Xp22.31 copy number variations in 87 fetuses: refined genotype-phenotype correlations by prenatal and postnatal follow-up.

BACKGROUND: Xp22.31 deletion and duplication have been described in various studies, but different laboratories interpret pathogenicity differently. OBJECTIVES: Our study aimed to refine the genotype-phenotype associations between Xp22.31 copy number variants in fetuses, with the aim of providing data support to genetic counseling. METHODS: We retrospectively analyzed karyotyping and single nucleotide polymorphism array results from 87 fetuses and their family members. Phenotypic data were obtained through follow-up visits. RESULTS: The percentage of fetuses carrying the Xp22.31 deletions (9 females, 12 males) was 24.1% (n = 21), while duplications (38 females, 28 males) accounted for 75.9% (n = 66). Here, we noted that the typical region (from 6.4 to 8.1 Mb, hg19) was detected in the highest ratio, either in the fetuses with deletions (76.2%, 16 of 21) or duplications (69.7%, 46 of 66). In female deletion carriers, termination of pregnancy was chosen for two fetuses, and the remaining seven were born without distinct phenotypic abnormalities. In male deletion carriers, termination of pregnancy was chosen for four fetuses, and the remaining eight of them displayed ichthyosis without neurodevelopmental anomalies. In two of these cases, the chromosomal imbalance was inherited from the maternal grandfathers, who also only had ichthyosis phenotypes. Among the 66 duplication carriers, two cases were lost at follow-up, and pregnancy was terminated for eight cases. There were no other clinical findings in the rest of the 56 fetuses, including two with Xp22.31 tetrasomy, for either male or female carriers. CONCLUSION: Our observations provide support for genetic counseling in male and female carriers of Xp22.31 copy number variants. Most of them are asymptomatic in male deletion carriers, except for skin findings. Our study is consistent with the view that the Xp22.31 duplication may be a benign variant in both sexes.

An assessment of the analytical performance of non-invasive prenatal testing (NIPT) in detecting sex chromosome aneuploidies: 34,717-patient sample in a single prenatal diagnosis Centre in China.

OBJECTIVE: The present study aimed to evaluate the efficacy of a non-invasive prenatal test (NIPT) in the detection of the sex chromosome aneuploidies (SCAs) at our prenatal diagnosis centre. METHODS: Among a cohort of 34,717 pregnancies, maternal plasma samples from our prenatal diagnosis centre were subject to analysis of SCAs using NIPT detection. Pregnant women with NIPT positive results of SCAs were recommended to undergo an invasive prenatal diagnosis (i.e. karyotyping and fluorescence in situ hybridization) to validate the prediction value of NIPT. RESULTS: From 34,717 clinical pregnancies, 229 (0.66%) pregnancies were identified with SCAs. Of these, 78 (34.1%) cases were positive for 45,X and 151 (65.9%) cases comprised a sex chromosome trisomy. Of the 229 positive NIPT results, 193 (84.3%) cases had accepted an invasive diagnosis involving karyotyping analysis of the amniotic fluid, which confirmed 67 cases (34.7%) as true positive, as well as 126 cases (65.3%) as false positive. The positive predictive values were 23.07%, 50%, 36% and 27.27% respectively. The remaining 36 (15.7%) cases declined a prenatal diagnosis. The termination rates of 45,X, 47,XXY, 47,XXX and 47,XYY were 20.5%,46%,12.9% and 11.5% respectively. CONCLUSIONS: NIPT demonstrated a lower accuracy in predicting monosomy X than sex chromosome trisomies. After invasive testing, the fetal chromosome with 45,X and 47,XXY were terminated more often than those with 47,XXX, 47,XYY. Because NIPT is a screening test, false positive/negative cases exist, and pre- and post-test counselling is essential for informing patients about the benefits and limitations of the test. Confirmatory testing of abnormal results is recommended prenatally or after birth, and the importance of confirmatory testing and benefits of early diagnosis should be addressed.

Prenatal Diagnosis and Genetic Analysis of 21q21.1-q21.2 Aberrations in Seven Chinese Pedigrees.

