INTRODUCTION — Approximately 3 percent of live births are affected by a major structural anomaly [1]. With advances in prenatal ultrasound, many of these anomalies are now identified before birth. The etiology is diverse and includes environmental factors, genetic factors, or a combination of both.
As the landscape of genetic testing rapidly evolves, clinicians are often left with many questions about the most appropriate testing methods to use for prenatal diagnosis (table 1). This topic will provide a reasonable approach to the genetic evaluation of a fetus with anomalies. Postnatal evaluation of the anomalous infant is reviewed separately. (See "Birth defects: Approach to evaluation".)
FREQUENCY OF CHROMOSOMAL ABNORMALITIES IN FETUSES WITH ANOMALIES — The finding of a fetal structural anomaly increases the possibility of a chromosomal abnormality or genetic molecular defect and should prompt further evaluation into genetic etiologies. The frequency of a chromosomal abnormality in this setting depends on several factors: the specific anomaly, the number of anomalies, and the combination of anomalies identified [2].
In several retrospective series of prenatally detected anomalies on ultrasound that prompted genetic studies, the frequency of fetal chromosomal abnormalities in cases of isolated and multiple fetal anomalies was [2-7]:
●Isolated fetal anomalies – 2 to 18 percent of cases
●Multiple fetal anomalies – 13 to 35 percent of cases
APPROACH TO EVALUATION OF THE FETUS WITH ANOMALIES
Overview — For patients with structural fetal abnormalities on ultrasound examination, standard clinical practice is to offer an invasive procedure for diagnostic genetic testing (algorithm 1) [8]. If a genetic etiology accounting for the abnormalities is determined, then well-informed counseling about prognosis, reproductive options, obstetric and pediatric management, and recurrence risks is possible.
The decision to undergo an invasive procedure for diagnostic testing is personal and must be based on the individual patient's values and goals. For patients to make informed decisions, pretest counseling should be provided by a clinician familiar with the suspected fetal diagnoses, genetic testing options, and alternatives to prenatal diagnostic testing, such as prenatal screening and postnatal diagnostic testing.
Depending on the gestational age at the time of diagnosis, chorionic villus sampling (CVS) or amniocentesis can be offered to obtain a fetal specimen for genetic testing. CVS is typically performed between 10 and 13 weeks of gestation (see "Chorionic villus sampling"). Amniocentesis is optimally performed at ≥15 weeks of gestation (see "Diagnostic amniocentesis"). When performed at a high-volume, experienced center, the procedure-related pregnancy loss rate for amniocentesis and CVS is estimated to range from approximately 1 in 300 to 1 in 1000 (0.1 to 0.3 percent) [9]. The observed pregnancy loss rate after CVS is higher than after amniocentesis because CVS is performed at an earlier gestational age when the background risk for spontaneous loss is higher.
Fetus with sonographic features consistent with a common trisomy — Our approach to the fetus with anomalies in whom a common trisomy is suspected based on ultrasound findings follows (see "Sonographic findings associated with fetal aneuploidy", section on 'Sonographic features of selected aneuploidies'):
●Begin with fluorescence in situ hybridization (FISH) – The authors' practice is to begin the genetic evaluation of these fetuses with interphase FISH for the major aneuploidies (chromosomes 13, 18, 21, X, and Y). The FISH results are typically available in 24 to 48 hours compared with the 7 to 10 days needed for conventional karyotype or chromosomal microarray analysis (CMA). Although FISH provides a rapid result, it also adds to the cost of the fetal evaluation, so it is also reasonable to proceed directly to a conventional karyotype or CMA. (See 'Fluorescence in situ hybridization' below.)
●If the FISH is consistent with aneuploidy, the results should be confirmed with a conventional karyotype. Although FISH on amniocytes is accurate, we recommend confirming abnormal FISH results with a karyotype to determine if the aneuploidy detected is secondary to an unbalanced translocation (representing a risk for a balanced translocation in a parent) or nondisjunction. This information is needed to determine recurrence risks. (See 'Conventional karyotype versus microarray' below and 'Posttest counseling' below.)
●If the FISH is not consistent with aneuploidy, we offer CMA instead of a conventional karyotype as this approach allows for a higher diagnostic yield. CMA can be performed on the same fetal specimen used for FISH. Before proceeding with CMA, patients should meet with a with a qualified clinician to review the spectrum of possible results and test limitations. (See 'Pretest and posttest counseling' below and 'Conventional karyotype versus microarray' below.)
