Noninvasive prenatal testing | |
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Other names | NIPT |
Specialty | Medical diagnosis, obstetrics and gynaecology |
Noninvasive prenatal testing (NIPT) is a method used to determine the risk for the fetus being born with certain chromosomal abnormalities, such as trisomy 21, trisomy 18 and trisomy 13. [1] [2] [3] This testing analyzes small DNA fragments that circulate in the blood of a pregnant woman. [4] Unlike most DNA found in the nucleus of a cell, these fragments are not found within the cells, instead they are free-floating, and so are called cell free fetal DNA (cffDNA). These fragments usually contain less than 200 DNA building blocks (base pairs) and arise when cells die, and their contents, including DNA, are released into the bloodstream. CffDNA derives from placental cells and is usually identical to fetal DNA. Analysis of cffDNA from placenta provides the opportunity for early detection of certain chromosomal abnormalities without harming the fetus. [5]
Non-Invasive Prenatal Testing, or NIPT, is a simple blood draw that screens for chromosomal abnormalities of a fetus while still in utero. When this screening was first performed it was used to determine the sex of a fetus, now it is also used to find aneuploidies in fetal DNA. [6] Aneuploidies are disorders in which a fetus has the incorrect number of chromosomes, either too many or not enough. [7] The use of ultrasound and biochemical markers to detect aneuploidies is usually done in the first and / or second trimester of pregnancy. [8] Aneuploidies is when a fetus retains an abnormal amount of haploid cells from their parents. However, both of these approaches have a high rate of false positive results of 2–7%. [9] If these tests indicate an increased risk of aneuploidy, then invasive diagnostic testing is used, such as amniocentesis or chorionic villus sampling. Many women, however, feel uncomfortable with the invasive testing, because of the risk associated with miscarriage, which is around 0.5%. [10] Noninvasive prenatal testing is an intermediate step between prenatal screening and invasive diagnostic testing. The only physical risk associated with the procedure is the blood draw and there is no risk of miscarriage. [11]
NIPT works by sampling cffDNA, which are small fragments of fetal blood DNA that comes from the placenta of the mother and flows in her blood vessels. Circulating cffDNA can be detected in maternal blood between the 5th and the 7th week of gestational age, [12] however more fetal DNA is available for analysis usually after 10 weeks, because the amount of fetal DNA increases over time. [13] cffDNA, RNA and intact fetal cells can all be used to assess the genetic status of the fetus non-invasively. Recent advances in DNA sequencing, such as massive parallel sequencing (MPS) and digital polymerase chain reaction (PCR), are currently under exploration for the detection of chromosomal aneuploidies via NIPT/NIPS. [14] [15] [16] [17]
Since 2014, noninvasive testing has identified aneuploidies in chromosomes 13, 16, 18, 21, 22, X and Y, including Down syndrome (caused by trisomy 21), Edwards syndrome (caused by trisomy 18), Patau syndrome (caused by trisomy 13), as well as sex chromosome aneuploidies, such as Turner syndrome (45, X) and Klinefelter syndrome (47, XXY). [18] [19] [20] These methods of cffDNA sequencing have sensitivity and specificity rates greater than 99% in identifying Trisomy 21. Sensitivity and specificity rates are lower for other aneuploidies, such as trisomy 18 (97–99% and > 99%, respectively), trisomy 13 (87–99% and > 99%, respectively), and 45, X (92–95% and 99%, respectively). The low false positive rate (1–3%) is one of the advantages of NIPT which allows pregnant women to avoid invasive procedures. [21] In the UK the Advertising Standards Authority has stated that one should not quote “Detection Rate” figures unless the figures are accompanied by (i.e. alongside)a robust "Positive Predictive Value" figure; and a clear explanations about what both figures mean. [22]
