Significant Chromosomal Abnormalities Research Articles

Prenatal chromosomal microarray analysis in a large Chinese cohort of fetuses with congenital heart defects: a single center study

Background and objectivesCongenital heart defect (CHD) is one of the most common birth defects. The aim of this cohort study was to evaluate the prevalence of chromosomal abnormalities and the clinical utility of chromosomal microarray analysis (CMA) in fetuses with different types of CHD, aiming to assist genetic counseling and clinical decision-making.MethodsIn this study, 642 fetuses with CHD were enrolled from a single center over a six-year period (2017–2022). Both conventional karyotyping and CMA were performed simultaneously on these fetuses.ResultsThe diagnostic yield of CMA in fetuses with CHD in our study was 15.3% (98/642). Our findings revealed a significant increase in the diagnostic yield of CMA compared to karyotyping in fetuses with CHD. Among CHD subgroups, the diagnostic yields were high in complex CHD (34.9%), conotruncal defects (28.6%), right ventricular outflow tract obstructive defects (RVOTO) (25.9%), atrioventricular septal defects (AVSD) (25.0%) and left ventricular outflow tract obstructive defects (LVOTO) (24.1%), while those in other CHD (10.6%) and septal defects (10.9%) were relatively low. The overall detection rate of clinically significant chromosomal abnormalities was significantly higher in the non-isolated CHD group compared to the isolated CHD group (33.1% vs. 9.9%, P < 0.0001). Interestingly, numerical chromosomal abnormalities were more likely to occur in the non-isolated CHD group than in the isolated CHD group (20.3% vs. 2.0%, P < 0.0001). The rate of termination of pregnancy (TOP)/Still birth in the non-isolated CHD group was significantly higher than that in the isolated CHD group (40.5% vs. 20.6%, P < 0.0001). Compared to the isolated CHD group, the detection rate of clinically significant chromosomal abnormalities was significantly higher in the group of CHD with soft markers (35.6% vs. 9.9%, P < 0.0001) and in the group of CHD with additional structural anomalies (36.1% vs. 9.9%, P < 0.0001).ConclusionsCMA is a reliable and high-resolution technique that should be recommended as the front-line test for prenatal diagnosis of fetuses with CHD. The prevalence of chromosomal abnormalities varies greatly among different subgroups of CHD, and special attention should be given to prenatal non-isolated cases of CHD, especially those accompanied by additional structural anomalies or soft markers.

Chromosomal analysis in pregnant women of advanced maternal age: indications for prenatal diagnosis.

The demographic of women of advanced maternal age (AMA), defined as those over 35 years, is expanding in response to the liberalization of China's three-child policy. A significant proportion of these women are electing to undergo noninvasive prenatal testing (NIPT). Nonetheless, next-generation sequencing (NGS) is the recommended method for prenatal screening among women of AMA in the world. Consequently, the decision between opting for NIPT or NGS has emerged as topic of considerable debate and interest within the medical community. The objective was to explore which prenatal screening and diagnosis is suitable for women of AMA with different comorbidities. In this retrospective study, 326 pregnant women with AMA were divided into 9 groups to investigate clinically significant copy number variation (CNV) in different amniocentesis indications by amniocentesis and NGS. Clinically significant chromosomal abnormalities were identified in 84 cases (25.8%). Among the 119 detected segmental imbalances, 16 cases (13.4%) exhibited pathogenic or likely pathogenic microdeletions or micro-duplications. The incidence of pathogenic or likely pathogenic CNVs was significantly higher in the AMA with soft ultrasound markers group compared to the general AMA group (11.5% vs. 1.1%; P=0.016). Additionally, the incidence of pathogenic or likely pathogenic CNVs was significantly higher in the AMA with NIPT group compared to the general AMA group (48.7% vs. 1.1%; P<0.001). The incorporation of soft ultrasound markers and NIPT significantly enhanced the detection rate of clinically significant CNVs in women of AMA by 10.4% and 47.6%, respectively. Furthermore, the detection rate of clinically significant CNVs increased by 37% in women of AMA who underwent NIPT, when soft ultrasound markers were present. The positive predictive value of NIPT in detecting sex chromosome aneuploidy notably improved from 57.9% to 80% with the inclusion of soft ultrasound markers. Therefore, the combination of NIPT and soft ultrasound markers in women of AMA should be strongly considered and recommended for prenatal diagnosis.