Fetus with sonographic features that do not primarily suggest a common trisomy — Our approach to the fetus with anomalies in whom a common trisomy is not suspected based on ultrasound findings follows (see "Sonographic findings associated with fetal aneuploidy", section on 'Sonographic features of selected aneuploidies'):
●Begin with CMA – The authors' practice is to begin the genetic evaluation of these fetuses with CMA because of its higher diagnostic yield compared with a conventional karyotype. Our approach is the same whether the anomaly appears to be isolated or multiple structural anomalies are observed. While studies have suggested that the risk for chromosomal abnormalities or genetic syndromes is higher when multiple anomalies are present, we believe that an isolated anomaly still warrants a thorough investigation when desired by the patient. Furthermore, an apparently isolated anomaly on prenatal ultrasound may not be isolated when the newborn is evaluated. (See 'Conventional karyotype versus microarray' below.)
●If CMA identifies a variant – Patients should discuss the significance of their results with a qualified clinician. (See 'Posttest counseling' below.)
●If CMA does not identify a variant – For patients interested in pursuing additional genetic testing after a nondiagnostic CMA, we review available testing options and, when appropriate, suggest targeted gene sequencing and gene panels instead of exome sequencing (ES) [10]. The targeted approach reduces some of the risk of finding genomic variants of uncertain clinical significance or incidental findings. Additionally, the turnaround time of such tests is typically shorter. We anticipate that this is an area that will change significantly in coming years as our understanding of ES expands. (See 'Gene sequencing' below.)
Options for patients who decline an invasive procedure — Patients who decline to have an invasive procedure for diagnostic genetic testing may choose to undergo cell-free DNA screening and use the results to inform further decision making, or they may choose to undergo postnatal diagnostic genetic testing.
Cell-free DNA screening
●Conventional cell-free DNA screening – A definitive prenatal genetic diagnosis can only be made through an invasive procedure to obtain a sample on which to perform one of the diagnostic tests described above. However, some patients decline invasive procedures because they feel the results would not impact their decision to carry the pregnancy to term or they may find the risk of fetal loss to be unacceptable. If we suspect trisomy 21, 18, 13, or a sex chromosome aneuploidy, we offer a cell-free DNA screening test to these patients to provide additional information about the risk of aneuploidy in the pregnancy, with appropriate pretest and posttest counseling. (See "Prenatal screening for common aneuploidies using cell-free DNA".)
•Result: no increased risk of trisomy 21, 18, 13, or a sex chromosome aneuploidy – Patients should be counseled that this result does not eliminate the possibility of a genetic condition in the fetus and can be falsely reassuring in the setting of a fetal anomaly [11,12]. It has been estimated that, in the setting of a fetal anomaly, 8 percent of chromosomal abnormalities detectable by conventional karyotype will be missed if cell-free DNA screening is performed instead of diagnostic testing. The magnitude of cell-free DNA underdiagnosis is expected to be even higher when compared with CMA [13]. It is estimated that cell-free DNA screening would miss 16 percent of cytogenetic abnormalities diagnosed by FISH, conventional karyotype, and CMA in fetuses with anomalies [14].
•Result: increased risk of trisomy 21, 18, 13, or a sex chromosome aneuploidy – Patients also need to understand that a cell-free DNA test result showing an increased risk of aneuploidy may be a false positive [15]. The positive predictive value of a positive test is higher in the setting of a comprehensive ultrasound examination by an experienced sonologist that clearly shows features of trisomy 18, trisomy 13, or triploidy, but even in this setting, prediction of fetal aneuploidy is not 100 percent accurate. In addition, a trisomy that results from an unbalanced rearrangement in the fetus could be inherited from a parent who carries a balanced rearrangement, which has implications for recurrence risk. Therefore, all cell-free DNA results indicating an increased risk for aneuploidy should be confirmed with diagnostic testing, either pre- or postnatally. Cell-free DNA results should also be confirmed prior to a pregnancy termination or any other irreversible procedure. (See "Sonographic findings associated with fetal aneuploidy", section on 'Trisomy 18 (Edward syndrome)' and "Sonographic findings associated with fetal aneuploidy", section on 'Trisomy 13 (Patau syndrome)' and "Sonographic findings associated with fetal aneuploidy", section on 'Triploidy'.)
