Version July 2025
INTRODUCTION —
Approximately 3 percent of live births are affected by a major structural anomaly, many of which are now identified prenatally by ultrasound. The etiology of congenital anomalies is diverse and includes environmental influences, genetic factors, or a combination of both.
Identification of a fetal anomaly should prompt a discussion about fetal genetic evaluation because of the increased possibility of an underlying genetic alteration. However, the landscape of genetic testing is rapidly evolving and often leaves clinicians and patients with many questions about the most appropriate test(s) to choose when such testing is desired. Genetic testing is voluntary and may be chosen or declined by patients based upon their values, beliefs, and other factors that are important to them.
This topic will provide a reasonable approach to the genetic evaluation of a fetus with anomalies. Postnatal evaluation of the infant with anomalies is reviewed separately. (See "Congenital anomalies: Approach to evaluation".)
FREQUENCY OF CHROMOSOMAL ABNORMALITIES AND SIGNIFICANT GENETIC VARIANTS —
The frequency of informative genetic studies when the fetus has a structural anomaly depends on several factors: the specific anomaly, the number of anomalies, the combination of anomalies identified, and the type of genetic testing [1].
In several retrospective series of sonographically detected fetal anomalies that prompted fetal genetic studies, the frequency of an abnormal karyotype was [1-6]:
●2 to 18 percent among fetuses with an isolated anomaly
●13 to 35 percent among fetuses with multiple anomalies
The identification of causative DNA changes is even higher when chromosomal microarray analysis (CMA, which detects duplications or deletions in a region of the chromosomes [copy number variants]) and sequencing (which detects pathogenic variants within a specific gene sequence) are performed.
APPROACH TO GENETIC EVALUATION OF THE FETUS WITH ANOMALIES
Offer diagnostic genetic testing — Standard clinical practice is to offer diagnostic genetic testing to patients with a structural fetal abnormality. Either chorionic villus sampling (CVS) or amniocentesis can be used to obtain a fetal specimen for this testing [7]. If the test results account for the observed abnormalities, then well-informed counseling about prognosis, reproductive options, obstetric and pediatric management, and recurrence risks is usually possible. Obstetric issues include whether in utero intervention is available and might be indicated, use of antenatal fetal surveillance (ultrasound, nonstress testing, biophysical profile), timing and route of delivery, and choice of facility for giving birth based on expected newborn needs (eg, level of care, palliative care, need for surgery).
The decision to undergo a procedure to obtain a fetal specimen for diagnosis is personal and must be based on the individual's values and goals. For patients to make informed decisions, pretest counseling should be provided by a clinician familiar with suspected fetal diagnoses, genetic testing options, spectrum of possible results, test limitations, risks of CVS and amniocentesis, and alternatives to prenatal diagnostic testing, such as the range of noninvasive prenatal screening options and postnatal diagnostic testing. Referral to a genetic counselor can aid these discussions. (See 'Pretest counseling' below.)
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 American College of Obstetricians and Gynecologists (ACOG) and Society for Maternal-Fetal Medicine (SMFM) estimated that the procedure-related pregnancy loss rate for a prenatal diagnostic procedure ranges from approximately 1 in 300 to 1 in 1000 (0.1 to 0.3 percent) in a 2016 practice bulletin [8]. Within this range, the observed pregnancy loss rate after CVS is thought to be higher than after amniocentesis because CVS is performed at an earlier gestational age when the background risk for spontaneous loss is higher. However, a 2019 meta-analysis has suggested that the procedure-related risk of pregnancy loss after amniocentesis and CVS is lower (less than 1 in 300) and may not be increased above the background risk of pregnancy loss [9].
Choice of test when a common aneuploidy is suspected — When one of the more common aneuploidies (eg, trisomy 21, 18, and 13; monosomy X; triploidy) is suspected based on ultrasound findings, we use the approach described in the algorithm (algorithm 1) and discussed below. These ultrasound findings are described in detail separately. (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 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 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 karyotype or CMA. (See 'Fluorescence in situ hybridization' below.)