Copy number variation sequencing for the products of conception: What is the optimal testing strategy

BackgroundCopy number variation sequencing (CNV-seq) is crucial in prenatal diagnosis, but its limitations in detecting polyploidy, maternal cell contamination (MCC), and uniparental disomy (UPD) restrict its application in the analysis of products of conception (POCs). This study aimed to investigate an optimal genetic testing strategy for POCs in the era of CNV-seq. MethodsCNV-seq and quantitative fluorescent polymerase chain reaction (QF-PCR) were performed in all 4,211 spontaneous miscarriage cases. Different testing strategies were compared and the optimal testing strategies were proposed. ResultsOf the 4,211 cases, 2561 (60.82%) exhibited clinically significant chromosomal abnormalities. CNV-seq alone, without QF-PCR, might misdiagnose 311 (7.39%) cases, including 278 polyploidy, 13 UPD, and 20 MCC. In 20 MCC cases identified by QF-PCR, CNV-seq successfully pinpointed the cause of miscarriage in 13 cases. Furthermore, in cases where QF-PCR suggested polyploidy, CNV-seq improved the diagnostic accuracy in 54 (1.28%) hypo/hypertriploidy cases. After comparing four different strategies, the sequential approach (initiating with CNV-seq followed by QF-PCR if necessary) emerged as advantageous, reducing approximately 70% of the cost associated with QF-PCR while maintaining result accuracy. ConclusionsWe propose an initial CNV-seq followed by QF-PCR if needed—an efficient and cost-effective strategy for the genetic analysis of POCs.

Experience of copy number variation sequencing applied in spontaneous abortion

PurposeWe evaluated the value of copy number variation sequencing (CNV-seq) and quantitative fluorescence (QF)-PCR for analyzing chromosomal abnormalities (CA) in spontaneous abortion specimens.MethodsA total of 650 products of conception (POCs) were collected from spontaneous abortion between April 2018 and May 2020. CNV-seq and QF-PCR were performed to determine the characteristics and frequencies of copy number variants (CNVs) with clinical significance. The clinical features of the patients were recorded.ResultsClinically significant chromosomal abnormalities were identified in 355 (54.6%) POCs, of which 217 (33.4%) were autosomal trisomies, 42(6.5%) were chromosomal monosomies and 40 (6.2%) were pathogenic CNVs (pCNVs). Chromosomal trisomy occurs mainly on chromosomes 15, 16, 18, 21and 22. Monosomy X was not associated with the maternal or gestational age. The frequency of chromosomal abnormalities in miscarriages from women with a normal live birth history was 55.3%; it was 54.4% from women without a normal live birth history (P > 0.05). There were no significant differences among women without, with 1, and with ≥ 2 previous miscarriages regarding the rate of chromosomal abnormalities (P > 0.05); CNVs were less frequently detected in women with advanced maternal age than in women aged ≤ 29 and 30–34 years (P < 0.05).ConclusionChromosomal abnormalities are the most common cause of pregnancy loss, and maternal and gestational ages are strongly associated with fetal autosomal trisomy aberrations. Embryo chromosomal examination is recommended regardless of the gestational age, modes of conception or previous abortion status.

MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing.

Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.

Comparison of Chromosomal Microarray Analysis and Noninvasive Prenatal Testing in Pregnant Women with Fetal Ultrasonic Soft Markers.

