Chromosomal microarray analysis vs.karyotyping for fetal ventriculomegaly:a meta-analysis

Background:Chromosomal abnormalities are important causes of ventriculomegaly(VM).In mild and isolated cases of fetal VM,obstetricians rarely give clear indications for pregnancy termination.We aimed to calculate the incidence of chromosomal abnormalities and incremental yield of chromosomal microarray analysis(CMA)in VM,providing more information on genetic counseling and prognostic evaluation for fetuses with VM.Methods:The Chinese language databases Wanfang Data,China National Knowledge Infrastructure,and China Biomedical Literature Database(from January 1,1991 to April 29,2020)and English language databases PubMed,Embase,and Cochrane Library(from January 1,1945 to April 29,2020)were systematically searched for articles on fetal VM.Diagnostic criteria were based on ultrasonographic or magnetic resonance imaging(MRI)assessment of lateral ventricular atrium width:≥10 to<15 mm for mild VM,and≥15 mm for severe VM.Isolated VM was defined by the absence of structural abnormalities other than VM detected by ultrasonography or MRI.R software was used for the meta-analysis to determine the incidence of chromosomal abnormalities and incremental yield of CMA in VM,and the combined rate and 95%confidence interval(CI)were calculated.Results:Twenty-three articles involving 1635 patients were included.The incidence of chromosomal abnormalities in VM was 9%(95%CI:5%-12%)and incremental yield of CMA in VM was 11%(95%CI:7%-16%).The incidences of chromosomal abnormalities in mild,severe,isolated,and non-isolated VM were 9%(95%CI:4%-16%),5%(95%CI:1%-11%),3%(95%CI:1%-6%),and 13%(95%CI:4%-25%),respectively.Conclusions:Applying CMA in VM improved the detection rate of abnormalities.When VM is confirmed by ultrasound or MRI,obstetricians should recommend fetal karyotype analysis to exclude chromosomal abnormalities.Moreover,CMA should be recommended preferentially in pregnant women with fetal VM who are undergoing invasive prenatal diagnosis.CMA cannot completely replace chromosome karyotype analysis.

Overview of genetic causes of recurrent miscarriage and the diagnostic approach

Recurring miscarriage(RM)is a frustrating reproductive complication with variable etiology.Numerous genetic defects have been known to play a crucial role in the etiology of RM.Chromosomal abnormalities are frequently detected,while other genetic defects cannot be diagnosed through routine research,such as cryptic chromosomal anomalies,single nucleotide polymorphism,single-gene defect,and gene copy number variation.Diagnostic laboratories have recently used variable advanced techniques to detect potential genetic abnormalities in couples with RM and/or in products of conception.Here we aim to summarize the known genetic causes of RM,with a focus on the new diagnostic techniques.Knowledge of the genetic profile of miscarriages is important for prognosis and potential counseling planning,as well as the prenatal diagnostic strategy in subsequent pregnancies.

Clinical Application of Chromosome Microarray Analysis in Han Chinese Children with Neurodevelopmental Disorders

Chromosome microarray analysis(CMA) is a cost-effective molecular cytogenetic technique that has been used as a first-line diagnostic test in neurodevelopmental disorders in the USA since 2011. The impact of CMA results on clinical practice in China is not yet well studied, so we aimed to better evaluate this phenomenon.We analyzed the CMA results from 434 patients in our clinic, and characterized their molecular diagnoses, clinical features, and follow-up clinical actions based on these results. The overall diagnostic yield for our patients was 13.6%(59 out of 434). This gave a detection rate of 14.7%for developmental delay/intellectual disability(DD/ID,38/259) and 12% for autism spectrum disorders(ASDs,21/175). Thirty-three recurrent(n≥2) variants were found, distributed at six chromosomal loci involving known chromosome syndromes(such as DiGeorge, Williams Beuren, and Angelman/Prader-Willi syndromes).The spectrum of positive copy number variants in our study was comparable to that reported in Caucasian populations, but with specific characteristics. Parental origin tests indicated an effect involving a significant maternal transmission bias to sons. The majority of patients with positive results(94.9%) had benefits, allowing earlier diagnosis(36/59), prioritized full clinical management(28/59), medication changes(7/59), a changed prognosis(30/59), and prenatal genetic counseling(15/59). Our results provide information on de novo mutations in Chinese children with DD/ID and/or ASDs. Our data showed that microarray testing provides immediate clinical utility for patients. It is expected that the personalized medical care of children with developmental disabilities will lead to improved outcomes in long-term developmental potential.We advocate using the diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility.

Age- and gender-dependent obesity in individuals with 16pl1.2 deletion

Recurrent genomic imbalances at 16p 11.2 are genetic risk factors of variable penetrance for developmental delay and autism.Recently, 16pl 1.2（chr16：29.5 Mb-30.1 Mb） deletion has also been detected in individuals with early-onset severe obesity.The penetrance of 16p11.2 deletion as a genetic risk factor for obesity is unknown.We evaluated the growth and body mass characteristics of 28 individuals with 16p11.2 （chr16：29.5 Mb-30.1 Mb） deletion originally ascertained for their developmental disorders by reviewing their medical records.We found that nine individuals could be classified as obese and six as overweight.These individuals generally had early feeding and growth difficulties,and started to gain excessive weight around 5-6 years of age.Thirteen out of the 18 deletion carriers aged 5 years and older（72%） were overweight or obese,whereas only two of 10 deletion carriers（20%） younger than five were overweight or obese.Males exhibited more severe obesity than females.Thus,the obesity phenotype of 16p11.2 deletion carriers is of juvenile onset,exhibited an age- and gender-dependent penetrance. 16p11.2 deletion appears to predispose individuals to juvenile onset obesity and in this case are similar to the well-described Prader-Willi syndrome（PWS）.Early detection of this deletion will provide opportunity to prevent obesity.

JAX-CNV:A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level

We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical diagnosis.JAX-CNV is thus developed for CNV detection from WGS data.The performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 samples.The result showed that JAX-CNV recalled 100%of these CNVs.Besides,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated CMAs.Experimental validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×coverage.For CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to WGS.JAX-CNV is available at https://github.com/TheJacksonLaboratory/JAX-CNV.

osaicism of Tetrasomy 18p： Clinical and Cytogenetic Findings in a Female Child

INTRODUCTION The tetrasomy 18p （OMIM 614290） is a very rare chromosomal abnormality, with a prevalence of 1/140,000-180,000 live births,Although it has been known in some countries, it has been seldom reported in China. Especially, mosaicism for tetrasomy 18p is even rare. Because of a very limited number of cases, the phenotypic spectrum of mosaic tetrasomy 18p, the complications, and prognosis are unknown. In this study, we reported a patient with mosaic tetrasomy 18p by conventional karyotyping analysis, high-resolution single nucleotide polymorphism （SNP） array, and fluorescence in situ hybridization （FISH）.

46,XY,9(p24)dup(2q35q37.3)with Cryptorchidism:A Case Report and Literature Review

A young boy with a facial abnormality was brought to our genetics clinic.Physical examination found bilateral cryptorchidism.Several clinical genetic tests,including chromosome microarray analysis(CMA),karyotyping,and azoospermia factor(AZF)microdeletions on the Y chromosome,were used to identify the genetic basis for this abnormality.The karyotype showed a duplication of the chromosome 2q35q37.3 fragment attached to chromosome 9(p24);CMA revealed 2q35q37.3(220,558,895-243,006,013)x3;the Y chromosome showed no AZF microdeletions;and the parent karyotypes were normal.Surgery has been planned to correct cryptorchidism a year after the original examination.A similar case was found previously.