4. Proposed workflow

The goal of prenatal genetic testing in fetuses with CAs is to determine if there is a genetic etiology and consequently enabling well-informed genetic counseling to the parents about the prognosis, reproductive options, obstetric and pediatric management, and recurrence risks.

If the results are normal we proceed with molecular karyotyping instead of a conventional karyotype as studies showed that this approach allows for the highest diagnostic yield. We use this approach whether the anomaly appears to be isolated or multiple anomalies are detected. In fetuses with normal results of molecular karyotyping, with multiple CAs, and a strong clinical indication for monogenic etiology, we proceed with WES; our approach involves sequencing the fetus as well as the biological parents (so-called trio sequencing), which increases the diagnostic yield by filtering out thousands of uninformative genomic variants as

Figure 3. Diagnostic algorithm for the prenatal genetic diagnostics of CAs. CAs, congenital anomalies; QF-PCR, quanti-

Genomic Testing for Prenatal Clinical Evaluation of Congenital Anomalies

http://dx.doi.org/10.5772/intechopen.73247

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tative fluorescence-polymerase chain reaction; NGS, next-generation sequencing.

In cases when CAs are lethal or have unfavorable prognosis, the parents often decide to terminate the pregnancy, but for the purpose of genetic counseling, it is still important to obtain the diagnosis. Accordingly, we shift the diagnostic process after the termination of the pregnancy. Thorough dysmorphological and pathohistological evaluation may give additional information on the specific phenotype and thus enables a more direct diagnostic approach in the aborted fetus. Otherwise, we use the diagnostic approach similar to the approach during

Different medical specialists are involved in the process of prenatal diagnosis of CAs. The role of a clinical geneticist in the whole pathway of genetic diagnostics of a pregnancy with CAs in a close collaboration with other medical specialists (obstetricians, surgeons, radiologists, pathologists, etc.) and a multidisciplinary approach is undisputed due to all the complexities of prenatal diagnostics of CAs, their clinical presentation and phenotype evaluation, choice of the right genetic testing strategies, interpretation of genetic testing results, and their communication

well as shortens the analysis turnaround time (less than 3 weeks at our institution).

the pregnancy.

to patients and families.

Different approaches of prenatal genetic diagnostics are used. Despite known evidence of important additional diagnostic yield of new genomic technologies to the etiology of CAs, most countries still use the traditional genetic diagnostic approach. Hereinafter we present a diagnostic workflow that is currently in use at our institution (Figure 3). It incorporates the use of new genomic technologies and is focused on the expected diagnostic yield and limited diagnostic time frame.

When fetal CAs are detected on an ultrasound examination, we offer an invasive procedure for diagnostic genetic testing.

In cases when specific chromosomal disorder (e.g., double bubble and trisomy 21) or monogenic syndrome is strongly suspected on the initial evaluation and single gene testing is straightforward (e.g., achondroplasia), we exclude common aneuploidies (trisomy 13, 18, and 21, and aneuploidies of sex chromosomes) first, using quantitative fluorescence-polymerase chain reaction (QF-PCR), and proceed with single gene testing, respectively.

When the specific clinical diagnosis is not apparent, we use a genomic approach for the detection of genetic etiology of CAs. Because aneuploidies represent the commonest genetic etiology of CAs, we first opt for QF-PCR to exclude the aneuploidies mentioned above.

Genomic Testing for Prenatal Clinical Evaluation of Congenital Anomalies http://dx.doi.org/10.5772/intechopen.73247 407

