胎儿先天性心脏畸形产前遗传学研究

目的 评估胎儿先天性心脏病(congenital heart diseases,CHD)遗传学异常情况,为孕期管理和遗传咨询提供依据.方法 对产前超声检查发现为先天性心脏畸形的胎儿共81例,采用绒毛活检/羊膜腔穿刺/脐静脉穿刺获取胎儿细胞,进行细胞培养染色体分析;对显带分析无染色体异常胎儿,采用短串联重复标记结合多重荧光定量PCR技术,检测其22q11.2区域微缺失和微重复情况,异常胎儿再用荧光原位杂交技术证实.结果 81例先天性心脏畸形胎儿,发现染色体异常34例,22q11.2微重复1例,总异常发现率为43.2%;合并心外畸形胎儿染色体异常率高于单纯心脏畸形胎儿(64.5%vs.28.0%).染色体异常中,18三体有19例,占染色体异常病例的54.3%.结论 先天性心脏畸形的胎儿染色体异常率高,尤以18三体最为常见;如合并心外畸形,染色体异常概率明显增加;对显带分析染色体正常胎儿则需进行22q11.2区域微缺失和微重复检测.先天性心脏畸形胎儿的遗传学检测有助于孕期管理和遗传咨询.     

Lessons from exome sequencing in prenatally diagnosed heart defects: A basis for prenatal testing

Congenital heart defects (CHDs) are the most common birth defect with 30%-40% being explained by genetic aberrations. With next generation sequencing becoming widely available, we sought to evaluate the clinical utility of exome sequencing (ES) in prenatally diagnosed CHD. We retrospectively analyzed the diagnostic yield as well as non-conclusive and incidental findings in 30 cases with prenatally diagnosed CHDs using ES, mostly as parent-child trios. A genetic diagnosis was established in 20% (6/30). Non-conclusive results were found in 13% (4/30) and incidental findings in 10% (3/30). There was a phenotypic discrepancy between reported prenatal and postnatal extracardiac findings in 40% (8/20). However, none of these additional, postnatal findings altered the genetic diagnosis. Herein, ES in prenatally diagnosed CHDs results in a comparably high diagnostic yield. There was a significant proportion of incidental findings and variants of unknown significance as well as potentially pathogenic variants in novel disease genes. Such findings can bedevil genetic counseling and decision making for pregnancy termination. Despite the small cohort size, our data serve as a first basis to evaluate the value of prenatal ES in CHD for further studies emerging in the near future.     

Prenatal exome sequencing: A useful tool for the fetal neurologist

Prenatal exome sequencing (pES) is a promising tool for diagnosing genetic disorders when structural anomalies are detected on prenatal ultrasound. The aim of this study was to investigate the diagnostic yield and clinical impact of pES as an additional modality for fetal neurologists who counsel parents in case of congenital anomalies of the central nervous system (CNS). We assessed 20 pregnancies of 19 couples who were consecutively referred to the fetal neurologist for CNS anomalies. pES had a diagnostic yield of 53% (10/19) with most diagnosed pregnancies having agenesis or hypoplasia of the corpus callosum (7/10). Overall clinical impact was 63% (12/19), of which the pES result aided parental decision making in 55% of cases (6/11), guided perinatal management in 75% of cases (3/4), and was helpful in approving a late termination of pregnancy request in 75% of cases (3/4). Our data suggest that pES had a high diagnostic yield when CNS anomalies are present, although this study is limited by its small sample size. Moreover, pES had substantial clinical impact, which warrants implementation of pES in the routine care of the fetal neurologist in close collaboration with gynecologists and clinical geneticists.     

The risk for congenital heart defects in offspring of individuals with congenital heart defects

