prenatal testing (NIPT) high-throughput sequencing based on second-generation sequencing technology. The Notice on Strengthening the Management of Products and Technologies Related to Clinical Use of Genetic Testing (Food and Drug Administration Office of Machinery Management [2014] No. 25) issued by the Department of Women and Children of the National Health and Family Planning Commission clearly describes the work of the pilot unit, specifically including: prenatal screening and prediagnostic consultation, scope of application, signing of informed consent, clinical data collection and specimen collection requirements, review and use of test reports, post-test clinical The work content includes: prenatal screening and diagnosis consultation, scope of application, informed consent, clinical data collection and specimen collection requirements, review and use of test reports, post-test clinical consultation, follow-up clinical services for high-risk pregnant women, follow-up, statistical reporting, and other related contents that need to be piloted in order to standardize the clinical services of high-throughput gene sequencing.
Southern Hospital of Southern Medical University was selected as one of the first units to receive the pilot work. The Director of Obstetrics and Gynecology Department of the hospital, Zhong Mei, was invited to be interviewed by China Obstetrics and Gynecology Network to give a professional interpretation of the Technical Specification for High-Throughput Genetic Sequencing Prenatal Screening and Diagnosis (Trial).
A definition of non-invasive prenatal screening
Classified according to different methods of obtaining fetal specimens, prenatal testing is divided into invasive and non-invasive. At present, invasive prenatal diagnosis is the gold standard for diagnosing fetal chromosomal disorders, which mainly refers to the collection of fetal cells or tissues through chorionic villus biopsy, amniocentesis and umbilical vein puncture to obtain fetal chromosomal information. The accuracy of invasive testing is 98%-99%, but is associated with a 0.5%-1% risk of miscarriage, as well as the risk of amniotic fluid leakage and intrauterine infection, so invasive prenatal diagnosis is currently used only to screen for high-risk, high-risk pregnancies or families that have had children with genetic disorders.
Traditional noninvasive prenatal tests include ultrasonography and maternal serology, which can be used to avoid risks to the fetus and the pregnant woman, but have limited sensitivity and specificity. In the last two decades, prenatal screening based on a combination of ultrasonography and maternal serological screening for various proteins or hormones has developed rapidly. The target diseases of prenatal serological screening are 21, 18-trisomy and neural tube defects, and their detection rates in early, mid and early combined with mid pregnancy are 83%, 81% and 94%-96%, respectively, with a false positive rate of about 5%. The high false positive rate of these methods brings greater clinical pressure and laboratory pressure for subsequent invasive prenatal diagnosis, which brings some unnecessary punctures.
In recent years, with the development of new generation high-throughput sequencing technology, non-invasive prenatal testing (NIPT) technology based on second-generation sequencing technology has emerged, referred to as non-invasive prenatal genetic testing.
How is non-invasive prenatal testing defined?
Studies have shown that a large number of free DNA fragments from the fetus are present in the peripheral blood of pregnant women for a long period of time throughout pregnancy, and the percentage of free fetal DNA is stable in the peripheral blood of pregnant women after about 7 weeks of pregnancy and increases slowly with the increase of pregnancy weeks.
The technique of non-invasive prenatal genetic testing is to extract only the free fetal DNA from the peripheral blood of the pregnant woman and use the new generation of high-throughput sequencing technology combined with bioinformatics analysis to detect the fetal genes. This effectively avoids the risks to the fetus and the pregnant woman caused by invasive tests such as chorionic villus biopsy, amniocentesis and umbilical vein puncture.
What diseases can be detected by the III non-invasive prenatal genetic test?
Currently in clinical use, prenatal testing is performed for chromosomal aneuploidy disorders, mainly trisomy 21 aka Down syndrome, trisomy 18, and trisomy 13.
There are various disorders in the research stage, like thalassemia, pseudohypertrophic muscular dystrophy (DMD), hemophilia, etc. With the increase of sequencing depth and the development of bioinformatics, more and more diseases will be able to be applied to clinical testing.
What are the target diseases and technical positioning of NIPT technology?
According to the expert consensus, the target diseases of this technology at the current stage of development should be clearly defined as fetal trisomy 21, trisomy 18 and trisomy 13, and the clinical application should be located at the “approximate level of prenatal diagnosis” and the “precise target diseases”. The main reasons are as follows.
The main reasons are as follows.
(1) The clinical validity of this technique for prenatal screening for trisomy 21, trisomy 18, and trisomy 13 has been well established in several clinical studies.
(2) False-negative cases and failed tests for trisomy 21, trisomy 18, trisomy 13, and sex chromosome abnormalities (2-5%) were present in all of these studies.
(3) These studies suggest a low compliance rate (about 25%) for the noninvasive diagnosis of sex chromosome abnormalities.
(4) From a technical point of view, cases of twin or multiple births, chimerism and chromosomal abnormalities in the parents are not suitable for NIPT analysis, which accounts for about 5% of all cases;
(5) Due to the limitations of the developmental process, the technology lacks effective screening indication for other chromosomal trisomies, structural abnormalities and microdeletion syndromes at this stage.
What are the advantages of non-invasive prenatal genetic testing?
(1) Traditional serological screening methods have a high risk of false positives and missed tests; the new technology has a high detection rate and a low false positive rate for the target disease. It can be used in early and middle pregnancy and even after 23 weeks of gestation.