This study aimed to assess the utility of chromosomal microarray analysis (CMA) and noninvasive prenatal testing (NIPT) in detecting clinically significant chromosomal abnormalities among fetuses presenting ultrasonic soft markers (USMs). A retrospective observational study, spanning from January 1, 2019, to September 30, 2022, enrolled 539 singleton pregnant women with fetal USMs at our center. Of these, 418 cases (77.6%) underwent NIPT, while 121 cases (22.4%) opted for invasive prenatal diagnosis post-appropriate genetic counseling. Cases with high-risk NIPT results proceeded to invasive prenatal diagnosis, where conventional karyotyping and CMA were concurrently performed. Further stratification was done based on the number of USMs, classifying cases into single-USM and multiple-USM groups. Of the 24 cases (4.5%) exhibiting abnormal findings, 17 presented numerical chromosomal abnormalities, 2 featured clinically significant copy number variations (CNVs), 3 showed variants of unknown significance (VOUS), 1 displayed LOH, and 1 exhibited chromosome nine inversion. Notably, 18 cases (75%) theoretically detectable by karyotyping (eg, sizes above 10Mb) and 16 cases (66.7%) detectable by NIPT for five common aneuploidies were identified. Six submicroscopic findings (25%) were exclusively detectable by CMA. The predominant clinically relevant aberrations were observed in the thickened nuchal-translucency (TNT) group (9/35, 25.7%), followed by the multiple soft markers group (3/32, 9.3%). In the NIPT group, the false positive rate was 1.22%, and the false negative rate was 0%. The prevalence of chromosome aneuploidy exceeded that of submicroscopic chromosomal imbalance in pregnant women with fetal USMs. NIPT demonstrated efficacy, particularly for soft markers like echogenic intracardiac focus. However, for those with TNT and multiple soft markers, invasive prenatal diagnosis, including CMA testing, is recommended as the primary investigative approach.

Defining the scope of extended NIPS in Western China: evidence from a large cohort of fetuses with normal ultrasound scans

BackgroundStandard noninvasive prenatal screening(NIPS) is an accurate and reliable method to screen for common chromosome aneuploidies, such as trisomy 21, 18 and 13. Extended NIPS has been used in clinic for not only aneuploidies but also copy number variants(CNVs). Here we aim to define the range of chromosomal abnormalities that should be able to identify by NIPS in order to be an efficient extended screening test for chromosomal abnormalities.MethodsA prospective study was conducted, involving pregnant women without fetal sonographic structural abnormalities who underwent amniocentesis. Prenatal samples were analyzed using copy number variation sequencing(CNV-seq) to identify fetal chromosomal abnormalities.ResultsOf 28,469 pregnancies included 1,022 (3.59%) were identified with clinically significant fetal chromosome abnormalities, including 587 aneuploidies (2.06%) and 435 (1.53%) pathogenic (P) / likely pathogenic (LP) CNVs. P/LP CNVs were found in all chromosomes, but the distribution was not uniform. Among them, P/LP CNVs in chromosomes 16, 22, and X exhibited the highest frequencies. In addition, P/LP CNVs were most common on distal ends of the chromosomes and in low copy repeat regions. Recurrent microdeletion/microduplication syndromes (MMS) accounted for 40.69% of total P/LP CNVs. The size of most P/LP CNVs (77.47%) was < 3 Mb.ConclusionsIn addition to aneuploidies, the scope of extended NIPS should include the currently known P/LP CNVs, especially the regions with recurrent MMS loci, distal ends of the chromosomes, and low copy repeat regions. To be effective detection should include CNVs of < 3 Mb. Meanwhile, sufficient preclinical validation is still needed to ensure the clinical effect of extended NIPS.

The Effect of Resolution Level and Targeted Design in the Diagnostic Performance of Prenatal Chromosomal Microarray Analysis

Introduction: This study was performed to assess the optimal resolution for prenatal testing by array comparative genomic hybridization (aCGH), aiming to balance between maximum diagnostic yield and minimal detection of variants of uncertain significance (VOUS). Methods: This was a prospective study using data of 2,336 fetuses that underwent invasive prenatal diagnosis, and the samples were analyzed by aCGH. In total, six different aCGH platforms were studied; four different resolutions (0.18 Mb, 0.5 Mb, 1 Mb, and 2 Mb) and two platform designs (whole-genome [WG] and targeted). The results of these designs were compared based on their diagnostic yield and VOUS rate. The performance of the different designs was further analyzed according to indication for invasive testing. Results: The diagnostic yield of copy number variants increased with increasing level of analysis. The detection rates of clinically significant chromosomal abnormalities were almost the same across our targeted array designs; 7.2% with 0.18 Mb backbone/0.05 Mb versus 7.1% with 0.5 Mb backbone/0.05 Mb (p >0.05). However, a significant difference in the rate of VOUS was observed; 9.4% with 0.18 Mb backbone/0.05 Mb versus 6% with 0.5 Mb backbone/0.05 Mb (p <0.001). After analyzing the results across different indications for testing, we found that the application of non-targeted platform designs and lower levels of resolution analysis (such as 1 Mb WG or 0.5 MbL/1 MbG WG) would offer similar diagnostic yield in most cases with major congenital anomalies, with lower VOUS rates. However, the sample size for many indication groups was too small to extract robust associations. Conclusion: It appears that the targeted array platform with 0.5 Mb backbone resolution and 0.05 Mb on targeted gene-rich regions is optimal for routine chromosomal microarray analysis use in prenatal diagnosis. It may be beneficial to individualize the minimum resolution in specific referral indications as the indications for invasive prenatal testing may be quite heterogeneous.