NIPT can determine paternity and may be able to determine fetal sex earlier in gestation than previous tests such as ultrasounds. It is recommended that the test be performed towards the end of the first trimester to the beginning of the second trimester, when there is enough cffDNA circulating in the mother's bloodstream to be detectable. [23] If the test is performed too early the test is more likely to yield a false negative result because there is not enough cffDNA in the sample. False negative results for NIPT would indicate that the fetus does not have a genetic abnormality when it actually does. [24] [25] It is also used to determine fetal Rhesus D, which can prevent mothers who are Rhesus D negative from undergoing unnecessary prophylactic treatment. [26] [27] Finally, it is used to detect genetic mutations, such as duplications or microdeletions, including 1p, 5p, 15q, 22q, 11q, 8q, and 4p. The sensitivity and specificity of these tests, however, for most have not yet been validated. [11]
The Natera SMART study however has shown that most cases of 22q11.2 deletion can be detected using SNP based NIPT/NIPS (Panorama) including smaller nested deletions whilst still maintaining a low false positive rate. [28] Single nucleotide polymorphism (SNP) NIPT can also detect Triploidy and can differentiate between maternal and "fetal" DNA which reduces the redraw rate and allows determination of gender for each fetus in twin pregnancies and can be done from 9 weeks of pregnancy. [29] [30]
For micro deletions such as DiGeorge syndrome, 1p36 deletion, Cri-du-chat syndrome, Wolf-Hirschhorn syndrome, Prader-Willi and Angelman syndromes, positive results can be incorrect as much as 85% of the time, according to a New York Times investigation. [31]
When a woman is pregnant the placenta will release small DNA fragments into her bloodstream (cffDNA) which can be sampled without disturbing the fetus in utero with an invasive procedure. [7] The NIPT testing uses chromosomal next generation sequencing to track the variation in fetal genes that could be signs of abnormalities. [32] A blood sample is taken from the perspective mother and the cffDNA is analyzed for several aneuploidies and other genetic markers. Once the blood test is obtained it is taken to the lab where a PCR test is performed to detect single fetal nucleotide variations.
NIPT is used to detect an array of genetic disorders including Trisomy 13 (Patau Syndrome), Trisomy 18 (Edward's Syndrome), and Trisomy 21 (Down Syndrome). [32] It can also be used to determine the sex and paternity of a child while still in utero. The most common genetic condition tested for is Trisomy 21. The test can also detect disorders that affect the sex-linked chromosomes such as Turner's Syndrome, Triple X Syndrome, and Klinefelter Syndrome. NIPT can also detect congenital heart disease such as atrioventricular septal defect, and this disease can also be a side effect in the conditions mentioned above. [33]
The NIPT test does not put the mother or the fetus in any type of danger compared to the other invasive tests that are available, making it the safest option for prenatal testing. Studies have found that the in the instance of detecting Trisomy 21 has a reliability value of 99.2%, which makes NIPT more reliable than other tests than are performed to determine the presence of these genetic disorders. [7] However, the test does have limitations. If the test is performed early during the first trimester there is a chance that it can yield false negative or positive results, and false positive results may cause unnecessary worry for prospective parents. Another concerning factor could be the cost to have these tests conducted, because some insurance companies will not cover the cost of the test if it's not deemed medically necessary. NIPT also may not be available in certain areas, limiting access to the test in these areas. There is also an ethical debate surrounding NIPT and eugenics, because the results of this test can lead to parents opting for abortion if the fetus tests positive for a genetic disorder. [34]
Amniocentesis is a medical procedure used primarily in the prenatal diagnosis of genetic conditions. It has other uses such as in the assessment of infection and fetal lung maturity. Prenatal diagnostic testing, which includes amniocentesis, is necessary to conclusively diagnose the majority of genetic disorders, with amniocentesis being the gold-standard procedure after 15 weeks' gestation.
Aneuploidy is the presence of an abnormal number of chromosomes in a cell, for example a human somatic cell having 45 or 47 chromosomes instead of the usual 46. It does not include a difference of one or more complete sets of chromosomes. A cell with any number of complete chromosome sets is called a euploid cell.