•No call result – It has been reported that 1 to 5 percent of cell-free DNA tests will report "no result" for trisomy 21, 18, and 13 and sex chromosome aneuploidies. The reasons for test failures are multiple and depend on the testing platform, performing laboratory characteristics, fetal fraction, and patient characteristics [16]. Further evaluation following a test failure can include repeating cell-free DNA screening with a second sample or proceeding with diagnostic testing. (See "Prenatal screening for common aneuploidies using cell-free DNA", section on 'No call or no result'.)
●Expanded cell-free DNA screening – Cell-free DNA screening for conditions other than trisomy 21, 18, 13, and sex chromosome aneuploidies is not recommended on a population-wide basis [17,18]. The use of expanded cell-free DNA screening (either microdeletion screening or "whole genome" coverage) has not been clinically validated in the setting of a fetus with anomalies. (See "Prenatal diagnosis of chromosomal imbalance: Chromosomal microarray", section on 'Need for an invasive procedure'.)
Patients who desire this level of information regarding the genetic status of their fetus should opt for diagnostic testing on amniocytes or chorionic villi. However, the authors have encountered patients who consider cell-free DNA screening to be an acceptable alternative to diagnostic testing. For these patients, the decision to proceed with expanded cell-free DNA screening should only be made after appropriate counseling by a qualified clinician regarding the limitations of this testing.
Postnatal testing — The approach to postnatal evaluation of the anomalous infant is reviewed separately. (See "Birth defects: Approach to evaluation".)
PRETEST AND POSTTEST COUNSELING
Pretest counseling — Appropriate pretest counseling is critical for patients who are making the decision to undergo genetic testing. The goal of this counseling is to help patients understand the benefits and limitations of testing, discuss possible test results, and help patients make informed decisions consistent with their own goals and values [19]. Ideally, a certified genetic counselor or a knowledgeable obstetric provider should provide this counseling. Pretest counseling following the diagnosis of a fetal anomaly includes a discussion of the following:
●All testing options:
•Invasive diagnostic tests – Chorionic villus sampling or amniocentesis, percutaneous umbilical cord blood sampling.
•Screening tests – Serum screening, ultrasound, cell-free DNA.
•No additional testing.
●Possible results:
•Aneuploidy or pathologic variant with defined phenotype.
•Copy number variants with variable phenotype.
•Variant of uncertain significance.
•Incidental findings, including nonpaternity, consanguinity, and adult-onset disease.
•Normal results.
●Patient's values and goals:
•Patient's general attitudes toward prenatal testing and screening.
•Views and availability of pregnancy termination.
•Views on parenting, fears of coping with the challenges of a child with disabilities.
●Potential psychosocial issues:
•The meaning that the specific diagnosis has for the family, the sense of loss of a normal pregnancy or baby, any significant discord between parents or relatives.
•Coping strategies, referrals, and awareness of available resources when appropriate.
●Pregnancy/postpartum management options:
•Options of pregnancy termination versus continuing the pregnancy with possible changes in antepartum, intrapartum, and postpartum/neonatal care. Patients who would elect to continue a pregnancy with a life-limiting diagnosis (fetal demise, intrapartum fetal death, or neonatal/infant death is expected), discussing the option of perinatal palliative care can provide support and guidance for families throughout the pregnancy and birth. Additional resources for caregivers can be found at the Perinatal Hospice and Palliative Care.
Posttest counseling — Following genetic testing, it is important that patients are given the opportunity to discuss the significance of their results with a qualified provider. This is important for patients with both abnormal and normal results:
●Abnormal results:
•Significance of results for the health of the fetus, before and after birth, including the limitations of prenatal phenotyping.
•Review patient's goals and values and pregnancy/postpartum management options as discussed during pretest counseling.
•Recommended follow-up after birth.
•Review recurrence risk and options for future pregnancies.
●Normal results:
•Discuss that, while normal results are reassuring, they do not eliminate the possibility of an underlying genetic condition in the fetus.
•Review options for additional evaluation after birth, including consultation with a medical geneticist if appropriate.
TESTING OPTIONS — Testing options are described below and summarized in the table (table 1).
Fluorescence in situ hybridization — Autosomal trisomies for 21, 18, and 13; sex chromosome aneuploidy; and triploidy account for 80 percent of clinically significant chromosomal conditions diagnosed prenatally [20]. Fluorescence in situ hybridization (FISH) can be used for rapid and accurate detection of aneuploidies involving chromosomes 21, 18, 13, X, and Y, with results typically available in 24 to 48 hours [20].