Prenatal diagnosis of ultrasound soft markers in a single medical center of mainland China

BackgroundThere are a few studies on the chromosomal aberration of Ultrasound soft markers (USMs). The aim of this study was to determine the detection rate of clinically significant chromosomal abnormalities (CSCA) in fetuses with different USMs. MethodsThis study included fetuses with USMs who underwent invasive prenatal diagnosis for karyotype and/or chromosomal microarray (CMA) by categorizing into two groups: a single USM (SUSM) and multiple USMs (MUSMs).ResultsOf the 358 cases with USMs, CSCA occurred in 3.09% (8/259) and 8.08% (8/99) of the SUSM and MUSM groups, respectively (P < 0.05). Of 16 cases identified with CSCA, theoretically 68.75% (11/16) could be detected by karyotype, while 31.25% (5/16) could be recognized only by CMA. Among CSCA cases, the most frequent USM was an absent or hypoplastic nasal bone (62.5%, 10/16). In cases with negative karyotypes and/or CMA, follow-up results were available in 307 cases, including 292 term deliveries, 6 preterm deliveries, 8 terminations of pregnancy due to USMs, and 1 still birth.ConclusionMUSMs increased the risk of chromosomal abnormalities. An absent or hypoplastic nasal bone was the most clinically significant marker either alone or in combination with other USMs. Most of SUSM had a good prognosis.

Identification of a Rare Variant of c.1777G>A (p.G593S) in the COL1A1 Gene as the Etiology of Recurrent Osteogenesis Imperfecta by Whole-Exome Sequencing.

BackgroundOsteogenesis imperfecta (OI) is a rare heterogeneous disorder typically featured by fragile bones and susceptibility to fracture. The aim of the present study was to explore the genetic etiology of familial recurrent OI and the genotype–phenotype correlation.MethodsKaryotyping, chromosomal microarray analysis, and whole-exome sequencing (WES) were performed to determine the genetic etiology of OI in the enrolled family. Western blotting analysis was carried out using the fetal skin tissue for type I collagen production analysis.ResultsAt the first pregnancy, a c.1777G>A mutation in the COL1A1 gene was detected in the fetus who exhibited skeletal dysplasia. In this second pregnancy, severe fetal skeletal dysplasia was also presented without significant chromosomal abnormality detected by karyotype and chromosomal microarray analysis in the fetus. Further WES results demonstrated a de novo missense mutation of c.1777G>A (p.G593S) in the fetus, which was classified as a pathogenic variant according to the ACMG guidelines. The recurrent mutation in the two fetuses hinted at the possible existence of gonadal mosaicism in the parents, while no mutation in the COL1A1 gene was identified in the DNA from the father's sperm. In addition, Western blot results demonstrated no reduced type I procollagen production in the affected fetus compared with the age-matched controls.ConclusionsTo the best of our knowledge, this is the first study that identified a rare variant of c.1777G>A in the COL1A1 gene that led to recurrent OI in the Chinese population. Additionally, we believe that this rare variant of c.1777G>A in the COL1A1 gene will lead to OI type II. The results of the present study further verify the application value of WES in identifying fetuses with ultrasound anomalies.

Pericentric inversion of chromosome 6 and male fertility problems.