Prenatal testing is a tool that can be used to detect some birth defects at various stages prior to birth. Prenatal testing consists of prenatal screening and prenatal diagnosis, which are aspects of prenatal care that focus on detecting problems with the pregnancy as early as possible. These may be anatomic and physiologic problems with the health of the zygote, embryo, or fetus, either before gestation even starts or as early in gestation as practicable. Screening can detect problems such as neural tube defects, chromosome abnormalities, and gene mutations that would lead to genetic disorders and birth defects, such as spina bifida, cleft palate, Down syndrome, trisomy 18, Tay–Sachs disease, sickle cell anemia, thalassemia, cystic fibrosis, muscular dystrophy, and fragile X syndrome. Some tests are designed to discover problems which primarily affect the health of the mother, such as PAPP-A to detect pre-eclampsia or glucose tolerance tests to diagnose gestational diabetes. Screening can also detect anatomical defects such as hydrocephalus, anencephaly, heart defects, and amniotic band syndrome.
Chorionic villus sampling (CVS), sometimes called "chorionic villous sampling", is a form of prenatal diagnosis done to determine chromosomal or genetic disorders in the fetus. It entails sampling of the chorionic villus and testing it for chromosomal abnormalities, usually with FISH or PCR. CVS usually takes place at 10–12 weeks' gestation, earlier than amniocentesis or percutaneous umbilical cord blood sampling. It is the preferred technique before 15 weeks.
Choroid plexus cysts (CPCs) are cysts that occur within choroid plexus of the brain. They are the most common type of intraventricular cyst, occurring in 1% of all pregnancies.
The triple test, also called triple screen, the Kettering test or the Bart's test, is an investigation performed during pregnancy in the second trimester to classify a patient as either high-risk or low-risk for chromosomal abnormalities.
Echogenic intracardiac focus (EIF) is a small bright spot seen in the baby's heart on an ultrasound exam. This is thought to represent mineralization, or small deposits of calcium, in the muscle of the heart. EIFs are found in about 3–5% of normal pregnancies and cause no health problems.
The Pallister–Killian syndrome (PKS), also termed tetrasomy 12p mosaicism or the Pallister mosaic aneuploidy syndrome, is an extremely rare and severe genetic disorder. PKS is due to the presence of an extra and abnormal chromosome termed a small supernumerary marker chromosome (sSMC). sSMCs contain copies of genetic material from parts of virtually any other chromosome and, depending on the genetic material they carry, can cause various genetic disorders and neoplasms. The sSMC in PKS consists of multiple copies of the short arm of chromosome 12. Consequently, the multiple copies of the genetic material in the sSMC plus the two copies of this genetic material in the two normal chromosome 12's are overexpressed and thereby cause the syndrome. Due to a form of genetic mosaicism, however, individuals with PKS differ in the tissue distributions of their sSMC and therefore show different syndrome-related birth defects and disease severities. For example, individuals with the sSMC in their heart tissue are likely to have cardiac structural abnormalities while those without this sSMC localization have a structurally normal heart.
A nuchal scan or nuchal translucency (NT) scan/procedure is a sonographic prenatal screening scan (ultrasound) to detect chromosomal abnormalities in a fetus, though altered extracellular matrix composition and limited lymphatic drainage can also be detected.
The genetics and abortion issue is an extension of the abortion debate and the disability rights movement. Since the advent of forms of prenatal diagnosis, such as amniocentesis and ultrasound, it has become possible to detect the presence of congenital disorders in the fetus before birth. Specifically, disability-selective abortion is the abortion of fetuses that are found to have non-fatal mental or physical defects detected through prenatal testing. Many prenatal tests are now considered routine, such as testing for Down syndrome. Women who are discovered to be carrying fetuses with disabilities are often faced with the decision of whether to abort or to prepare to parent a child with disabilities.
