Prevalence of chromosomal abnormalities and 22q11.2 deletion in conotruncal and non-conotruncal antenatally diagnosed congenital heart diseases in a Chinese population

Evaluating High-Confidence Genes in Conotruncal Cardiac Defects by Gene Burden Analyses

Background In nonsyndromic conotruncal cardiac defects, the use of next-generation sequencing for clinical diagnosis is increasingly adopted, but gene-disease associations in research are only partially translated to diagnostic panels, suggesting a need for evidence-based consensus. Methods and Results In an exome data set of 245 patients with conotruncal cardiac defects, we performed burden analysis on a high-confidence congenital heart disease gene list (n=132) with rare (<0.01%) and ultrarare (absent in the Genome Aggregation Database) protein-altering variants. Overall, we confirmed an excess of rare variants compared with ethnicity-matched controls and identified 2 known genes (GATA6, NOTCH1) and 4 candidate genes supported by the literature (ANKRD11, DOCK6, NPHP4, and STRA6). Ultrarare variant analysis was performed in combination with 3 other published studies (n=1451) and identified 3 genes (FLT4, NOTCH1, TBX1) to be significant, whereas a subgroup analysis involving 391 Chinese subjects identified only GATA6 as significant. Conclusions We suggest that these significant genes in our rare and ultrarare burden analyses warrant prioritization for clinical testing implied for rare inherited and de novo variants. Additionally, associations on ClinVar for these genes were predominantly variants of uncertain significance. Therefore, a more stringent assessment of gene-disease associations in a larger and ethnically diverse cohort is required to be prudent for future curation of conotruncal cardiac defect genes.

Prenatal screening of DiGeorge (22q11.2 deletion) syndrome by abnormalities of the great arteries among Thai pregnant women

Objective

22q11.2DS (deletion syndrome) is one of the common serious anomalies resulting in high perinatal morbidity and mortality rate. Nevertheless, prenatal diagnosis of 22q11.2DS in Southeast Asia has never been described and its prevalence in prenatal series has never been explored. The objective of this study was to describe the experience of prenatal diagnosis of 22q11.2DS in the Thai population and to determine its prevalence among fetuses prenatally diagnosed with abnormalities of the great arteries.

Methods

A prospective study was conducted on pregnant Thai women prenatally diagnosed with abnormalities of the great arteries in the second trimester. The recruited cases were investigated for fetal 22q11.2 deletion by in situ hybridization with a probe specific to the DiGeorge/VCFS TUPLE 1 region located on chromosome 22 for the locus D22S75, and 22qter for a telomere specific sequence clone as the control region.

Results

Five out of the 42 (11.9%) fetuses with abnormalities of the great arteries meeting the inclusion criteria were proven to have 22q11.2DS. The most common abnormalities were the tetralogy of Fallot (or variants) and right-sided aortic arch, followed by a thymic hypoplasia.

Conclusion

As observed in the western countries, we have documented that, among pregnant Thai women, 22q11.2DS is highly prevalent in fetuses with abnormalities of the great arteries (approximately 12%). This information is important when counselling couples to undergo prenatal testing for 22q11.2DS, since this information is vital in the patients' decision of termination or continuation of pregnancy and in a well-prepared management of the affected child.

Effect quantification and value prediction of factors in noninvasive detection for specific fetal copy number variants by semiconductor sequencing

Background

The detection limit of noninvasive prenatal testing (NIPT) by next generation sequencing for any given fetal copy number variants (CNV) can be influenced by several factors. In this study, we quantified the effects and predicted the value of parameters for CNVs detection by NIPT.

Methods

Genomic DNA from patient's leucocytes with 3.16 Mb microdeletion in 22q11.21 was mixed with DNA from aborted fetal tissues without CNV at various concentrations by an enzyme digestion method. Abnormal DNA at 0% served as negative control. Sequencing of mixture samples (at 0%, 4%, 12%, and 20%) by Ion Proton Sequencer was performed at flow 500, with WISECONDOR as the pipeline in CNV‐calling and bin of 500, 750 and 1,000 kb for counting unique reads. The parameters were evaluated with Box–Behnken design. The region with Z score ≦−3 was marked as a potential microdeletion.

Results

The equation of Z score depending on fetal fraction, unique read number and bin size was obtained by Box–Behnken design. The negative effect was quantified as the coefficient in the equation. The smallest values of these parameters were defined as 4 M unique read number, and 10.08% fetal DNA concentration at bin of 750 kb for detecting subchromosomal microdeletion of 3.16 Mb.

Conclusion

The quantification of effect and value of parameters as well as the method used in this study can benefit the establishment of quality standards for CNVs detection and interpretation of CNVs detection results.