●If the FISH is consistent with aneuploidy – We recommend obtaining a karyotype both for confirmation and to determine if the aneuploidy is due to nondisjunction or secondary to an unbalanced translocation (which means a parent may have a balanced translocation). This determination is needed to calculate recurrence risks. The karyotype can be performed using cells from the same specimen obtained for FISH. (See 'Chromosomal microarray and karyotype' below.)
●If the FISH is not consistent with aneuploidy – We recommend CMA instead of a karyotype because CMA has a higher diagnostic yield. CMA can be performed on the same fetal specimen used for FISH. (See 'Chromosomal microarray and karyotype' below.)
Choice of test when findings are not suggestive of a common aneuploidy — We use the approach in the algorithm (algorithm 1) and discussed below when ultrasound findings are not suggestive of one of the more common aneuploidies (eg, trisomy 21, 18, and 13; monosomy X; triploidy), which are described separately. (See "Sonographic findings associated with fetal aneuploidy", section on 'Sonographic features of selected aneuploidies'.)
●Begin with CMA – We begin with CMA because of its higher diagnostic yield compared with a karyotype. Our approach is the same whether an isolated or multiple structural anomalies are observed. While the yield of CMA is higher in fetuses with multiple anomalies, 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 'Chromosomal microarray and karyotype' below.)
CMA results are classified as benign, likely benign, variant of unknown significance (VUS), likely pathogenic, and pathogenic. (See "Prenatal diagnosis of chromosomal imbalance: Chromosomal microarray".)
●If CMA identifies a pathogenic or likely pathogenic variant, a qualified clinician should discuss the significance of the results with the patient. (See 'Posttest counseling' below.)
●If CMA is nondiagnostic, we review available molecular testing options with patients interested in pursuing additional genetic testing. (See 'Advanced testing options' below.)
Options for patients who decline a diagnostic procedure — Patients who decline to have a diagnostic procedure for genetic testing may choose to undergo cell-free DNA (cfDNA) screening and/or expanded carrier screening and use the results to inform further decision-making, or they may choose to undergo postnatal diagnostic genetic testing (algorithm 1).
Cell-free DNA screening
●Standard prenatal cell-free DNA screening – A definitive prenatal genetic diagnosis can only be made if CVS or amniocentesis is performed to obtain a fetal sample for diagnostic testing. However, some patients decline to have an invasive procedure because they consider the risk of fetal loss unacceptable and the results would not impact their decision to carry the pregnancy to term. For these patients, we offer a cfDNA screening test to provide additional information about the fetal risk of aneuploidy, with appropriate pretest and posttest counseling. (See "Prenatal screening for common fetal aneuploidies: Cell-free DNA test".)
•cfDNA result: Low risk of trisomy 21, 18, 13, or a sex chromosome aneuploidy– Patients with a low-risk result should be counseled about the frequency and causes of false-negative results (ie, fetus is affected but the result indicates a low risk of 21, 18, 13 or sex chromosome aneuploidy). They also need to understand that the result does not eliminate the possibility of a fetal genetic condition other than trisomy 21, 18, 13, or a sex chromosome aneuploidy, especially in the setting of a fetal anomaly [10,11]. (See "Prenatal screening for common fetal aneuploidies: Cell-free DNA test", section on 'False-negative cfDNA test results'.)
It has been estimated that, in the setting of a fetal anomaly, performing a cfDNA screening test alone will miss 8 percent of chromosomal abnormalities detectable by a karyotype and 16 percent of cytogenetic abnormalities diagnosed by CMA [12,13]. The frequency of missed genetic diagnosis varies by gestational age: it is <10 percent in the first trimester but almost 20 percent in the late second or third trimester. The difference reflects the high frequency of sonographic abnormalities associated with trisomy 21, 18, and 13 that are detectable in early pregnancy (eg, enlarged nuchal translucency, cystic hygroma, cardiac anomalies); better detection of other structural anomalies later in gestation compared with the first trimester; and the association of these other anomalies with less common chromosome imbalances.
•cfDNA result: Increased risk of trisomy 21, 18, 13, or a sex chromosome aneuploidy – Patients also need to understand that a cfDNA test result showing an increased risk of one of these aneuploidies may be a false positive (ie, the fetus is unaffected). (See "Prenatal screening for common fetal aneuploidies: Cell-free DNA test", section on 'False-positive cfDNA test results'.)