(2) Non-invasive prenatal genetic diagnosis only collects a small amount of maternal blood and extracts free fetal DNA from it for testing. It requires less information, is convenient to obtain material, the process is simpler and quality control is relatively easy. There is room for further development of the technology.
(3) Traditional prenatal diagnosis uses invasive sampling methods, which have risks of infection and miscarriage; it can effectively reduce the number of subsequent invasive prenatal diagnosis and solve the problem of insufficient technical strength of prenatal diagnosis.
VI What are the limitations of non-invasive prenatal genetic testing?
(1) The number of target diseases for screening is still small, narrowing the range of diseases for subsequent prenatal diagnosis.
(2) Dual/multiple births, chimerism and chromosomal abnormalities in parents are not suitable for screening by this technology.
(3) Non-invasive prenatal genetic screening still cannot replace invasive prenatal diagnostic testing (if the non-invasive test result is positive, amniotic fluid or cord blood puncture is still required for definitive diagnosis).
What is the accuracy of non-invasive prenatal genetic testing?
The technology has a high detection rate and a low false positive rate for the target diseases. The overall detection rate for common chromosomal aneuploidy abnormalities such as trisomy 21 is over 99%, and the false-positive rate is about 0.1%, which is much better than the efficiency of current prenatal serological screening.
However, the target diseases for screening are now only trisomy 21, trisomy 18, and trisomy 13, and humans have 23 pairs of chromosomes, so there is no way to know about the other chromosomes. Invasive prenatal diagnosis is still the gold standard for diagnosing fetal chromosomal disorders.
VIII Who is suitable for non-invasive prenatal genetic testing?
(1) Pregnant women who cannot undergo invasive prenatal diagnosis, like those with preterm miscarriage, fever, bleeding tendency, untreated infection, etc.
(2) Pregnant women with critical high risk for prenatal screening (e.g. risk rate of 1/270-1/1000).
(3) Pregnant women of advanced age (age >35 years) when not combined with other high-risk factors for chromosomal disorders
(4) Pregnant women with precious child pregnancies who knowingly refuse interventional prenatal diagnosis
(5) Pregnant women who are extremely anxious about interventional prenatal diagnosis
(6) Pregnant women who cannot get an appointment for prenatal diagnosis.
Under what circumstances is non-invasive prenatal genetic testing not suitable?
(1) Pregnant women with abnormal prenatal ultrasound examination
(2) Pregnant women with twin or multiple births
(3) When either of the couple has a definite chromosomal structure or number abnormality.
(4) Pregnant women whose fetus is suspected of having microdeletion syndrome, other chromosomal abnormalities or genetic disorders
(5) Pregnant women who have received allogeneic blood transfusion, transplantation, stem cell therapy, or immunotherapy.
When can I have non-invasive prenatal genetic testing?
In the Obstetrics and Gynecology Department of Southern Hospital of Southern Medical University, pregnant women from 9 weeks to 26 weeks of pregnancy can have their blood drawn for non-invasive prenatal genetic screening.
What do I need to do before having a non-invasive prenatal genetic test?
This test does not require fasting, so pregnant women can have the test after meals.
The following is the data of non-invasive prenatal testing (NIPT) based on second-generation sequencing technology in Southern Hospital: 2010-2014, 1080 cases were done in 5 years, 10 abnormalities were found, 8 cases of trisomy 21 and 2 cases of sex chromosome abnormalities. The final diagnosis was confirmed by amniocentesis: 8 cases of trisomy 21 and 1 case of sex chromosome abnormality. There was one case of sex chromosome abnormality which was false positive. There were no cases of missed diagnosis.
Can twelve high-throughput sequencing technologies be used for genetic diagnosis of genetic diseases?
Current studies have shown that whole-genome sequencing of single-gene genetic disease lines using high-throughput sequencing technology can identify disease-causing mutations. This makes it possible to make high-speed and precise genetic diagnosis of genetic diseases with many causative genes and high genetic heterogeneity. In addition, with the decreasing cost and time of sequencing, personal genome sequencing may become the basis for personalized healthcare.
Can high-throughput sequencing technology replace gene chips?
High-throughput sequencing technology can obtain millions or even millions of sequences at a time, and therefore has the potential to replace “gene chip” technology.
Since the detection range of gene chips depends on the information of probes on the chips, they can only detect the characteristics of known sequences and lack the ability to find new genes, whereas high-throughput sequencing can make up for the shortcomings of gene chips.
However, high-throughput sequencing technology has been established for a short period of time, the technology is not very mature, and its information reserve is also very limited; while gene chip technology has been developed for more than 20 years, and its experimental technology and later data analysis theory have been very mature and complete, and a huge public database has been accumulated, so gene chip technology will still dominate for a short period of time. However, it is believed that in the near future, high-throughput sequencing technology will become more and more mature and be more widely used.
The announcement of the list of high-throughput pilot units brings confidence to the whole industry, meaning that the genetic testing industry will be “lawful” and the whole industry order will be rational and normal. For families with rare diseases and pregnant women with genetic testing needs, there will be a formal channel for genetic testing, which can help these families avoid genetic risks and have healthy next generation, which is a good thing for the country and the people!