The positive predictive value for FISH is high, reported to be 100 percent for trisomies 21, 18, and 13, and 98.5 percent for 45,X [21]. However, confirmatory testing with a conventional karyotype is required to determine if a translocation is present. Normal FISH results also require additional testing, either through a conventional karyotype or chromosomal microarray analysis (CMA), as alternations in chromosome structure and less common aneuploidies would be missed if FISH was used in isolation. (See "Tools for genetics and genomics: Cytogenetics and molecular genetics", section on 'Fluorescence in situ hybridization'.)
Conventional karyotype versus microarray — Conventional karyotyping has been the standard for prenatal diagnosis, but use of CMA is increasing. CMA detects small (10 to 100 kb) gains and losses of genetic material (called copy number variants [CNV]) that would not be identified by traditional karyotyping yet have the potential to lead to significant phenotypic abnormalities. By contrast, conventional karyotyping has a resolution of only 5 to 10 Mb, which is far larger. Additionally, CMA does not require cell culture, which reduces the turnaround time for results. In a systematic review of prenatal CMA, a clinically significant CNV was detected in 5.6 percent (95% CI 4.7-6.6 percent) of euploid fetuses with an ultrasound anomaly restricted to one anatomic system and in 9.1 percent (95% CI 7.5-10.8 percent) of euploid fetuses with multiple anomalies [22]. These estimates are similar to other reviews in which significant CNV in euploid fetuses with ultrasound anomalies ranged from 5.1 to 10.0 percent [23,24].
The greater depth of molecular analysis with CMA increases the likelihood of a diagnosis but is accompanied by identification of background variability and genetic diseases not associated with the fetal anomaly being evaluated (ie, incidental findings), which increases the complexity of prenatal counseling. For example, CMA may detect variants of unknown significance, previously unsuspected genetic variants in one or both parents, or fetal genes associated with adult-onset diseases. In addition, while CMA has improved resolution over conventional karyotype, this technique will not identify some clinical significant genetic findings, such as gene sequence changes that might affect gene function, balanced structural rearrangements, and unbalanced translocation versus free-lying nondisjunction. (See "Prenatal diagnosis of chromosomal imbalance: Chromosomal microarray", section on 'Benefits and limitations of CMA'.)
Many professional societies, including the American College of Obstetricians and Gynecologists (ACOG) and the Society for Maternal-Fetal Medicine (SMFM), have recommended use of CMA for prenatal diagnosis. The ACOG committee opinion states that CMA is recommended instead of a karyotype when the fetus has one or more major structural abnormalities identified on ultrasound [25]. ACOG has also stated that CMA should be made available to any patient choosing to undergo invasive diagnostic testing. (See "Prenatal diagnosis of chromosomal imbalance: Chromosomal microarray" and "Genomic disorders: An overview".)
Gene sequencing — When chromosomal analysis, including CMA, is nondiagnostic, the next step in the genetic evaluation is testing for specific genetic conditions through molecular genetic studies. Clinicians should inform the laboratory that this additional testing might be requested if cytogenetic results are nondiagnostic. The testing is performed on fetal DNA from cultured chorionic villi or amniocytes obtained at the time of the diagnostic procedure; if an adequate sample is obtained, DNA can often be directly extracted from chorionic villi or amniocytes without culture and thus shorten the time to results. If an adequate cultured or direct sample from the original procedure is not available, then a second procedure may be required. Patients must also be aware that parental blood samples are often required for confirmatory testing.
In the postnatal setting, molecular genetic studies often involve consultation with a medical geneticist and targeted testing based on recognized patterns of anomalies and other clinical findings. Testing may include molecular genetic analysis, such as sequencing of single genes, gene panels, or exome sequencing (ES) [26]. While the presence of a fetal anomaly increases the risk for an underlying genetic condition, the ability to test and value of testing for specific conditions prenatally can be more challenging. For example, prenatal prognostic counseling is complicated because the characteristic phenotype may be incomplete prenatally, the disorder may evolve from the time of initial diagnosis and counseling to late pregnancy, and disorders identified prenatally may have more benign or more deleterious outcomes than the same disorders identified postnatally [27]. Additionally, genetic testing can be a long process, and the rapid turnaround time required for prenatal testing often limits this process.
Targeted gene sequencing — Targeted gene sequencing refers to testing of a specific gene or genes known to be associated with a genetic condition. Single gene testing in the prenatal period often relies on a positive family history and a previously identified pathogenic variant [28]. For example, achondroplasia is caused by genetic alterations in FGFR3. When achondroplasia is suspected clinically, sequencing FGFR3 can confirm the diagnosis [29].