All cfDNA results indicating an increased risk for aneuploidy should be confirmed with diagnostic testing, either pre- or postnatally. cfDNA results should be confirmed prenatally prior to a pregnancy termination or any other irreversible prenatal procedure. The positive predictive value of cfDNA for predicting an aneuploid fetus is higher in the setting of a comprehensive ultrasound examination by an experienced sonologist that clearly shows features of one of these disorders, but even in this setting, prediction of one of these aneuploidies is not 100 percent accurate. We counsel patients with positive cfDNA screening results on the positive predictive value based on their specific pretest probability. Although we do not recommend this, some patients with cfDNA results showing >97 percent probability of trisomy have rejected diagnostic testing and moved directly to termination. (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'.)
Confirmation of cfDNA results is also important because a trisomy that results from an unbalanced rearrangement in the fetus could be inherited from a parent who carries a balanced rearrangement, which is not detected with cfDNA screening but has implications for recurrence risk.
•cfDNA result: nonreportable – One to 5 percent of cfDNA tests will report "no result" for trisomy 21, 18, and 13, and sex chromosome aneuploidies. The reasons for nonreportable results (test failures) are multiple and depend on the testing platform, performing laboratory characteristics, fetal fraction, and patient characteristics. Further evaluation following a nonreportable result can include repeating cfDNA screening with a second sample or moving on to diagnostic testing as these patients are at increased risk for aneuploidy. (See "Prenatal screening for common fetal aneuploidies: Cell-free DNA test", section on 'Test failures (no result)'.)
●Expanded cell-free DNA screening – cfDNA screening for genetic conditions other than trisomy 21, 18, 13, and sex chromosome aneuploidies is not recommended on a population-wide basis [14-16]. The use of expanded cfDNA screening (either for microdeletion/microduplication screening, monogenic disorders, or whole genome coverage) has not been clinically validated in the setting of a fetus with anomalies. However, this is an evolving area with new studies suggesting clinical value of more expanded screening strategies [17,18]. (See "Cell-free DNA screening for fetal conditions other than the common aneuploidies".)
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 expanded cfDNA screening, which is commercially available, an acceptable alternative to diagnostic testing. For these patients, the decision to obtain expanded cfDNA screening should only be made after appropriate counseling by a qualified clinician regarding the limitations of this testing.
Expanded carrier screening — Expanded carrier screening uses next-generation sequencing (NGS) to analyze select genes that are associated with autosomal recessive or X-linked conditions. Patients who initially decline diagnostic testing may consider this testing to better inform decision-making. One study found that 3.2 percent of newborns (7 of 222) with structural anomalies were diagnosed with a condition that would have been detected (ie, positive parental screening result) on an expanded carrier screening panel of 500 conditions [19]. This study suggests that when diagnostic testing is declined, expanded carrier screening can be considered after pretest counseling. If the expanded carrier screening is negative (ie, an inherited single gene disorder associated with the ultrasound anomalies is not identified), the family should not be overly reassured and postnatal testing for genetic etiologies is still recommended. (See "Preconception and prenatal panethnic expanded carrier screening".)
Postnatal testing — Genetic testing after birth is another option. The approach to postnatal evaluation of the infant with congenital anomalies is reviewed separately. (See "Congenital anomalies: Approach to evaluation".)
Pretest and posttest counseling
Pretest counseling — Appropriate pretest counseling (up-to-date, balanced, accurate information) that is patient-centered is critical for patients who are making the decision to undergo genetic testing. The goal is to help patients understand the benefits as well as the limitations of testing, discuss possible test results, and help patients make informed decisions consistent with their own goals and values [20]. 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:
●Patient values and goals:
•General attitudes toward prenatal testing and screening.
•Desires regarding the level of information provided by testing.
•Views about and availability of pregnancy termination.
●Prenatal testing options and procedures, and the options of no prenatal testing or postnatal testing
●Possible results:
•Aneuploidy or a pathologic variant with defined phenotype.
•Copy number variants (CNVs) with variable phenotype.
•Variants of uncertain significance.