BACKGROUND: Congenital heart defects (CHDs) occur in approximately 1% of all live births. Although most CHDs are of unknown etiology, a family history of CHDs is a known risk factor, and offspring of individuals with CHDs are at a higher risk of having CHDs. The aim of this study was to investigate the relative risk for CHDs to offspring of individuals with CHDs. METHODS: The prevalence rates of CHDs in offspring of 203 individuals with CHDs and 282 individuals without CHDs were investigated. The study participants completed a questionnaire that included information on medical and reproductive history, lifestyle indicators, and family history of CHDs and other congenital malformations. The prevalence rates of CHDs in offspring were calculated. RESULTS: The prevalence of CHDs was 3.1% (18/575) in offspring of individuals with CHDs and 1.3% (8/589) in offspring of individuals without CHDs. The adjusted odds ratio for CHDs to offspring of parents with CHDs was 1.73 (95% confidence interval [95% CI] 0.89-2.44, p=0.02). The estimated relative risk for offspring to females with CHD was higher than for males [2.3 (95% CI 1.1-4.7, p=0.03) versus 1.31 (95% CI 0.48-4.30, p=0.66), respectively]. There was no suggestion of association between CHDs and maternal smoking, alcohol consumption, and use of medication during pregnancy. CONCLUSIONS: Offspring of parents with CHDs are at a higher risk for CHDs compared with the general population. Couples where one member is affected with CHD should receive pre-conceptional or pre-natal genetic counseling and should be informed about the magnitude of the potential risk of CHDs to the offspring.     

Diagnostic yield of clinical exome sequencing in adulthood in medical genetics clinics

Clinical exome sequencing (ES) is the most comprehensive genomic test to identify underlying genetic diseases in Canada. We performed this retrospective cohort study to investigate the diagnostic yield of clinical ES in adulthood. Inclusion criteria were: (1) Adult patients ≥18 years old; (2) Patients underwent clinical ES between January 1 and December 31, 2021; (3) Patients were seen in the Department of Medical Genetics. We reviewed patient charts. We applied American College of Medical Genetics and Genomics and the Association for Molecular Pathology variant classification guidelines for interpretation of variants. Non-parametric Fisher's exact statistical test was used. Seventy-seven patients underwent clinical ES. Fourteen different genetic diseases were confirmed in 15 patients: FBXO11, MYH7, MED13L, NSD2, ANKRD11 (n = 2), SHANK3, RHOBTB2, CDKL5, TRIO, TCF4, SCN1, SMAD3, POGZ, and EIF2B3 diseases. The diagnostic yield of clinical ES was 19.5%. Patients with a genetic diagnosis had a significantly higher frequency of neurodevelopmental disorders than those with no genetic diagnosis (p = 0.00339). The diagnostic yield of clinical ES was the highest in patients with seizures (35.7%), and with progressive neurodegenerative diseases (33.3%). Clinical ES is a helpful genomic test to provide genetic diagnoses to the patients who are referred to medical genetic clinics due to suspected genetic diseases in adulthood to end their diagnostic odyssey. Targeted next generation sequencing panels for specific phenotypes may decrease the cost of genomic test in adulthood.     

Prenatal course of metaphyseal anadysplasia associated with homozygous mutation in MMP9 identified by exome sequencing

Metaphyseal anadysplasia (MANDP) is a rare autosomal recessive form of skeletal dysplasia characterized by normal length at birth and transitory bowing of the legs. Although several families with MANDP have been reported, homozygous mutations in the matrix metalloproteinase type 9 (MMP9) gene have been described in only one consanguineous family, and thus the pre and postnatal phenotypic spectrum is still obscure. A clinically similar but more severe type is caused by autosomal‐dominant inheritance and is caused by mutations in matrix metalloproteinase type 13 gene (MMP13). Here, we report the prenatal and early postnatal course of two affected sib fetuses with early sonographic evidence of long bone shortening and postnatally no metaphyseal changes. Whole‐exome sequencing revealed homozygous mutation in MMP9 in both fetuses suggesting a diagnosis of MANDP. We propose that MANDP should be considered in pregnancies with early prenatal shortening of the long bones without associated finding of lethal skeletal dysplasias. In addition, the finding of homozygous mutation in non‐consanguineous parents of Jewish‐Caucasus ancestry may suggest unawareness of such relation or the occurrence of a founder mutation in this gene.     

Prenatal presentation and diagnosis of Baraitser‐Winter syndrome using exome sequencing

Baraitser‐Winter cerebrofrontofacial syndrome (BWCFF) is a rare autosomal dominant developmental disorder associated with missense mutations in the genes ACTB or ACTG1. The classic presentation of BWCFF is discerned by the combination of unique craniofacial characteristics including ocular coloboma, intellectual disability, and hypertelorism. Congenital contractures and organ malformations are often present, including structural defects in the brain, heart, renal, and musculoskeletal system. However, there is limited documentation regarding its prenatal presentation that may encourage healthcare providers to be aware of this disorder when presented throughout pregnancy. Herein we describe a case of a pregnancy with large cystic hygroma and omphalocele. Whole exome sequencing (WES) was performed and a de novo, heterozygous, likely pathogenic mutation in ACTB was detected, c.1004G>A (p.Arg335His), conferring a diagnosis of BWCFF.     