As a significant chromosomal structural abnormality, chromosomal inversion is closely related to male infertility. For inversion carriers, the interchromosomal effect explains male infertility, but its specific mechanism remains unclear. Additionally, inversion carriers with different chromosomes have different clinical manifestations. Therefore, genetic counseling is difficult in clinical practice. Herein, four male carriers of pericentric inversion in chromosome 6 have been described. Two patients showed asthenospermia, one showed azoospermia, and the wife of the remaining patient had recurrent miscarriages. Through a literature search, the association between the breakpoint of pericentric inversion in chromosome 6 and male fertility problems are also discussed in this study. Overall, important genes related to asthenospermia in chromosome 6p21 were found, which may be related to the clinical phenotype. These results suggest that physicians should focus on the breakpoints of inversion in genetic counseling.

Significance of Low Maternal Serum Β-hCG Levels in the Assessment of the Risk of Atypical Chromosomal Abnormalities

Introduction: The introduction of prenatal cell-free DNA as a screening test has surpassed traditional combined first-trimester screening (cFTS) in the detection of common trisomies. However, its current limitation in detecting only common trisomies is affecting the diagnostic yield for other clinically significant chromosomal abnormalities. Methods: In efforts to optimize the detection of fetuses with genetic abnormalities, we have analyzed the relationship between the cFTS risk score and biomarkers with atypical chromosomal abnormalities. Furthermore, we have evaluated the impact of prenatal cell-free DNA screening on the detection of chromosomal abnormalities in our population. For these purposes, we performed a retrospective study of 877 singleton pregnancies who underwent chromosomal microarray analysis (CMA) between 2013 and 2020 and for whom cFTS data were available. Results: The results demonstrated that low levels of free beta-human chorionic gonadotropin (β-hCG) (≤0.37 multiples of the median) and increased fetal nuchal translucency (NT) (≥3.5 mm) were statistically associated with the presence of atypical chromosomal abnormalities. In fact, the risk of pathogenic CMA results increased from 6 to 10% when fetal NT was increased and from 6 to 20% when a low serum β-hCG level was detected in the high-risk cFTS group. Moreover, our results showed that altered serum levels of β-hCG can have a substantial impact on the early detection of clinically relevant copy number variants. Discussion/Conclusion: Traditional cFTS can potentially identify a substantial proportion of atypical chromosomal aberrations, and women with increased NT or low maternal serum β-hCG levels are at increased risk of having pathogenic CMA results. Our results may help clinicians and women decide whether invasive testing or prenatal cell-free DNA screening testing is more appropriate for each situation.

Expanding the application of non-invasive prenatal testing in the detection of foetal chromosomal copy number variations

PurposeThe aim of this study was to assess the detection efficiency and clinical application value of non-invasive prenatal testing (NIPT) for foetal copy number variants (CNVs) in clinical samples from 39,002 prospective cases.MethodsA total of 39,002 pregnant women who received NIPT by next-generation sequencing (NGS) with a sequencing depth of 6 M reads in our centre from January 2018 to April 2020 were enrolled. Chromosomal microarray analysis (CMA) was further used to diagnose suspected chromosomal aneuploidies and chromosomal microdeletion/microduplication for consistency assessment.ResultsA total of 473 pregnancies (1.213%) were positive for clinically significant foetal chromosome abnormalities by NIPT. This group comprised 99 trisomy 21 (T21, 0.254%), 30 trisomy 18 (T18, 0.077%), 25 trisomy 13 (T13, 0.064%), 155 sex chromosome aneuploidy (SCA, 0.398%), 69 rare trisomy (0.177%), and 95 microdeletion/microduplication syndrome (MMS, 0.244%) cases. Based on follow-up tests, the positive predictive values (PPVs) for the T21, T18, T13, SCA, rare trisomy, and MMS cases were calculated to be 88.89%, 53.33%, 20.00%, 40.22%, 4.88%, and 49.02%, respectively. In addition, the PPVs of CNVs of < 5 Mb, 5–10 Mb, and > 10 Mb were 54.55%, 38.46%, and 40.00%, respectively. Among the 95 cases with suspected CNVs, 25 were diagnosed as true positive and 26 cases as false positive; follow-up prenatal diagnosis by CMA was not performed for 44 cases. Moreover, among the 25 true positive cases, 10 were pathogenic, 3 were likely pathogenic, and 12 were of uncertain significance.ConclusionNIPT is not only suitable for screening T21, T18, T13, and SCA but also has potential significance for CNV detection. As combined with ultrasound, extended NIPT is effective for screening MMS. However, NIPT should not be recommended for whole-chromosome aneuploidy screening.