•Incidental findings, including nonpaternity, consanguinity, and variants in the fetus and/or parent associated with adult-onset disease.
•Normal (ie, benign, likely benign) results. Normal results do not guarantee absence of a disorder as no test can detect all disorders.
•Nonreportable result on cfDNA screening.
●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.
•Fears of coping with the challenges of a child with disabilities; 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. For patients who would elect to continue a pregnancy with a life-limiting diagnosis (ie, a 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 Perinatal Hospice and Palliative Care.
Posttest counseling — Following genetic testing, it is important to give patients an opportunity to discuss the significance of their results with a qualified provider. This is important even when results are normal.
●Abnormal results:
•Discuss the certainty of the diagnosis and whether further testing is indicated.
•Discuss the significance of the results for the health of the fetus, before and after birth, including the limitations of prenatal phenotyping.
•Review the patient’s goals and values and pregnancy/postpartum management options as discussed during pretest counseling.
•Consider referral to a pediatric subspecialist with expertise in the identified condition.
•Discuss recommended follow-up after birth.
•Review recurrence risk and options for future pregnancies.
•Refer to vetted online parent support resources.
●Normal results:
•Discuss that, while normal results are reassuring, they do not eliminate the possibility of an underlying genetic condition in the fetus. Discuss advanced testing options (sequencing), if appropriate.
•Explain that variants of uncertain significance may be reclassified in the future and found to be disease causing.
•If the patient elected to have prenatal sequencing and it is uninformative, explain that additional features may be identified in the newborn or child, which may lead to a sequencing result becoming informative.
•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).
Initial testing options
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 [21]. 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 [21]. FISH can also be used to detect other chromosome abnormalities when appropriate probes are available.
The concordance rates between FISH and karyotype of uncultured amniocytes are high, reportedly >99 percent [22]. However, confirmatory testing with a karyotype is required to determine if a translocation is present. Normal FISH results also require additional testing, either through karyotype or CMA, because 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'.)
Chromosomal microarray and karyotype — Karyotyping has been the standard for prenatal diagnosis, but use of CMA is increasing. Advantages of CMA are:
●CMA detects small (typically 50 to 100 kb) gains and losses of genetic material (called copy number variants [CNVs]) that would not be identified by traditional karyotyping yet have the potential to lead to significant phenotypic abnormalities. By contrast, karyotyping typically has a resolution of only 5 to 10 Mb.
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 [23]. 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 [24,25].
●CMA does not require cell culture, thus reducing the turnaround time for results.
The greater depth of molecular analysis with CMA increases the likelihood of a diagnosis, but the likelihood of incidental findings is also increased, 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 karyotype, CMA will not identify some clinically significant genetic findings, such as gene sequence changes that might affect gene function, balanced structural rearrangements, and unbalanced translocations. (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 abnormality identified on ultrasound [26]. 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".)
Advanced testing options — When chromosomal analysis, including CMA, is nondiagnostic, the next step in the genetic evaluation is testing for specific genetic conditions through use of molecular genomic techniques. Advanced sequencing techniques such as NGS may be used to interrogate a single gene, a panel of selected genes, the exome (ES, the protein-coding genes that make up 1 to 2 percent of the genome), or the entire genome (GS). Sequencing options have the advantage of higher diagnostic yield and have gained support because of increasing knowledge that the defining features of a phenotype may not manifest until later in the gestation (after the time of diagnostic testing) and the fetal phenotype may be different from the classic pediatric presentation.
We recommend additional counseling with a prenatal genetic counselor or clinical geneticist prior to proceeding with this testing. The targeted approach has the advantage of reducing the chances of finding genomic variants of uncertain clinical significance or incidental findings, and the turnaround time is typically shorter than ES or GS. However, selection of a gene panel targeted to a fetal finding does not provide the opportunity to examine other clinically significant conditions [27].
General principles when considering advanced genetic testing
●Utilize appropriate expertise – 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.
●Inform the laboratory about the possibility of advanced testing – Clinicians should inform the laboratory if advanced testing will be considered in cases of nondiagnostic cytogenetic results from CMA because the testing can be performed on fetal DNA from cultured chorionic villi or amniocytes obtained at the time of the diagnostic procedure. If an adequate initial 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.