Low maternal serum alpha-fetoprotein levels and congenital diaphragmatic defects

We report on 2 cases of fetal congenital diaphragmatic defects with normal chromosomes among 105 patients referred for evaluation for low maternal serum alpha-fetoprotein (MSAFP) levels. The mechanism for this striking association is not clear. The association of low MSAFP levels and congenital diaphragmatic defects may have importance for MSAFP screening programs.     

Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population

Neuromuscular diseases (NMDs) include a broad range of disorders affecting muscles, nerves and neuromuscular junctions. Their overlapping phenotypes and heterogeneous genetic nature have created challenges in diagnosis which calls for the implementation of massive parallel sequencing as a candidate strategy to increase the diagnostic yield. In this study, total of 45 patients, mostly offspring of consanguineous marriages were examined using whole exome sequencing. Data analysis was performed to identify the most probable pathogenic rare variants in known NMD genes which led to identification of causal variants for 33 out of 45 patients (73.3%) in the following known genes: CAPN3, Col6A1, Col6A3, DMD, DYSF, FHL1, GJB1, ISPD, LAMA2, LMNA, PLEC1, RYR1, SGCA, SGCB, SYNE1, TNNT1 and 22 novel pathogenic variants were detected. Today, the advantage of whole exome sequencing in clinical diagnostic strategies of heterogeneous disorders is clear. In this cohort, a diagnostic yield of 73.3% was achieved which is quite high compared to the overall reported diagnostic yield of 25% to 50%. This could be explained by the consanguineous background of these patients and is another strong advantage of offering clinical exome sequencing in diagnostic laboratories, especially in populations with high rate of consanguinity.     

Whole exome sequencing identifies multiple diagnoses in congenital glaucoma with systemic anomalies

The genetic basis of congenital glaucoma with systemic anomalies is largely unknown. Whole exome sequencing (WES) in 10 probands with congenital glaucoma and variable systemic anomalies identified pathogenic or likely pathogenic variants in three probands; in two of these, a combination of two Mendelian disorders was found to completely explain the patients' features whereas in the third case only the ocular findings could be explained by the genetic diagnosis. The molecular diagnosis for glaucoma included two cases with compound heterozygous or homozygous pathogenic alleles in CYP1B1 and one family with a dominant pathogenic variant in FOXC1; the second genetic diagnosis for the additional systemic features included compound heterozygous mutations in NPHS1 in one family and a heterozygous 18q23 deletion in another pedigree. These findings show the power of WES in the analysis of complex conditions and emphasize the importance of CYP1B1 screening in patients with congenital glaucoma regardless of the presence/absence of other systemic anomalies.     

Diagnostic exome sequencing identifies a heterozygous MBD5 frameshift mutation in a family with intellectual disability and epilepsy

Methyl-CpG-binding domain 5 (MBD5)-associated neurodevelopmental disorder caused by 2q23.1 or MBD5-specific mutation has been recently identified as a genetic disorder associated with autism spectrum disorders. Phenotypic features of 2q23.1 deletion or disruption of MBD5 gene include severe intellectual disability, seizure, significant speech impairment, sleep disturbance, and autistic-like behavioural problems. Here we report a 7-year-old girl with intellectual disability and epilepsy without previous clinical diagnosis. Diagnostic exome sequencing identified a novel frameshift mutation c.254_255delGA (p.Arg85Asnfs*6) in the MBD5 gene of the proband and her father. The proband's father with normal intelligence showed subclinical manifestations observed in subsequent investigations. Clinical manifestations, disease course, and molecular findings of the involvement of MBD5 gene in this family suggest an unusual MBD5-related neurodevelopmental disorder. Moreover, this report demonstrates the critical role of next-generation sequencing technique in characterizing such a rare disorder with variable or no clinical manifestation and providing opportunity to develop effective preventive measures such as pre-implantation genetic diagnosis.     