Some genetic conditions are associated with genetic changes in multiple genes. For example, Noonan syndrome has been associated with pathogenic variants in PTPN11, SOS1, KRAS, RAF1, NRAS, BRAF, and MAP2K1. If Noonan syndrome is suspected clinically, then sequencing a panel of the genes associated with Noonan syndrome through massively parallel sequencing (MPS) can confirm the diagnosis [30]. (See "Noonan syndrome", section on 'Diagnosis'.)
The decision regarding which test to perform, and the interpretation of molecular genetic results can be complex, and usually should be done in consultation with a provider specializing in genetic testing, such as a certified genetic counselor or medical geneticist.
Exome sequencing — ES uses MPS to sequence the exome (regions of the genome that are known to encode proteins). The exome includes approximately 1 percent of the genome but is thought to contain 85 percent of disease-causing mutations [31]. ES platforms vary in their depth of sequencing (ie, the number of times a specific nucleotide is sequenced). The greater the depth, the higher the likelihood that an identified sequence alteration is truly present and the lower the risk that true sequence changes will be missed. ES does not sequence the remainder of the DNA (99 percent); for this reason, some sequence abnormalities, such as those occurring in promoter regions, would not be detected by ES.
●Diagnostic performance – In a meta-analysis of the diagnostic yield of exome sequencing (ES) for prenatal diagnosis of fetal structural anomalies when karyotype/chromosomal microarray (CMA) was normal (72 reports from 2010 to 2021, 4350 anomalous fetuses), the pooled incremental yield of ES was 31 percent (95% CI 26-36) [32]. Incremental diagnostic yield was higher for cases in which a multidisciplinary team with expertise in genetics suspected a monogenic etiology than in unselected cases (42 versus 15 percent). The incremental diagnostic yield also varied among phenotypic subgroups, ranging from 53 percent for isolated skeletal abnormalities, 29 percent for multisystem anomalies, and 11 percent for cardiac anomalies to 2 percent for isolated enlarged nuchal translucency. Diagnoses were strictly defined as variants classified as pathogenic/likely pathogenic and deemed to be causing the fetal phenotype, while possibly diagnostic, probably diagnostic, or potentially relevant diagnoses were excluded.
●Challenges to clinical use – While the findings described above are promising for the use of ES technology in the genetic evaluation of the fetus with anomalies, challenges remain for the routine clinical use [33-35]:
•Interpreting results from ES is a very lengthy process, and results may not be available quickly enough for patients who are making decisions about pregnancy termination.
•Much of the phenotypic data for specific sequence changes is incomplete, which makes interpretation of identified variants more difficult.
•Ethical issues involving when to report secondary or incidental findings have not been resolved.
•There is an ongoing need for reanalysis of results as information accrues after the initial analysis.
•The cost of ES can be substantial, and insurance coverage is limited.
Given the complexities involved in interpretation of results, timeliness of results, and meaningful patient/family counseling, the decision to proceed with this type of testing should be made in consultation with a clinician specializing in genetic testing, such as a certified genetic counselor or medical geneticist. (See "Next-generation DNA sequencing (NGS): Principles and clinical applications".)
The following statements reflect the key points of a 2022 International Society for Prenatal Diagnosis updated position statement endorsed by SMFM on the use of genome-wide sequencing for fetal diagnosis [36]:
●The routine use of prenatal sequencing as a diagnostic test on fetal tissue obtained from an invasive prenatal procedure for indications other than fetal anomalies (including upon parental request) is not currently supported due to insufficient validation data and knowledge about its benefits and pitfalls.
●Prenatal sequencing may be beneficial in the following settings:
•A fetus with a single major anomaly or with multiple organ system anomalies that are suggestive of a possible genetic etiology, but no genetic diagnosis was found after microarray, or in select situations with no microarray result, following a multidisciplinary review and consensus, in which there is a fetus with a multiple anomaly 'pattern' that strongly suggests a single gene disorder.
•A personal (maternal or paternal) history of a prior undiagnosed fetus (or child) affected with a major single anomaly or multiple anomalies suggestive of a genetic etiology, and a recurrence of similar anomalies in the current pregnancy without a genetic diagnosis after karyotype or microarray. If such parents present for preconception counseling and no sample is available from the affected proband, or if a fetal sample cannot be obtained in an ongoing pregnancy, it is appropriate to offer sequencing for both biological parents to look for shared carrier status for autosomal recessive mutations that might explain the fetal phenotype.