Background: Chromosomal aberrations contribute to human phenotypic diversity and disease susceptibility, but it is difficult to assess their pathogenic effects in the clinic. Therefore, it is of great value to report new cases of chromosomal aberrations associated with normal phenotypes or clinical abnormalities. Methods: This was a retrospective analysis of seven pedigrees that carried 21q21.1-q21.2 aberrations. G-banding and single-nucleotide polymorphism array techniques were used to analyze chromosomal karyotypes and copy number variations in the fetuses and their family members. Results: All fetuses and their family members showed normal karyotypes in seven pedigrees. Here, it was revealed that six fetuses carried maternally inherited 21q21.1-q21.2 duplications, ranging from 1 to 2.7 Mb, but none of the mothers had an abnormal phenotype. In one fetus, an 8.7 Mb deletion of 21q21.1-q21.2 was found. An analysis of the pedigree showed that the deletion was also observed in the mother, brother, and maternal grandmother, but no abnormal phenotypes were found. Conclusion: This study identified 21q21.1-q21.2 aberrations in Chinese pedigrees. The carriers of 21q21.1-q21.2 duplications had no clinical consequences based on their phenotypes, and the 21q21.1-q21.2 deletion was transmitted through three generations of normal individuals. This provides benign clinical evidence for pathogenic assessment of 21q21.1-q21.2 duplication and deletion, which was considered a variant of uncertain significance and a likely pathogenic variant in previous reports.

A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center.

OBJECTIVE: To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS: A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS: Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS: NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.

Prenatal diagnosis of familial submicroscopic duplication at 18q22.3 without phenotypic abnormalities.

OBJECTIVE: To report a case of familial submicroscopic duplication at 18q22.3 without phenotypic abnormalities. CASE REPORT: Here, we reported two different cases with novel copy number variation at chromosome 18q22.3: one carried a maternally inherited 2.36 Mb microduplication, and the other carried a patrilineally inherited 1.74 Mb microduplication. The HumanCytoSNP-12 array allows for the visualization of the CNVs and maps the breakpoints. Both parents with the microduplication at 18q22.3 as well as their foetuses had normal phenotypes; the infants were regularly followed up after one year of age, and no abnormalities were found, including abnormalities related to growth, intelligence and sexual development. CONCLUSION: Our report showed that the duplication of 18q22.3 (chr18:68,606,012-71,287,101) might represent a benign variant.

[Factors affecting the failure of non-invasive prenatal testing and the feasibility analysis of retesting].

OBJECTIVE: To explore the cause for the failure of non-invasive prenatal testing (NIPT) and feasibility of repeated testing. METHODS: Clinical data, test results and pregnancy outcomes of 40 311 pregnant women who received NIPT test from January 2011 to December 2018 were reviewed. RESULTS: Among all the pregnant women, 1116 cases failed in the first test, 9 cases (0.81%) had fetal free DNA concentration lower than 4%, 663 cases (59.41%) were retested after the establishment of Z value gray area, and the remainder 444 cases (39.78%) needed to be retested after the blood collection due to the fetal free DNA concentration lower than 4%. After retesting, 1069 cases (95.78%) obtained effective NIPT results. The results showed that 53 cases were at high risk (6 cases for trisomy 21, 6 cases for trisomy 18, 13 cases for trisomy 13, 16 cases for sex chromosomal abnormality, 12 cases for chromosomal copy number variation). Forty-eight cases were selected for invasive prenatal diagnosis, and 2 cases of 47, XXY and 2 CNV were confirmed. A total of 47 cases (0.12%) did not obtain results because the concentration of fetal free DNA was lower than 4%. Only 16 cases (34%) chose invasive prenatal diagnosis. CONCLUSION: Repeated detection of the gray area of Z value can reduce the false positive rate of NIPT and invasive prenatal diagnosis, and the feasibility of repeated detection is high. In the case of fetal free DNA concentration lower than 4%, the success rate of obtaining effective NIPT results by re-sampling and re-detection increases with the increase of gestational age, but may delay the diagnosis for fetal aneuploidies. Therefore, personalized estimation should be made according to gestational age and clinical indications. It is suggested that pregnant women should choose invasive prenatal diagnosis when they have failed in the retest.

Detection of fetal trisomy and single gene disease by massively parallel sequencing of extracellular vesicle DNA in maternal plasma: a proof-of-concept validation.