●Address limitations of prenatal versus postnatal testing – While the presence of a fetal anomaly increases the risk for an underlying monogenic condition, the ability to test and the value of testing for specific conditions prenatally can be more challenging compared with the postnatal setting. Identification of a pathogenic variant is not a clinical diagnosis; clinical diagnosis requires correlation of the genetic test result, fetal findings (phenotype), and family history.
Prenatal prognostic counseling is complicated because the resolution of ultrasound imaging of minor anatomic abnormalities is limited; functional features of a phenotype (eg, neurodevelopmental impairment) are generally not possible to detect prenatally; the characteristic phenotype may be poorly defined or incomplete prenatally; the phenotype may evolve after initial diagnosis and counseling; and disorders identified prenatally may have more benign or more deleterious outcomes than the same disorders identified postnatally [28].
●Discuss issues regarding time to make a diagnosis – Advanced genetic testing can be a long process, which can be a problem prenatally when time-sensitive decisions need to be made regarding possible pregnancy termination, pregnancy management, route of birth, site of birth, and level of neonatal care.
●Discuss trio-based sequencing – Diagnostic sequencing for fetal indications is best done as a trio analysis (where fetal and both parental samples are sequenced and analyzed together); thus, patients should understand that parental blood samples are often required for confirmatory testing. The trio approach is more informative than duo analysis (one parent and the fetus) and helps to exclude uninformative variants, identify de novo fetal variants, and determine inheritance of recessive variants.
Issues related to misattributed parentage (eg, mistaken paternity, nondisclosed relationship, nondisclosure of a donor) should be addressed during pretest counseling.
●Discuss the potential for incidental findings – Ethical issues involving when to report secondary or incidental fetal and parental findings (variants for genetic disorders unrelated to the phenotype being investigated) have not been resolved. Medically actionable genes (eg, cardiovascular disease or cancer predisposition genes) are generally assessed and reported as secondary findings when established interventions are available for preventing or significantly reducing morbidity and mortality.
●Discuss future reanalysis of results – There is ongoing need for reanalysis of results as information in database resources accrues after the initial analysis. Reanalysis may also be considered postnatally if a new phenotype is observed in the proband.
●Discuss cost – Insurance coverage is limited, but the cost of advanced genetic testing continues to decrease.
Targeted gene sequencing — Targeted gene sequencing refers to testing 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 [29]. For example, achondroplasia is caused by genetic alterations in FGFR3. When achondroplasia is suspected clinically, sequencing FGFR3 can confirm the diagnosis [30].
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 NGS can confirm the diagnosis [31]. (See "Noonan syndrome", section on 'Diagnosis'.)
Targeted gene panels are typically less expensive than exome or genome sequencing. A gene panel is a reasonable consideration when the phenotype is clear, such as a skeletal dysplasia. If results of the gene panel are nondiagnostic, then additional genetic testing may still be warranted. However, whole genome and exome sequencing (ES) are rapidly replacing the use of targeted gene panels as these methods allow agnostic interrogation of the genome/exome, which is advantageous since many prenatal phenotypes are nonspecific.
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 NGS 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 variants [32]. 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 within the exomes 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. In addition, relevant genes may be missed because of technical issues, and ES typically does not detect triplet repeat disorders, small insertions and deletions between 100 and 100,000 base pairs, structural variants (rearrangements and translocations), or some CNVs [33].
In a meta-analysis of the diagnostic yield of ES for prenatal diagnosis of fetal structural anomalies when karyotype/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) [34]. Diagnoses were strictly defined as variants classified as pathogenic/likely pathogenic and deemed to be causing the fetal phenotype; variants classified as possibly diagnostic, probably diagnostic, or potentially relevant diagnoses were excluded. The incremental diagnostic yield was affected by several factors; for example, it 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). It 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. By comparison, in morphologically normal fetuses, the diagnostic yield of prenatal ES based on parental request varies from 0.5 to 3 percent [35-39].