A prenatally diagnosed case of Donnai‐Barrow syndrome: Highlighting the importance of whole exome sequencing in cases of consanguinity

Donnai‐Barrow syndrome (DBS) is an autosomal recessive disorder characterized by typical craniofacial features, vision and hearing loss, intellectual disability, agenesis of the corpus callosum (ACC), congenital diaphragmatic hernia (CDH), and omphalocele. This condition is associated with loss‐of‐function mutations in the LRP2 gene. Few cases have been described in the literature. In our case, CDH and ACC were prenatally diagnosed by ultrasound, and the fetus was the product of a first‐degree union. Single‐nucleotide polymorphism‐microarray showed large regions of homozygosity. Whole exome sequencing (WES) was performed and revealed a homozygous frameshift pathogenic variant in LRP2 (c.6978dupG). Here, we present a case of DBS, which diagnosed prenatally via WES in a fetus with CDH and ACC.     

Implementation of fetal clinical exome sequencing: Comparing prospective and retrospective cohorts

PurposeWe compared the diagnostic yield of fetal clinical exome sequencing (fCES) in prospective and retrospective cohorts of pregnancies presenting with anomalies detected using ultrasound. We evaluated factors that led to a higher diagnostic efficiency, such as phenotypic category, clinical characterization, and variant analysis strategy.MethodsfCES was performed for 303 fetuses (183 ongoing and 120 ended pregnancies, in which chromosomal abnormalities had been excluded) using a trio/duo-based approach and a multistep variant analysis strategy.ResultsfCES identified the underlying genetic cause in 13% (24/183) of prospective and 29% (35/120) of retrospective cases. In both cohorts, recessive heterozygous compound genotypes were not rare, and trio and simplex variant analysis strategies were complementary to achieve the highest possible diagnostic rate. Limited prenatal phenotypic information led to interpretation challenges. In 2 prospective cases, in-depth analysis allowed expansion of the spectrum of prenatal presentations for genetic syndromes associated with the SLC17A5 and CHAMP1 genes.ConclusionfCES is diagnostically efficient in fetuses presenting with cerebral, skeletal, urinary, or multiple anomalies. The comparison between the 2 cohorts highlights the importance of providing detailed phenotypic information for better interpretation and prenatal reporting of genetic variants.     

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

Phenotype‐based filtering and prioritization contribute to the interpretation of genetic variants detected in exome sequencing. However, it is currently unclear how extensive this phenotypic annotation should be. In this study, we compare methods for incorporating phenotype into the interpretation process and assess the extent to which phenotypic annotation aids prioritization of the correct variant. Using a cohort of 29 patients with congenital myasthenic syndromes with causative variants in known or newly discovered disease genes, exome data and the Human Phenotype Ontology (HPO)‐coded phenotypic profiles, we show that gene‐list filters created from phenotypic annotations perform similarly to curated disease‐gene virtual panels. We use Exomiser, a prioritization tool incorporating phenotypic comparisons, to rank candidate variants while varying phenotypic annotation. Analyzing 3,712 combinations, we show that increasing phenotypic annotation improved prioritization of the causative variant, from 62% ranked first on variant alone to 90% with seven HPO annotations. We conclude that any HPO‐based phenotypic annotation aids variant discovery and that annotation with over five terms is recommended in our context. Although focused on a constrained cohort, this provides real‐world validation of the utility of phenotypic annotation for variant prioritization. Further research is needed to extend this concept to other diseases and more diverse cohorts.     

Prenatal diagnosis of congenital sialidosis

Sasagasako N, Miyahara S, Saito N, Shinnoh N, Kobayashi T, Goto I. Prenatal diagnosis of congenital sialidosis.
Clin Genet 1993: 44: 8–11. © Munksgaard, 1993
A case of prenatally diagnosed congenital sialidosis is described in a 21-week-old male fetus, which was the fifth product of non-consanguineous parents. The proband, the second product, was diagnosed as having sialidosis by the enzyme assay in peripheral leukocytes after birth. At the 17th week of pregnancy, the fetus at risk was proven to have isolated sialidase deficiency after analyzing a sample of the cultured amniotic fluid cells. There were many cytoplasmic vacuoles and increased amounts of sialyloligosaccharides in the tissue of the aborted fetus, while the amount and the pattern of gangliosides in the central nervous system were normal.