BACKGROUND: During human pregnancy, placental trophectoderm cells release extracellular vesicles (EVs) into maternal circulation. Trophoblasts also give rise to cell-free DNA (cfDNA) in maternal blood, and has been used for noninvasive prenatal screening for chromosomal aneuploidy. We intended to prove the existence of DNA in the EVs (evDNA) of maternal blood, and compared evDNA with plasma cfDNA in terms of genome distribution, fragment length, and the possibility of detecting genetic diseases. METHODS: Maternal blood from 20 euploid pregnancies, 9 T21 pregnancies, 3 T18 pregnancies, 1 T13 pregnancy, and 2 pregnancies with FGFR3 mutations were obtained. EVs were separated from maternal plasma, and confirmed by transmission electronic microscopy (TEM), western blotting, and flow cytometry (FACS). evDNA was extracted and its fetal origin was confirmed by quantitative PCR (qPCR). Pair-end (PE) whole genome sequencing was performed to characterize evDNA, and the results were compared with that of cfDNA. The fetal risk of aneuploidy and monogenic diseases was analyzed using the evDNA sequencing data. RESULTS: EVs separated from maternal plasma were confirmed with morphology by TEM, and protein markers of CD9, CD63, CD81 as well as the placental specific protein placental alkaline phosphatase (PLAP) were confirmed by western blotting or flow cytometry. EvDNA could be successfully extracted for qPCR and sequencing from the plasma EVs. Sequencing data showed that evDNA span on all 23 pairs of chromosomes and mitochondria, sharing a similar distribution pattern and higher GC content comparing with cfDNA. EvDNA showed shorter fragments yet lower fetal fraction than cfDNA. EvDNA could be used to correctly determine fetal gender, trisomies, and de novo FGFR3 mutations. CONCLUSIONS: We proved that fetal DNA could be detected in EVs separated from maternal plasma. EvDNA shared some similar features to plasma cfDNA, and could potentially be used to detect genetic diseases in fetus.

Genome-wide detection of additional fetal chromosomal abnormalities by cell-free DNA testing of 15,626 consecutive pregnant women.

Cell-free DNA (cfDNA) testing for common fetal trisomies (T21, T18, T13) is highly effective. However, the usefulness of cfDNA testing in detecting other chromosomal abnormalities is unclear. We evaluated the performance of cfDNA testing for genome-wide abnormalities, and analyzed the incremental yield by reporting extra abnormalities. We performed genome-wide cfDNA testing in 15,626 consecutive pregnancies prospectively enrolled in this study. cfDNA testing results were reported and counseling was given depending on the presence of extra chromosomal abnormalities. cfDNA testing identified 190 cases (1.2%) of chromosomal abnormalities including 100 common trisomies and 90 additional abnormalities. By expanding the cfDNA reporting range to genome-wide abnormalities, the false positive rate increased to 0.39% (P<0.001) and positive predictive value (PPV) was reduced to 65.58% (P=0.42). However, the detection yield increased from 0.44% to 0.65% (P=0.014), and cfDNA testing detected 38.61% (39/101) additional abnormalities with no ultrasound and biochemical screening findings. cfDNA testing outperformed biochemical screening by showing 60 times higher true positive rate and fewer false negative results. Genome-wide cfDNA testing significantly increased the diagnostic yield by detecting extra abnormalities, especially those without diagnostic indications. Genome-wide cfDNA testing has fewer false positive and false negative results compared with biochemical screening.

Targeted next-generation sequencing identification of mutations in patients with disorders of sex development.

BACKGROUND: The identification of causative mutations is important for treatment decisions and genetic counseling of patients with disorders of sex development (DSD). Here, we designed a new assay based on targeted next-generation sequencing (NGS) to diagnose these genetically heterogeneous disorders. METHODS: All coding regions and flanking sequences of 219 genes implicated in DSD were designed to be included on a panel. A total of 45 samples were used for sex chromosome dosage validation by targeted sequencing using the NGS platform. Among these, 21 samples were processed to find the causative mutation. RESULTS: The sex chromosome dosages of all 45 samples in this assay were concordant with their corresponding karyotyping results. Among the 21 DSD patients, a total of 11 mutations in SRY, NR0B1, AR, CYP17A1, GK, CHD7, and SRD5A2 were identified, including five single nucleotide variants, three InDels, one in-frame duplication, one SRY-positive 46,XX, and one gross duplication with an estimated size of more than 427,038 bp containing NR0B1 and GK. We also identified six novel mutations: c.230_231insA in SRY, c.7389delA in CHD7, c.273C>G in NR0B1, and c.2158G>A, c.1825A>G, and c.2057_2065dupTGTGTGCTG in AR. CONCLUSIONS: Our assay was able to make a genetic diagnosis for eight DSD patients (38.1%), and identified variants of uncertain clinical significance in the other three cases (14.3%). Targeted NGS is therefore a comprehensive and efficient method to diagnose DSD. This work also expands the pathogenic mutation spectrum of DSD.