Confined placental mosaicism (CPM) represents a discrepancy between the chromosomal makeup of the cells in the placenta and the cells in the fetus. CPM was first described by Kalousek and Dill in 1983. CPM is diagnosed when some trisomic cells are detected on chorionic villus sampling and only normal cells are found on a subsequent prenatal test, such as amniocentesis or fetal blood sampling. In theory, CPM is when the trisomic cells are found only in the placenta. CPM is detected in approximately 1-2% of ongoing pregnancies that are studied by chorionic villus sampling (CVS) at 10 to 12 weeks of pregnancy. Chorionic villus sampling is a prenatal procedure which involves a placental biopsy. Most commonly when CPM is found it represents a trisomic cell line in the placenta and a normal diploid chromosome complement in the baby. However, the fetus is involved in about 10% of cases.
Trisomy 16 is a chromosomal abnormality in which there are 3 copies of chromosome 16 rather than two. It is the most common autosomal trisomy leading to miscarriage, and the second most common chromosomal cause. About 6% of miscarriages have trisomy 16. Those mostly occur between 8 and 15 weeks after the last menstrual period.
Sequenom, Inc. is an American company based in San Diego, California. It develops enabling molecular technologies, and highly sensitive laboratory genetic tests for NIPT. Sequenom's wholly owned subsidiary, Sequenom Center for Molecular Medicine (SCMM), offers multiple clinical molecular genetics tests to patients, including MaterniT21, plus a noninvasive prenatal test for trisomy 21, trisomy 18, and trisomy 13, and the SensiGene RHD Fetal RHD genotyping test.
Ravinder (Rav) Dhallan is the chairman and chief executive officer of Ravgen.
Natera, Inc. is a clinical genetic testing company based in Austin, Texas that specializes in non-invasive, cell-free DNA (cfDNA) testing technology, with a focus on women’s health, cancer, and organ health. Natera’s proprietary technology combines novel molecular biology techniques with a suite of bioinformatics software that allows detection down to a single molecule in a tube of blood. Natera operates CAP-accredited laboratories certified under the Clinical Laboratory Improvement Amendments (CLIA) in San Carlos, California and Austin, Texas.
Cell-free fetal DNA (cffDNA) is fetal DNA that circulates freely in the maternal blood. Maternal blood is sampled by venipuncture. Analysis of cffDNA is a method of non-invasive prenatal diagnosis frequently ordered for pregnant women of advanced maternal age. Two hours after delivery, cffDNA is no longer detectable in maternal blood.
Diana W. Bianchi is the director of the U.S. National Institutes of Health Eunice Kennedy Shriver National Institute of Child Health and Human Development, a post often called “the nation’s pediatrician.” She is a medical geneticist and neonatologist noted for her research on fetal cell microchimerism and prenatal testing. Bianchi had previously been the Natalie V. Zucker Professor of Pediatrics, Obstetrics, and Gynecology at Tufts University School of Medicine and founder and executive director of the Mother Infant Research Institute at Tufts Medical Center. She also has served as Vice Chair for Research in the Department of Pediatrics at the Floating Hospital for Children at Tufts Medical Center.
The anomaly scan, also sometimes called the anatomy scan, 20-week ultrasound, or level 2 ultrasound, evaluates anatomic structures of the fetus, placenta, and maternal pelvic organs. This scan is an important and common component of routine prenatal care. The function of the ultrasound is to measure the fetus so that growth abnormalities can be recognized quickly later in pregnancy, to assess for congenital malformations and multiple pregnancies, and to plan method of delivery.
Trisomy X, also known as triple X syndrome and characterized by the karyotype 47,XXX, is a chromosome disorder in which a female has an extra copy of the X chromosome. It is relatively common and occurs in 1 in 1,000 females, but is rarely diagnosed; fewer than 10% of those with the condition know they have it.
Dame Lyn Susan Chitty is a British physician and Professor of Genetics and Fetal Medicine at University College London. She is the deputy director of the National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre. She is the 2022 president of the International Society for Prenatal Diagnosis. Her research considers non-invasive prenatal diagnostics. She was made a Dame in the 2022 New Year Honours.
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