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Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

ABSTRACT: The genetic etiology of non-aneuploid fetal structural abnormalities is typically investigated by karyotyping and array-based detection of microscopically detectable rearrangements, and submicroscopic copy-number variants (CNVs), which collectively yield a pathogenic finding in up to 10% of cases. We propose that exome sequencing may substantially increase the identification of underlying etiologies. We performed exome sequencing on a cohort of 30 non-aneuploid fetuses and neonates (along with their parents) with diverse structural abnormalities first identified by prenatal ultrasound. We identified candidate pathogenic variants with a range of inheritance models, and evaluated these in the context of detailed phenotypic information. We identified 35 de novo single-nucleotide variants (SNVs), small indels, deletions or duplications, of which three (accounting for 10% of the cohort) are highly likely to be causative. These are de novo missense variants in FGFR3 and COL2A1, and a de novo 16.8 kb deletion that includes most of OFD1. In five further cases (17%) we identified de novo or inherited recessive or X-linked variants in plausible candidate genes, which require additional validation to determine pathogenicity. Our diagnostic yield of 10% is comparable to, and supplementary to, the diagnostic yield of existing microarray testing for large chromosomal rearrangements and targeted CNV detection. The de novo nature of these events could enable couples to be counseled as to their low recurrence risk. This study outlines the way for a substantial improvement in the diagnostic yield of prenatal genetic abnormalities through the application of next-generation sequencing.

SUBMITTER: Carss KJ

PROVIDER: S-EPMC4030780 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

Carss Keren J KJ Hillman Sarah C SC Parthiban Vijaya V McMullan Dominic J DJ Maher Eamonn R ER Kilby Mark D MD Hurles Matthew E ME

Human molecular genetics 20140129 12

The genetic etiology of non-aneuploid fetal structural abnormalities is typically investigated by karyotyping and array-based detection of microscopically detectable rearrangements, and submicroscopic copy-number variants (CNVs), which collectively yield a pathogenic finding in up to 10% of cases. We propose that exome sequencing may substantially increase the identification of underlying etiologies. We performed exome sequencing on a cohort of 30 non-aneuploid fetuses and neonates (along with t ...[more]

PMID: 24476948

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Project description:BackgroundTo explore the significance of multiple ultrasonic soft indexes such as Nuchal translucency (NT) in detection of cardiac structural malformations and chromosome abnormalities in fetal systematic screening in the first trimester, and to understand the value of combined transvaginal ultrasound (TVUS) in congenital heart disease (CHD) screening.MethodsA total of 3,356 pregnant women who underwent early NT screening were screened by systematic ultrasound to monitor and evaluate the sensitivity and specificity of NT, tricuspid valve (TV), ductus venosus (DV) in the diagnosis of fetal CHD. According to the different intervals of NT thickening, the patients were divided into four groups, the detection rates of CHD and abnormal karyotypes in each group were compared, and the consistency of transabdominal and combined transvaginal ultrasonography was compared.ResultsA total of 3,356 cases of early pregnancy were examined by NT. A total of 66 cases of CHD were detected, and the detection rate was 1.97%. Among the 66 CHD cases, 14 cases underwent chromosome karyotype examination and 12 of those cases had abnormal results. With the increase of NT thickness, the detection rates of cardiac structural abnormalities and chromosomal abnormalities all showed a linear increasing trend. The sensitivity of the NT ≥2.5 mm group was as high as 63.64%, and the ductus venosus α wave (DVα) reverse specificity, and the positive likelihood ratio was 99.57% and 53.41%, respectively. The sensitivity of the 3 indicators combined was 66.67%, which was higher than that of any single index, and the area under the receiver operating characteristic (ROC) curve of these 3 indicators combined was the largest (AUC: 0.86). 4. Seventy patients in total were examined by combined TVUS. There is no statistical difference between the two.ConclusionsA positive linear correlation was found between NT thickness and the detection rate of fetal cardiac structural abnormality and chromosome abnormality. Early pregnancy NT screening combined with TV blood flow spectrum and DV blood spectrum screenings has high specificity and sensitivity in the diagnosis of CHD. Combined transabdominal and TVUS in early pregnancy can reduce the rates of misdiagnosis and missed diagnosis of fetal CHD.

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Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

Publications

Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

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