[Prenatal diagnosis of a case with combined Wolf-Hirschhorn syndrome and Jacobsen syndrome].

OBJECTIVE: To detect chromosomal imbalance in a fetus with complex congenital heart disease, and to correlate the genotype with the phenotype. METHODS: Routine G-banding was carried out to analyze the karyotypes of the fetus and its parents, and single nucleotide polymorphisms array (SNP-array) was used for delineating fine genomic aberrations. The detected aberrations were confirmed with multiplex ligation-dependent probe amplification (MLPA). RESULTS: The fetus and its parents all showed a normal karyotype, while array-SNP has detected a 13.87 Mb duplication at 4p16.3-p15.33 and a 15.65 Mb deletion at 11q23.3-q25 in the fetus. The results were confirmed by the MLPA assay. CONCLUSION: The partial trisomy 4p (Wolf-Hirschhorn syndrome) and partial monosomy 11q (Jacobsen syndrome) probably underlie the complex heart defects detected in the fetus. Analysis of the karyotypes of its parents offered no help for the determination of the aberrant type and recurrent risk. Compared with routine karyotype analysis, aberrant regions can be identified with array-SNP with greater resolution and accuracy. This has provided useful information for prenatal diagnosis and genetic counseling.

A robust approach for blind detection of balanced chromosomal rearrangements with whole-genome low-coverage sequencing.

Balanced chromosomal rearrangement (or balanced chromosome abnormality, BCA) is a common chromosomal structural variation. Next-generation sequencing has been reported to detect BCA-associated breakpoints with the aid of karyotyping. However, the complications associated with this approach and the requirement for cytogenetics information has limited its application. Here, we provide a whole-genome low-coverage sequencing approach to detect BCA events independent of knowing the affected regions and with low false positives. First, six samples containing BCAs were used to establish a detection protocol and assess the efficacy of different library construction approaches. By clustering anomalous read pairs and filtering out the false-positive results with a control cohort and the concomitant mapping information, we could directly detect BCA events for each sample. Through optimizing the read depth, BCAs in all samples could be blindly detected with only 120 million read pairs per sample for data from a small-insert library and 30 million per sample for data from nonsize-selected mate-pair library. This approach was further validated using another 13 samples that contained BCAs. Our approach advances the application of high-throughput whole-genome low-coverage analysis for robust BCA detection-especially for clinical samples-without the need for karyotyping.

CpG island methylation status of miRNAs in esophageal squamous cell carcinoma.

Previous studies on esophageal squamous cell carcinoma (ESCC) indicated that it contains much dysregulation of microRNAs (miRNAs). DNA hypermethylation in the miRNA 5' regulatory region is a mechanism that can account for the downregulation of miRNA in tumors (Esteller, N Engl J Med 2008;358:1148-59). Among those dysregulated miRNAs, miR-203, miR-34b/c, miR-424 and miR-129-2 are embedded in CpG islands, as is the promoter of miR-34a. We investigated their methylation status in ESCC by bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP). The methylation frequency of miR-203 and miR-424 is the same in carcinoma and in the corresponding non-tumor tissues. The methylation ratio of miR-34a, miR-34b/c and miR-129-2 is 66.7% (36/54), 40.7% (22/54) and 96.3% (52/54), respectively in ESCC, which are significantly higher than that in the corresponding non-tumor tissues(p < 0.01). Quantitative RT-PCR analysis in clinical samples suggested that CpG island methylation is significantly correlated with their low expression in ESCC, 5-aza-2'-deoxycytidine (DAC) treatment partly recovered their expression in EC9706 cell line. We conclude that CpG island methylation of miR-34a, miR-34b/c and miR-129-2 are frequent events and important mechanism for their low expression in ESCC. DNA methylation changes have been reported to occur early in carcinogenesis and are potentially good early indicators of carcinoma (Laird, Nat Rev Cancer 2003;3:253-66). The high methylation ratio of miR-129-2 indicated its potential as a methylation biomarker in early diagnosis of ESCC.