than a month's time. This significantly increases the utility of this test in prenatal diagnosis. Sequencing of parental samples along with the fetal sample may also be used to facilitate the timely interpretation of the sequencing results. Furthermore, we believe that limiting the set of reported variants to known and clear pathogenicity is also an option in order to limit the complexity of the analysis only to clinically actionable and conclusive results. Furthermore, as in other genome-wide analysis approaches, NGS-based diagnostics inherently raise the issues of incidental findings and variants of uncertain clinical significance. Due to limited time and other specificities in prenatal diagnostics, several approaches should be employed to address these issues. These include (1) limiting the gene target to genes with overlapping clinical symptoms and signs and (2) limiting the reported variants to definitely pathogenic and likely pathogenic variant classes. Furthermore, efficient collaboration within a multidisciplinary team is often crucial in clarifying the clinical relevance of identified variants. Opting for this approach, it is possible to utilize diagnostic advantages of NGS-based approaches while reducing the chance of encountering uncertain and unsolicited findings. Nevertheless, extensive genetic counseling should be offered to patients while stressing the possibility of identifi-

The goal of prenatal genetic testing in fetuses with CAs is to determine if there is a genetic etiology and consequently enabling well-informed genetic counseling to the parents about the prognosis, reproductive options, obstetric and pediatric management, and recurrence risks.

Different approaches of prenatal genetic diagnostics are used. Despite known evidence of important additional diagnostic yield of new genomic technologies to the etiology of CAs, most countries still use the traditional genetic diagnostic approach. Hereinafter we present a diagnostic workflow that is currently in use at our institution (Figure 3). It incorporates the use of new genomic technologies and is focused on the expected diagnostic yield and limited

When fetal CAs are detected on an ultrasound examination, we offer an invasive procedure for

In cases when specific chromosomal disorder (e.g., double bubble and trisomy 21) or monogenic syndrome is strongly suspected on the initial evaluation and single gene testing is straightforward (e.g., achondroplasia), we exclude common aneuploidies (trisomy 13, 18, and 21, and aneuploidies of sex chromosomes) first, using quantitative fluorescence-polymerase

When the specific clinical diagnosis is not apparent, we use a genomic approach for the detection of genetic etiology of CAs. Because aneuploidies represent the commonest genetic etiology of CAs, we first opt for QF-PCR to exclude the aneuploidies mentioned above.

chain reaction (QF-PCR), and proceed with single gene testing, respectively.

cation of VUS findings and incidental findings.

406 Congenital Anomalies - From the Embryo to the Neonate

4. Proposed workflow

diagnostic time frame.

diagnostic genetic testing.

Figure 3. Diagnostic algorithm for the prenatal genetic diagnostics of CAs. CAs, congenital anomalies; QF-PCR, quantitative fluorescence-polymerase chain reaction; NGS, next-generation sequencing.

If the results are normal we proceed with molecular karyotyping instead of a conventional karyotype as studies showed that this approach allows for the highest diagnostic yield. We use this approach whether the anomaly appears to be isolated or multiple anomalies are detected.

In fetuses with normal results of molecular karyotyping, with multiple CAs, and a strong clinical indication for monogenic etiology, we proceed with WES; our approach involves sequencing the fetus as well as the biological parents (so-called trio sequencing), which increases the diagnostic yield by filtering out thousands of uninformative genomic variants as well as shortens the analysis turnaround time (less than 3 weeks at our institution).

In cases when CAs are lethal or have unfavorable prognosis, the parents often decide to terminate the pregnancy, but for the purpose of genetic counseling, it is still important to obtain the diagnosis. Accordingly, we shift the diagnostic process after the termination of the pregnancy. Thorough dysmorphological and pathohistological evaluation may give additional information on the specific phenotype and thus enables a more direct diagnostic approach in the aborted fetus. Otherwise, we use the diagnostic approach similar to the approach during the pregnancy.

Different medical specialists are involved in the process of prenatal diagnosis of CAs. The role of a clinical geneticist in the whole pathway of genetic diagnostics of a pregnancy with CAs in a close collaboration with other medical specialists (obstetricians, surgeons, radiologists, pathologists, etc.) and a multidisciplinary approach is undisputed due to all the complexities of prenatal diagnostics of CAs, their clinical presentation and phenotype evaluation, choice of the right genetic testing strategies, interpretation of genetic testing results, and their communication to patients and families.
