Expanded chromosomal microarray comprising screening for spinal muscular atrophy and monogenic diseases in prenatal diagnosis
Prenatal Genetics
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Primary Categories:
- Laboratory Genetics
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Secondary Categories:
- Laboratory Genetics
Introduction:
Copy number variant platforms, as critical supports for genetic diagnosis, have been routinely implemented in prenatal diagnosis. Nevertheless, numerous severe conditions with underlying single-gene defects are not included in current invasive prenatal screening. As a fatal genetic disease that leads to severe muscle weakness, SMA affects approximately 1 in 12,000 people worldwide. The molecular diagnosis of SMA patients and carriers consists of the detection of the absence of exon 7 (110 bp) of the SMN1 gene. Notably, the preemptive diagnosis and intervention with disease-modifying treatment in neonates prior to symptom onset demonstrates superior outcomes compared to post-symptomatic administration in SMA management. According to the Guidelines for spinal muscular atrophy, carrier screening is recommended as part of population-based genetic screening. Consequently, an expanded chromosomal microarray analysis was developed, employing a meticulously designed single nucleotide polymorphism chip incorporating additional probes to enhance its capability in screening for spinal muscular atrophy and diagnosing monogenic disorders.
Methods:
Between March 2022 and July 2023, 498 pregnant women who underwent invasive prenatal diagnostic procedures at our hospital were enrolled, including 13 with twin pregnancies. All 511 fetal specimens were collected by amniocentesis or chorionic villus sampling. Three distinct diagnostic approaches—expanded chromosomal microarray, karyotype analysis and low-depth genome sequencing—were employed for the evaluation of aneuploidies and multigenic copy number variations. These variations were detected and analyzed in a blinded manner. SMN1 exonic copy number variations were validated using multiplex ligation-dependent probe amplification, while single nucleotide variations were confirmed via Sanger sequencing.
Results:
Overall, expanded chromosomal microarray identified genetic abnormalities in 90 out of 511 cases (16.6%). The detection rate was significantly higher than the rates observed with low-depth genome sequencing (66 out of 511 cases, 12.9%) and conventional chromosome karyotyping (42 out of 511 cases, 8.2%). Expanded chromosomal microarray not only detected aneuploidies (mosaicism above 20%) and copy number variations in 62 cases (12.1%) identified by low-depth genome sequencing but also detected 9 cases with regions of homozygosity, 10 cases (2.0%) with exonic deletions (SMN1 and DMD), and 12 cases (2.3%) with single nucleotide variations.
Conclusion:
Compared with low-depth genome sequencing, expanded chromosomal microarray increased the detection rate by 4.7% (24/511). Likewise, compared with traditional chromosomal microarrays, expanded chromosomal microarray increased the detection rate by 3.9% (20/511). Furthermore, the detection rate of spinal muscular atrophy carriers in this study (1.6%, 8/511) was consistent with carrier frequency in the local population. Although the expanded chromosomal microarray has limited accuracy for detecting single nucleotide variations, its screening capacity was significantly enhanced when complemented with Sanger sequencing validation. This approach, with its capability to accurately identify not only copy number variations but also exonic deletions and regions of homozygosity within an acceptable timeframe of 2-3 weeks, highlights its potential as a potent prenatal diagnostic tool, particularly in screening for SMN1 exonic copy number variations with improved yield. This study provides further evidence that ECMA is a comprehensive diagnostic tool capable of detecting aneuploidies with mosaicisms exceeding 20% and multigene CNVs and facilitates the screening of conditions such as exonic CNVs of SMA, DMD, and other SNVs associated with monogenic disorders. Furthermore, it also underscores the clinical characteristics of participants, thereby offering valuable demographic insights and elucidating the indications for prenatal and genetic testing within the studied cohort. Furthermore, it also underscores the clinical characteristics of participants, thereby offering valuable demographic insights and elucidating the indications for prenatal and genetic testing within the studied cohort.
Copy number variant platforms, as critical supports for genetic diagnosis, have been routinely implemented in prenatal diagnosis. Nevertheless, numerous severe conditions with underlying single-gene defects are not included in current invasive prenatal screening. As a fatal genetic disease that leads to severe muscle weakness, SMA affects approximately 1 in 12,000 people worldwide. The molecular diagnosis of SMA patients and carriers consists of the detection of the absence of exon 7 (110 bp) of the SMN1 gene. Notably, the preemptive diagnosis and intervention with disease-modifying treatment in neonates prior to symptom onset demonstrates superior outcomes compared to post-symptomatic administration in SMA management. According to the Guidelines for spinal muscular atrophy, carrier screening is recommended as part of population-based genetic screening. Consequently, an expanded chromosomal microarray analysis was developed, employing a meticulously designed single nucleotide polymorphism chip incorporating additional probes to enhance its capability in screening for spinal muscular atrophy and diagnosing monogenic disorders.
Methods:
Between March 2022 and July 2023, 498 pregnant women who underwent invasive prenatal diagnostic procedures at our hospital were enrolled, including 13 with twin pregnancies. All 511 fetal specimens were collected by amniocentesis or chorionic villus sampling. Three distinct diagnostic approaches—expanded chromosomal microarray, karyotype analysis and low-depth genome sequencing—were employed for the evaluation of aneuploidies and multigenic copy number variations. These variations were detected and analyzed in a blinded manner. SMN1 exonic copy number variations were validated using multiplex ligation-dependent probe amplification, while single nucleotide variations were confirmed via Sanger sequencing.
Results:
Overall, expanded chromosomal microarray identified genetic abnormalities in 90 out of 511 cases (16.6%). The detection rate was significantly higher than the rates observed with low-depth genome sequencing (66 out of 511 cases, 12.9%) and conventional chromosome karyotyping (42 out of 511 cases, 8.2%). Expanded chromosomal microarray not only detected aneuploidies (mosaicism above 20%) and copy number variations in 62 cases (12.1%) identified by low-depth genome sequencing but also detected 9 cases with regions of homozygosity, 10 cases (2.0%) with exonic deletions (SMN1 and DMD), and 12 cases (2.3%) with single nucleotide variations.
Conclusion:
Compared with low-depth genome sequencing, expanded chromosomal microarray increased the detection rate by 4.7% (24/511). Likewise, compared with traditional chromosomal microarrays, expanded chromosomal microarray increased the detection rate by 3.9% (20/511). Furthermore, the detection rate of spinal muscular atrophy carriers in this study (1.6%, 8/511) was consistent with carrier frequency in the local population. Although the expanded chromosomal microarray has limited accuracy for detecting single nucleotide variations, its screening capacity was significantly enhanced when complemented with Sanger sequencing validation. This approach, with its capability to accurately identify not only copy number variations but also exonic deletions and regions of homozygosity within an acceptable timeframe of 2-3 weeks, highlights its potential as a potent prenatal diagnostic tool, particularly in screening for SMN1 exonic copy number variations with improved yield. This study provides further evidence that ECMA is a comprehensive diagnostic tool capable of detecting aneuploidies with mosaicisms exceeding 20% and multigene CNVs and facilitates the screening of conditions such as exonic CNVs of SMA, DMD, and other SNVs associated with monogenic disorders. Furthermore, it also underscores the clinical characteristics of participants, thereby offering valuable demographic insights and elucidating the indications for prenatal and genetic testing within the studied cohort. Furthermore, it also underscores the clinical characteristics of participants, thereby offering valuable demographic insights and elucidating the indications for prenatal and genetic testing within the studied cohort.