Analysis of the effect of expanded non-invasive prenatal testing in prenatal screening population during pregnancy

To explore the clinical effect of expanded non-invasive prenatal testing (NIPT-plus) for prenatal screening. The screening result, prenatal diagnosis and pregnancy outcome of 3700 pregnant women who volunteered NIPT-plus screening at our center from September 2018 to December 2019 were reviewed. Among the 3700 pregnant women, 74(2.0%) were scored positive for clinically significant fetal chromosomal abnormalities and underwent NIPT-plus screening. Sixty three women with a high risk underwent invasive prenatal diagnosis, among whom 19 were diagnosed, which yielded a positive predictive value (PPVs) of 30.2% (19/63). Statistical analysis showed that NIPT-plus has higher PPVs for common aneuploidies and low-to-medium PPVs for sex chromosome aneuploidies and microdeletion/microduplication syndromes. As a screening technique, NIPT-plus has broader applications compared with conventional techniques, and has reference value for clinicians and pregnant women during pregnancy.

Reply

We thank Drs Jing and Li for their thoughtful comments on our study1 and their reflections on prenatal screening for 22q11.2 deletion. They raise important points on which we would like to comment further and provide clarification. Drs Jing and Li suggest that ultrasound is more sensitive than cell-free DNA (cfDNA) testing in screening for 22q11.2 deletion, citing a study by Schindewolf et al.2. However, that study was intended to document the ultrasound findings seen most frequently in pregnancies with a 22q11.2 deletion in the second and third trimesters, not to determine the sensitivity of ultrasound for fetal 22q11.2 deletion. To our knowledge, this has not been evaluated in any study. Nonetheless, we agree that prenatal ultrasound findings have been well described by Schindewolf et al. and others and suggest that cfDNA screening in the first trimester can complement, not replace, second-trimester ultrasound as a screening tool for 22q11.2 deletion. As Drs Jing and Li note, the collective prevalence of other fetal microduplications and microdeletions is not insignificant, even when ultrasound is normal, and there is broad consensus that chorionic villus sampling or amniocentesis with microarray analysis should be offered whenever evaluation of a pregnancy for submicroscopic genomic alterations is desired. Similar to Drs Jing and Li, we would also welcome a method for accurate, genome-wide non-invasive prenatal screening with demonstrated clinical utility for detecting chromosomal imbalances at a resolution comparable to that of microarray, but currently available technologies fall short of this goal. In a prospective head-to-head comparison of genome-wide cfDNA testing and chromosomal microarray testing in 198 pregnancies, Guseh and colleagues showed that expanded non-invasive genome-wide screening has a lower detection rate for clinically significant chromosomal abnormalities when compared with that of chromosomal microarray analysis, and that pathogenic subchromosomal imbalances (< 7 Mb) contribute substantially to the missed abnormalities3. A clinical trial from The Eunice Kennedy Shriver National Institute of Child Health and Human Development showed that > 50% of (likely) pathogenic subchromosomal imbalances identified by chromosomal microarray analysis in anatomically normal fetuses are < 5 Mb in size4. We would also like to clarify a minor point. The cfDNA test evaluated in our study is described as ‘targeted’ in order to differentiate it from ‘genome-wide’ cfDNA testing because of the different technological design of the two approaches. It is not a standalone test for 22q11.2 deletion, as might have been misinterpreted from the phrasing. The Harmony® test screens for trisomy 21, trisomy 18 and trisomy 13, with the option of screening for sex chromosome aneuploidy and/or 22q11.2 deletion from the same blood collection. In many respects, we agree with Drs Jing and Li and support an approach to prenatal screening in which the benefits of cfDNA testing, ultrasound and diagnostic testing are incorporated to guide pregnancy management and improve outcome in 22q11.2 deletion syndrome and other prenatally diagnosable conditions.