ES typically identifies approximately 40,000 sequence variants. Bioinformatic algorithms are used for filtering, annotating, and prioritizing the genetic information from ES for clinical interpretation. This process narrows the number of variants down to those with a known (>99 percent) or likely (90 to 99 percent) genotype‐pathologic phenotype association. When the probability of pathogenicity is <90 percent but the variant is not clearly benign and without health consequences, it is considered a variant of uncertain significance. However, laboratories vary in their interpretation of gene variants, in part because of a lack of publicly available prenatal databases and standardized prenatal curation [33]. Trio analysis (fetus and both biological parents) has higher diagnostic yields [40].
The American College of Medical Genetics and Genomics recommend considering ES for a fetus with ultrasound anomalies when karyotype and CMA are nondiagnostic [41]. However, they suggest considering targeted gene testing as the initial test, if a specific diagnosis is suspected.
Given the complexities involved in the 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".)
Whole genome sequencing — Whole genome sequencing (WGS) analyzes both the exonic and intronic (noncoding) regions of the genome, thus it is a more comprehensive technique for detecting sequence variation than ES. It can identify even very small CNVs (below the resolution of microarray), other structural variants, expansions of short tandem repeats, mitochondrial disorders, and some coding exons not detected by ES [33]. Despite more comprehensive genomic assessment, turnaround time is often faster than for ES. However, ES analysis is more reliable for identifying mosaic sequence variants than WGS because of its higher sequencing depth [42].
The following statements reflect some of the key points of a 2022 International Society for Prenatal Diagnosis updated position statement endorsed by SMFM on the use of WGS for fetal diagnosis [43]:
●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 expanded carrier screening for both biological parents to look for shared carrier status for autosomal recessive variants that might explain the fetal phenotype.
The document also discussed quality standards, analysis, variant interpretation, and reporting of results (including incidental findings) from diagnostic or research laboratories.
Methylation studies — Methylation studies are useful when genetic disorders resulting from abnormal methylation or imprinting are suspected. For example, Beckwith-Wiedemann syndrome is in the differential diagnosis of omphalocele and is best detected with methylation studies. ES and GS will typically not detect disorders resulting from abnormal methylation. (See "Beckwith-Wiedemann syndrome".)
APPROACH TO THE EVALUATION OF THE FETUS WITH "SOFT MARKERS" AND NO STRUCTURAL ANOMALIES —
A detailed description of soft markers is available separately. (See "Sonographic findings associated with fetal aneuploidy", section on 'Soft markers'.)
Soft markers detected BEFORE aneuploidy screening
●Isolated soft marker – Our approach depends on the marker and is shown in the table (table 2). A detailed ultrasound examination is important to ensure as technically possible that the soft marker is isolated (eg, the short long bones are morphologically normal and other signs suggestive of growth restriction are absent, the profile is normal except for the absent nasal bone).
●Two or more soft markers
•Diagnostic testing approach – For patients with ≥2 soft markers who have not had aneuploidy screening, we suggest counseling and discussion of the option of diagnostic testing, as described in the algorithm (algorithm 2). If the patient elects this approach, we begin the evaluation with interphase fluorescence in situ hybridization (FISH) for the common aneuploidies. Patients are given the option of chromosomal microarray analysis (CMA) or karyotype if FISH is nondiagnostic. Other clinicians may omit FISH and go directly to CMA or karyotype. Patients may have a preference for one approach versus the other after pretest counseling [8].
In contrast to pregnancies with fetal structural anomalies, data are limited on the value of CMA versus 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) [44]. 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 karyotype have a clinically significant CMA finding [45].
•Cell-free DNA screening approach – For patients with ≥2 soft markers who have not had aneuploidy screening and decline diagnostic testing but are interested in further evaluation, we offer cell-free DNA (cfDNA) screening because this is the most sensitive single noninvasive test for the common aneuploidies.
If results from cfDNA 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. (See 'Cell-free DNA screening' above.)
Soft markers detected AFTER 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 cfDNA screening. The Society for Maternal-Fetal Medicine (SMFM) recommends not offering diagnostic testing solely for the indication of an isolated soft marker when prior aneuploidy screening shows no increased risk of the targeted aneuploidies [46]. 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 cfDNA screening, from access to diagnostic genetic testing or devalue the utility of diagnostic genetic testing within that subgroup. Therefore, for patients whose cfDNA screening or serum screening shows no increased risk, our approach is as follows:
●Isolated soft marker – Our approach depends on the soft marker, as shown in the table (table 2).