●Diagnostic sequencing for fetal indications is best done as a trio analysis (fetal and both parental samples are sequenced and analyzed together).
●Genotype-phenotype correlation for genetic disorders identified in the fetal period is limited because of the resolution of ultrasound imaging, especially with regard to dysmorphia, the fetal phenotype may differ from that in the newborn/child, and the fetal phenotypes of many conditions have not been well described.
●Pretest counseling, interpretation of results, and posttest counseling are highly complex and are best conducted in consultation with a multidisciplinary team with expertise and experience in both the clinical and laboratory aspects of prenatal diagnosis and fetal sequencing.
The document also discussed quality standards, analysis, variant interpretation, and reporting of results (including incidental findings) from diagnostic or research laboratories.
APPROACH TO THE EVALUATION OF THE FETUS WITH "SOFT MARKERS" AND NO STRUCTURAL ANOMALIES
Soft markers detected BEFORE cell-free DNA or biochemical marker aneuploidy screening — A soft marker (echogenic intracardiac focus, echogenic bowel, choroid plexus cyst, single umbilical artery, urinary tract dilation, slightly shortened humerus and/or femur, thickened nuchal fold, absent or hypoplastic nasal bone) is a relatively common finding on second-trimester ultrasound examination. Soft markers are not structural anomalies, but may be indicators of an increased risk for aneuploidy [37]. The presence of multiple soft markers increases the risk for certain aneuploidies; however, when only an isolated soft marker is detected, the effect on the a priori risk of aneuploidy is relatively small, unless it is a thickened nuchal fold [38,39]. (See "Sonographic findings associated with fetal aneuploidy".)
The management of an isolated soft marker is summarized in the table (table 2) and is discussed below.
●For patients with ≥2 soft markers who have not had aneuploidy screening, we suggest counseling and discussion of the option of invasive diagnostic testing (algorithm 2). If the patient elects to take this approach, we begin our evaluation with interphase fluorescence in situ hybridization (FISH) for the common aneuploidies. Patients are given the option of chromosomal microarray analysis (CMA) or conventional karyotype if FISH is nondiagnostic. Other clinicians may omit FISH and go directly to CMA or conventional karyotype. Patients may have a preference for one approach versus the other after pretest counseling [9].
In contrast to pregnancies with fetal structural anomalies, data are limited on the value of CMA versus conventional karyotyping when soft markers are identified on ultrasound. In a retrospective analysis that stratified CMA detection rates by specific ultrasound findings, CMA was abnormal in 2.6 percent of fetuses with isolated soft markers (2 of 77) [40]. Given the small number of cases in this study, it is not possible to draw definitive conclusions about the value of CMA when only soft markers are detected. However, from a large multicenter trial, we know that 1.7 percent of structurally normal fetuses with a normal conventional karyotype have a clinically significant CMA finding [41].
●For patients with ≥2 soft markers who have not had aneuploidy screening and decline invasive diagnostic testing but are interested in further evaluation, the authors offer cell-free DNA screening because this is the most sensitive single test for the common aneuploidies.
If results from cell-free DNA screening show no increased risk for trisomy 21, 18, 13, or sex chromosome anomalies, then patients can be reassured and typically continue with routine prenatal care. However, as discussed previously, we always stress that a normal screening result does not eliminate the possibility of a genetic condition in the fetus.
Soft markers detected AFTER cell-free DNA or biochemical marker aneuploidy screening — By the time of the second-trimester anatomy ultrasound, many patients have already completed aneuploidy screening through first- or second-trimester maternal biochemical marker screening or cell-free DNA screening. If soft markers are detected on ultrasound examination after blood screening tests, we suggest the following approach:
●For patients whose first- or second-trimester biochemical marker screening shows no increased risk, our approach depends to the number and type of soft markers:
•Isolated soft marker – We provide counseling and reassurance.
-Some isolated soft markers, such as thickened nuchal fold, absent nasal bone, and echogenic bowel, are more strongly associated with fetal aneuploidy. In such cases, additional genetic counseling and cell-free DNA screening may be warranted. (See 'Evaluation for other disorders' below.)
-Some soft markers in euploid fetuses are associated with specific disorders (eg, echogenic bowel has been associated with cystic fibrosis). Evaluation for these disorders should be addressed, when appropriate, during counseling and options for prenatal diagnosis discussed. (See "Fetal echogenic bowel".)