English

BACKGROUND Infertility is the inability to become a parent of a child even after one year of intercourse involving male and female partner without any contraceptives. There are many causes for infertility, Y chromosome microdeletion is one among that. Partial or complete deletion of the proximal Yq region, which contains azoospermic factor (AZF) locus, leads to infertility. Along with genetic and biochemical factors the ethno-geographical reasons also play an important role in infertility. The present study was done to identify the association of genetic and hormonal factors in the development of infertility in azoospermic males of southern Kerala. METHODS Retrospectively screened the medical records of 2100 infertile males of the Department of Reproductive Medicine of Sree Avittom Tirunal Hospital, Government Medical College, Thiruvananthapuram for a period from January 2017 to December 2019. Stringent inclusion criterias were taken to select patients for the molecular study and finally 46 were selected. Structural and numerical chromosome abnormalities were detected using karyotyping and microdeletion was identified using polymerase chain reaction. Electro-chemiluminescence immunoassay method was used for the quantification of reproductive hormones. Demographic data of selected patients were collected from the medical records. RESULTS The cytogenetic results showed that among the selected patients, 10.86 % had Klinefelter syndrome and one person had De la Chapelle syndrome. Partial microdeletion in AZFa, b or c regions have been observed in 13.63 % of the patients. The hormonal analysis showed significant change in concentration of reproductive hormones irrespective of genetic defects. Demographic data showed that the majority of participated patients are unskilled/skilled laborers, economically poor and are from urban areas. CONCLUSIONS The study concludes that among the selected patients, 24.49 % have clinically significant chromosomal abnormalities like Klinefelter syndrome, De la Chappelle syndrome and partial microdeletion on the AZF region. Irrespective of genetic defects, significant changes in the concentration of reproductive hormones are also observed. KEYWORDS Azoospermia, Infertility, Karyotyping, Y Chromosome Microdeletion

Utility of noninvasive genome-wide screening: a prospective cohort of obstetric patients undergoing diagnostic testing

PurposeCopy-number variant (CNV) assessment is recommended for patients undergoing prenatal diagnostic testing. Noninvasive screening tests have not been extensively validated for CNV detection. The objective of this study was to compare the ability of genome-wide noninvasive prenatal screening (NIPS) to chromosomal microarray to detect clinically significant findings. MethodsWe prospectively enrolled 198 subjects at the time of consent for diagnostic prenatal testing. Genome-wide NIPS results were compared with diagnostic testing results to assess NIPS test performance (n = 160, 38 subjects without microarray results excluded). Cohen’s kappa statistic was used to assess test agreement. ResultsGenome-wide NIPS did not detect clinically significant chromosomal abnormalities at the same rate as diagnostic testing, κ = 0.75 (95% confidence interval [CI], 0.62–0.87). When excluding CNVs <7 Mb and findings outside the limits of genome-wide NIPS, test agreement improved, κ = 0.88 (0.79–0.97) driven by agreement for common aneuploidies (κ = 1.0). However, among patients with an abnormal fetal survey, agreement was only fair, κ = 0.38 (0.08–0.67). ConclusionWhile NIPS is an excellent screening test for common aneuploidies, genome-wide NIPS misses clinically significant findings detected on routine diagnostic testing. False positive and false negative cases highlight the importance of pretest counseling regarding NIPS limitations, especially in the setting of fetal anomalies.

Copy number variation sequencing combined with quantitative fluorescence polymerase chain reaction in clinical application of pregnancy loss.

In this study, we evaluated the feasibility of the combining CNV-seq and quantitative fluorescence polymerase chain reaction (QF-PCR) for miscarriage analysis in clinical practice. Over a 35-month period, a total of 389 fetal specimens including 356 chorionic villi and 33 fetal muscle tissues were analyzed by CNV-seq and QF-PCR. Relationships between the risk factors (e.g., advanced maternal age, abnormal pregnancy history, and gestational age) and incidence of these chromosomal abnormalities were further analyzed by subgroup. Clinically significant chromosomal abnormalities were identified in 58.95% cases. Aneuploidy was the most common abnormality (46.84%), followed by polyploidy (8.16%) and structural chromosome anomalies (3.95%). In sub-group analysis, significant differences were found in the total frequency of chromosomal abnormalities between the early abortion and the late abortion group, as well as in the distribution of chromosomal abnormalities between the advanced and the younger maternal age group. Meanwhile, the results of the logistic regression analysis identified a trend suggesting that the percentage of fetal chromosomal abnormalities is significantly higher in advanced maternal age, lesser gestational age, and lesser number of prior miscarriages. Our study suggests that CNV-seq and QF-PCR are efficient and reliable technologies in the fetal chromosome analysis of miscarriages and could be used as a routine selection method for the genetic analysis of spontaneous abortion.