●Two or more soft markers – We offer genetic counseling to discuss invasive diagnostic testing options, as shown in the algorithm (algorithm 3).
Prenatal 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".)
●Thickened 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 long bones – (See "Approach to prenatal diagnosis of life-limiting skeletal dysplasias".)
●Nonisolated choroid plexus cysts – (See "Sonographic findings associated with fetal aneuploidy", section on 'Choroid plexus cysts'.)
Role of postnatal genetic testing after detection of soft markers — Most soft markers resolve by the third trimester. Prenatal detection of soft markers is not an indication for postnatal genetic evaluation unless the neonate has signs of aneuploidy or another genetic disorder on clinical examination.
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
●Frequency of chromosomal abnormalities in the fetus with one or more anomalies – The frequency of a chromosomal abnormality depends on the specific fetal anomaly, the number of anomalies, and the combination of anomalies. In general:
•2 to 18 percent of fetuses with an isolated anomaly have a chromosomal abnormality
•13 to 35 percent of fetuses with multiple anomalies have a chromosomal abnormality
The identification of causative DNA changes is even higher when genetic testing for copy number variants (CNVs; eg, chromosomal microarray analysis [CMA]) and sequence pathogenic variants are performed. (See 'Frequency of chromosomal abnormalities and significant genetic variants' above.)
●Prenatal screening and testing – Prenatal screening and diagnostic tests are voluntary and such tests may be chosen or declined by patients based upon their values, beliefs, and the issues that they feel are most important. (See 'Introduction' above.)
●Counseling – Appropriate pretest and posttest counseling is essential for all patients electing to proceed with genetic testing. (See 'Pretest and posttest counseling' above and 'General principles when considering advanced genetic testing' above.)
●Approach to fetal genetic testing in patients who accept an invasive procedure
•Initial testing – We offer diagnostic genetic testing (which requires either chorionic villus sampling [CVS] or amniocentesis) to all patients with a structural fetal anomaly, as described in the algorithm (algorithm 1). The decision to proceed with an invasive procedure for diagnostic 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 genetic evaluation of the fetus with anomalies' above.)
•Advanced testing – If initial testing is nondiagnostic, we suggest referral to a genetics specialist to discuss possible additional genetic testing and, if additional molecular testing is desired, the choice of test (table 1). Identification of a pathogenic variant is not a clinical diagnosis; clinical diagnosis requires correlation of the genetic test result, fetal findings (phenotype), and family history. (See 'Advanced testing options' above.)
Based on the clinical scenario, a targeted gene panel, exome sequencing (ES), or whole exome sequencing should be considered for further evaluation.
●Approach to fetal genetic testing in patients who decline an invasive procedure – For patients who decline an invasive procedure for diagnostic genetic testing, noninvasive screening via cell-free DNA (cfDNA) is an option. Patients should be counseled about the limitations of cfDNA screening in the setting of fetal anomalies: normal results can be falsely reassuring since the results are limited to trisomy 21, 18, 13 or sex chromosome aneuploidy, and abnormal results may be falsely positive. (See 'Options for patients who decline a diagnostic procedure' above.)
●Approach to patients with fetal soft markers but no structural anomalies
•No previous aneuploidy screening – The approach to management of an isolated soft marker is summarized in the table (table 2). For patients with two or more soft markers, we suggest genetic counseling to review options for diagnostic testing and cfDNA screening (algorithm 2). (See 'Soft markers detected BEFORE aneuploidy screening' above.)
•Previous aneuploidy screening – For patients whose aneuploidy screening results show a low risk for the targeted aneuploidies but a subsequent ultrasound examination identifies a soft marker, our approach depends on the number of soft markers (see 'Soft markers detected AFTER 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 (SMFM) (table 2). 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. Some isolated soft markers, such as thickened nuchal fold and absent/hypoplastic nasal bone, are more strongly associated with fetal aneuploidy. In such cases, additional genetic counseling and testing may be warranted.
-Two or more soft markers – We offer additional genetic counseling and discussion of diagnostic testing (algorithm 3).