-Soft ultrasound findings that are likely normal variants in this setting include echogenic intracardiac focus, choroid plexus cyst, sandal gap toe, and clinodactyly.
•Two or more soft markers – We offer genetic counseling to discuss cell-free DNA screening and diagnostic testing options (algorithm 3).
●For patients whose cell-free DNA screening shows no increased risk, our approach depends to the number and type of soft markers:
•Isolated soft marker – The Society for Maternal-Fetal Medicine (SMFM) recommends not offering diagnostic testing solely for the indication of an isolated soft marker when prior cell-free DNA screening shows no increased risk of the targeted aneuploidies [42]. We agree with SMFM that an isolated soft marker should not be overemphasized in these patients and that some soft markers should be described as a normal variant. However, we feel that it is important to ensure that guidelines do not disproportionately restrict subgroups of patients, such as those with a soft marker after cell-free DNA screening, from access to diagnostic genetic testing or devalue the utility of diagnostic genetic testing within that subgroup.
Some soft markers in euploid fetuses are associated with specific disorders or may warrant additional ultrasound evaluation/monitoring, which should be addressed during counseling. A falsely-reassuring cell-free DNA result is unlikely but probably higher with the following soft markers than with the normal variants described above (urinary tract dilation, single umbilical artery, echogenic bowel, thickened nuchal fold, absent nasal bone, shortened humerus or femur). (See 'Evaluation for other disorders' below.)
•Two or more soft markers – We offer genetic counseling to discuss invasive diagnostic testing options (algorithm 4).
As most soft markers resolve by the third trimester, we recommend not performing postnatal genetic evaluation unless there are signs of aneuploidy on clinical examination.
Evaluation for other disorders — Some soft markers are associated with disorders other than aneuploidy, which may require additional evaluation, including diagnostic testing. For example, echogenic bowel has been associated with blood in the bowel lumen, cystic fibrosis, growth restriction, infection, and gastrointestinal obstruction. Urinary tract dilation has been associated with kidney abnormalities. Evaluation of these fetuses depends on the specific marker.
●Urinary tract dilation – (See "Fetal hydronephrosis: Etiology and prenatal management", section on 'Congenital anomalies of the kidney and urinary tract (CAKUT)'.)
●Single umbilical artery – (See "Single umbilical artery".)
●Echogenic bowel – (See "Fetal echogenic bowel".)
●Thick nuchal fold – (See "Sonographic findings associated with fetal aneuploidy", section on 'Thick nuchal fold'.)
●Hypoplastic nasal bone – (See "Sonographic findings associated with fetal aneuploidy", section on 'Second-trimester absent nasal bone'.)
●Shortened humerus or femur – (See "Approach to prenatal diagnosis of the lethal (life-limiting) skeletal dysplasias".)
●Nonisolated choroid plexus cysts – (See "Sonographic findings associated with fetal aneuploidy", section on 'Choroid plexus cysts'.)
INFORMATION FOR PATIENTS — UpToDate offers two types of patient education materials, "The Basics" and "Beyond the Basics." The Basics patient education pieces are written in plain language, at the 5th to 6th grade reading level, and they answer the four or five key questions a patient might have about a given condition. These articles are best for patients who want a general overview and who prefer short, easy-to-read materials. Beyond the Basics patient education pieces are longer, more sophisticated, and more detailed. These articles are written at the 10th to 12th grade reading level and are best for patients who want in-depth information and are comfortable with some medical jargon.
Here are the patient education articles that are relevant to this topic. We encourage you to print or e-mail these topics to your patients. (You can also locate patient education articles on a variety of subjects by searching on "patient info" and the keyword(s) of interest.)
●Basics topics (see "Patient education: Genetic testing (The Basics)")
SUMMARY AND RECOMMENDATIONS
●The frequency of a chromosomal abnormality in the fetus with one or more anomalies depends on the specific anomaly, the number of anomalies, and the combination of anomalies identified.
•Isolated fetal anomaly – 2 to 18 percent of cases
•Multiple fetal anomalies – 13 to 35 percent of cases
(See 'Frequency of chromosomal abnormalities in fetuses with anomalies' above.)
●Approach to pregnancies with a fetus with anomalies
•Patients who accept an invasive procedure – We offer an invasive procedure for genetic testing to all patients with a structural fetal anomaly identified on ultrasound examination. The decision to proceed with prenatal testing is personal and must take into account the individual patient's goals and values. Other options include noninvasive screening and postnatal testing. (See 'Approach to evaluation of the fetus with anomalies' above.)