Prenatal and perinatal outcomes of twin pregnancy discordant for one fetus with nuchal translucency above the 95th percentile

Objective To compare prenatal and perinatal outcomes of twin pregnancies in which one twin the nuchal translucency (NT) was above the 95th percentile in dichorionic twins (DCT) and monochorionic twins (MCT). Method In this retrospective study, 93 twin pregnancies (186 fetuses) in which one twin the NT was above the 95th percentile and the co-twin had normal NT were analyzed. Results of of G-banding and Chromosomal microarray (CMA), ultrasound findings and pregnancy outcomes were reviewed. Results Totally, 57 pregnancies (114 fetuses) were DCT and 36 pregnancies (72 fetuses) were MCT. Karyotyping and CMA results shown that clinically significant chromosomal abnormalities were found in 16 fetuses, including 13 aneuploidies, 2 chromosomal mosaic and 1 pathological Copy number variations (CNVs) (14 were DCT and 2 were MCT). Overall, the incidence of fetal chromosomal abnormalities was 12.3% (14/114) in DCT and 2.8%(2/72) in MCT (χ2 = 3.932, p = 0.047). Among the cases with normal prenatal diagnosis result, structural abnormalities were found in four fetuses (4.0%, 4/100) in DCT and two fetuses (2.9%, 2/70) in MCT (p > 0.999). There were one intrauterine fetal demises (IUFD) and two miscarry in DCT. One IUFD, three subsequently developed Twin-to-Twin Transfusion Syndrome (TTTS) and four developed selective intrauterine growth restriction (sIUGR) in MCT. Totally, the overall fetal survival rate was 85.1% (97/114) in DCT and 80.6% (58/72) in MCT (χ2 = 0.653, p = 0.419). Conclusion Compared to MCT, the incidence of chromosomal abnormalities in DCT discordant for one fetus with NT above the 95th percentile was higher. The risk of structural abnormalities and the rate of fetal survival for both MCT and DCT was similar.

Systematic analysis of copy-number variations associated with early pregnancy loss.

Embryonic numerical and structural chromosomal abnormalities are the most common cause of early pregnancy loss. However, the role of submicroscopic copy-number variations (CNVs) in early pregnancy loss is unclear, and little is known about the critical regions and candidate genes for miscarriage, because of the large size of structural chromosomal abnormalities. The aim of this study was to identify potential miscarriage-associated submicroscopic CNVs and critical regions of large CNVs as well as candidate genes for miscarriage. Over a 5-year period, 5180 fresh miscarriage specimens were investigated using quantitative fluorescent polymerase chain reaction/CNV sequencing or chromosomal microarray analysis. Statistically significant submicroscopic CNVs were identified by comparing the frequency of recurrent submicroscopic CNVs between cases and a published control cohort. Furthermore, genes within critical regions of miscarriage-associated CNVs were prioritized by integrating the Residual Variation Intolerance Score and the human gene expression dataset for identification of potential miscarriage candidate genes. Results without significant maternal-cell contamination were obtained in 5003 of the 5180 (96.6%) cases. Clinically significant chromosomal abnormalities were identified in 59.1% (2955/5003) of these cases. Three recurrent submicroscopic CNVs (microdeletions in 22q11.21, 2q37.3 and 9p24.3p24.2) were significantly more frequent in miscarriage cases, and were considered to be associated with miscarriage. Moreover, 44 critical regions of large CNVs were observed, including 14 deletions and 30 duplications. There were 309 genes identified as potential miscarriage candidate genes through gene-prioritization analysis. We identified potential miscarriage candidate CNVs and genes. These data demonstrate the importance of CNVs in the etiology of miscarriage and highlight the importance of ongoing analysis of CNVs in the study of miscarriage. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.