A functional varient in microRNA-146a is associated with risk of esophageal squamous cell carcinoma in Chinese Han.

MicroRNAs are a new class of non-proteincoding, small RNAs that function as tumor suppressors or oncogenes. They participate in diverse biological pathways and function as gene regulators. A G>C polymorphism (rs2910164), which is located in the sequence of miR-146a precursor, results in a change from G:U to C:U in its stem region. However, it remains largely unknown whether this single nucleotide polymorphism (SNP) may alter esophageal squamous cell carcinoma (ESCC) susceptibility. In the current study, we evaluated association between rs2910164 and ESCC susceptibility in a case-control study of 444 sporadic ESCC patients and 468 matched cancer-free controls in a Chinese Han population. Compared with rs2910164 variant genotype CC, genotype GG was associated with increased risk of ESCC (Odds Ratio, 2.39, 95% Confidence Interval, 1.36-4.20). In the smokers, the risk of rs2910164 GG genotype was more notable (Odds Ratio, 3.17, 95% Confidence Interval, 1.71-4.46). In the stratification analyses, we also found there was a strong correlation between rs2910164 C/G variant and the clinical TNM stage (P < 0.01). These findings suggest that this functional SNP in pre-miR-146a could contribute to ESCC susceptibility and clinical outcome.

A functional variation in pre-microRNA-196a is associated with susceptibility of esophageal squamous cell carcinoma risk in Chinese Han.

MicroRNAs (miRNAs) are small, non-protein-coding RNAs that function as tumour suppressors or oncogenes. A single nucleotide change in the sequence of pre-miRNA can affect miRNA expression, so single-nucleotide polymorphisms (SNPs) in pre-miRNA may be biomarkers for biomedical applications. In this study, we performed a genetic association study between the SNP (rs11614913) in pre-miRNA-196a and esophageal squamous cell carcinoma (ESCC) susceptibility in a case-control study. We found that the homozygote CC of this SNP increased the risk of ESCC compared with the homozygote TT and the risk was more evident among smokers than non-smokers. Therefore, this functional SNP may be a biomarker for ESCC outcome.

Polymorphisms of decoy receptor 3 are associated with risk of esophageal squamous cell carcinoma in Chinese Han.

Decoy receptor 3 (DcR3) is a soluble receptor without transmembrane and intracellular sequences in its peptide. It can bind to and inactivate the apoptosis-inducing ligand FasL, LIGHT, and TL1A. The aims of this study are to genotype the two polymorphisms in the promotor of DcR3 in esophageal squamous cell cancer patients and controls and analyze the association between individual genetic variation and susceptibility to esophageal squamous cell carcinoma (ESCC). A total of 444 Chinese ESCC patients and 468 matched cancer-free controls were evaluated for the two single nucleotide polymorphisms (SNPs) in DCR3. Polymorphisms were genotyped using the SNPShot technique. The expression of DCR3 in cancer tissues was detected by reverse transcription-polymerase chain reaction. There were significant differences in the allele's distribution of the two SNPs among ESCC cases and controls (P < 0.01). Compared with the 147TT genotype, the 147CC genotype was associated with significant elevated risk of ESCC (odds ratio, 1.89; 95% confidence interval, 1.30-2.96). The risk of 147CC genotype was more notable (odds ratio, 2.19; 95% confidence interval, 1.32-3.64) in the smokers than in the nonsmokers (odds ratio, 1.25; 95% confidence interval, 0.59-2.69). In the stratification analyses, we also found there was a strong correlation between 147 CC and the clinical TNM stage (P < 0.01). Furthermore, significant difference in DCR3 expression in ESCC tissues was found between subgroups with different 147C/T variant. Our finding suggested that DcR3 promoter polymorphism 147C/T might influence the susceptibility to ESCC in the Chinese Han population, maybe by influencing DcR3 expression.