-For structural anomalies consistent with a common trisomy, we begin the evaluation with interphase fluorescence in situ hybridization (FISH) for the common aneuploidies (trisomies 21, 18, and 13; sex chromosome aneuploidy; and triploidy) (algorithm 1). Chromosomal microarray analysis (CMA) is performed if FISH is normal, and confirmatory conventional karyotype or CMA is performed if FISH is abnormal. Although FISH provides a rapid result, it also adds to the cost of the fetal evaluation, so it is also reasonable to proceed directly to CMA. Referral to a genetics specialist is recommended if the patient desires additional genetic testing (eg, gene sequencing).
-For structural anomalies not commonly associated with an aneuploidy detected by FISH, we begin the genetic evaluation with CMA (algorithm 1). Referral to a genetics specialist is recommended if the patient desires additional genetic testing.
•Patients who decline an invasive procedure – If the patient declines invasive testing, noninvasive screening via cell-free DNA is an option. It is critical that patients be counseled about the limitations of cell-free DNA screening in the setting of fetal anomalies as normal results can be falsely reassuring and abnormal results may be falsely positive. (See 'Options for patients who decline an invasive procedure' above.)
●Counseling – Appropriate pretest and posttest counseling is essential for all patients electing to proceed with genetic testing. (See 'Pretest and posttest counseling' above.)
●Testing options – Prenatal genetic testing options include fluorescence in situ hybridization, conventional karyotype, chromosomal microarray, gene sequencing, and exome sequencing. (See 'Testing options' above.)
●Approach to pregnancies with fetal soft markers and no structural anomalies
•Patients with no previous noninvasive screening and two or more soft markers – (See 'Soft markers detected BEFORE cell-free DNA or biochemical marker aneuploidy screening' above.)
-For patients with no fetal structural anomalies but two or more soft markers on ultrasound and no previous cell-free DNA or biochemical marker aneuploidy screening, we suggest diagnostic testing (algorithm 2). If the patient elects this approach, we begin our evaluation with interphase FISH for the common aneuploidies. Patients are given the option of CMA or traditional karyotype if FISH is normal.
-For patients with no fetal structural anomalies who have two or more soft markers and decline invasive testing but are interested in further evaluation, we offer cell-free DNA screening (algorithm 2). If results from cell-free DNA screening show no increased risk for trisomy 21, 18, 13, or sex chromosome anomalies, then we provide reassurance and typically continue with routine prenatal care. However, as discussed previously, we always stress that a negative result does not eliminate the possibility of a genetic condition in the fetus.
•Patients with previous negative (no increased risk) noninvasive (biochemical) screening – For patients who have had negative (no increased risk) first- or second-trimester biomarker aneuploidy screening followed by identification of a soft marker, our approach depends on the number and type of soft markers (see 'Soft markers detected AFTER cell-free DNA or biochemical marker aneuploidy screening' above):
-An isolated soft marker – We provide counseling and reassurance. Importantly, some isolated soft markers, such as thickened nuchal fold and absent/hypoplastic nasal bone are more strongly associated with fetal aneuploidy. Some soft markers in euploid fetuses are associated with specific disorders (eg, echogenic bowel has been associated with cystic fibrosis). Evaluation for these disorders should be addressed, when appropriate, during counseling and options for prenatal diagnosis discussed (table 2).
-Two or more soft markers – We offer genetic counseling to discuss cell-free DNA screening and diagnostic testing options (algorithm 3).
•Patients with previous negative (no increased risk) noninvasive (cell-free DNA) screening – For patients who have had negative (no increased risk) cell-free DNA screening followed by identification of a soft marker, our approach depends on the number of soft markers (see 'Soft markers detected AFTER cell-free DNA or biochemical marker aneuploidy screening' above):
-An isolated soft marker – We offer reassurance that this is likely a normal variant and the chance the fetus has one of the common aneuploidies targeted by screening is very low, in line with recommendations from the Society for Maternal-Fetal Medicine. However, soft markers in euploid fetuses may be associated with specific disorders (eg, urinary tract dilation may be a sign of congenital anomalies of the kidney and urinary tract [CAKUT]). This should be addressed during counseling and options for prenatal diagnosis discussed.
-Two or more soft markers – We offer additional genetic counseling and discussion of diagnostic testing (algorithm 4).
