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Next-generation sequencing for copy number variants is often used as a follow-up investigation of unusual fetal ultrasound results and is capable of detecting copy number variations with a resolution of ∼0.1 Mb. In a prenatal setting, observation and subsequent management of pregnancies with a fetal variant of uncertain significance remains problematic for counseling. This study aimed to follow the decision-making processes in pregnancies with a fetal variant of uncertain significance and prospectively assess copy number variation interpretations and implications under the newer 2020 American College of Medical Genetics and Genomics guidelines. In a single prenatal unit, prospective chromosome testing using copy number variation sequencing for 8030 fetuses with unexpected noninvasive findings identified 139 pregnancies with a copy number variation classified as a variant of uncertain significance according to the 2015 American College of Medical Genetics and Genomics guidelines current at the time. Parent-of-origin testing was subsequently performed to determine if the copy number variation was inherited or de novo. All couples were offered specialized genetic counseling to assist in pregnancy management decisions. For the continued pregnancies that reached term, newborns were clinically assessed for evidence of any disease at 0 to 10 months and/or at 2 to 4 years of age. Of the 139 variants of uncertain significance found, most (78%) were inherited with no evidence of disease in the carrier parent. On the basis of primary ultrasound findings combined with results from noninvasive prenatal screening tests, most inherited variant of uncertain significance pregnancies were continued, whereas most pregnancies involving de novo variants of uncertain significance were terminated. From clinical follow-up of the 113 live births, only 5 showed any evidence of a phenotype that was not apparently related to the original variant of uncertain significance. Prospective reanalysis of the 139 variants of uncertain significance using recent 2020 American College of Medical Genetics and Genomics guidelines changed the status of 24 variants of uncertain significance, with 15 reclassified as benign and 9 as pathogenic. However, the 5 children born with an inherited variant of uncertain significance reclassified as pathogenic showed no evidence of a disease phenotype on clinical follow-up. The severity of fetal ultrasound findings combined with results from parent-of-origin testing were the key drivers in pregnancy management decisions for patients. According to birth outcomes from continued pregnancies, most variants of uncertain significance proved to be apparently benign in nature and potentially of low risk of adverse disease outcome. There was a discordance rate of 17% for variant of uncertain significance scoring between the 2015 and 2020 American College of Medical Genetics and Genomics guidelines for defining a variant of uncertain significance, suggesting that difficulties remain for predicting true pathogenicity. Nonetheless, with increasing knowledge of population copy number variation polymorphisms, and a more complete assessment for alternative genetic causes, patients having prenatal assessments should feel less anxious when a fetal variant of uncertain significance is identified. [ABSTRACT FROM AUTHOR]

Background Non-invasive methods to assess the foetal genome during pregnancy will provide new opportunities to offer pregnant women a more comprehensive genetic diagnosis of their established foetus. The aim of this study was to determine the presence and frequency of foetal cells in transcervical cell (TCC) mucus samples from pregnant women and determine their suitability for early prenatal diagnosis. Methods Syncytiotrophoblasts in aspirated TCC mucus samples were identified by immunostaining with the foetal-specific antibody NDOG1. Genetic analysis of foetal cells was performed by laser capture microdissection and quantitative fluorescent PCR (QF-PCR). Results In 116 of 207 (56%) TCC samples, abundant syncytiotrophoblasts were retrieved. However, when TCC samples were stratified for the presence of chorionic villous fragments, syncytiotrophoblasts were identified in 85 of 109 (78%) samples. Significant numbers of syncytiotrophoblasts were found in TCC samples collected between 6 and 9 weeks of gestation (mean 741, range 25–2884). QF-PCR analysis of NDOG1 positive syncytiotrophoblasts and matching maternal DNA confirmed their foetal origin and correct foetal cell sexing was achieved in 97% of TCC samples. The one discordant sex diagnosis was associated with a dizygotic dichorionic twin pregnancy resulting from the implantation of a female T21 embryo and a normal male embryo, where the female T21 foetus had succumbed at 6 weeks of gestation and was vanishing. Conclusions Syncytiotrophoblasts can be successfully isolated from TCC samples and represent a suitable source of cells for genetic analysis of the established foetus in early pregnancy. The study highlights a vanishing twin as a potential cause for discordant non-invasive prenatal test results. [ABSTRACT FROM AUTHOR]

This study investigated a pregnancy where the fetus was diagnosed with monosomy 18p by invasive amniocentesis and karyotyping. Additional noninvasive prenatal diagnosis, which detects fetal chromosome abnormalities in the circulating cell-free plasma DNA originating from the placenta revealed a related 18p monosomy/18q trisomy, suggesting confined placental mosaicism. Based on recent observations of chromosomal instability in the early preimplantation embryo, this study speculates on the possible embryonic origin(s) of these related but discordant chromosome 18 aneuploidies in the placental and fetal tissues. The findings highlight the potential fo r both false-positive and -negative noninvasive prenatal diagnosis results in pregnancies where there is either confined placental mosaicism or placental mosaicism. [ABSTRACT FROM AUTHOR]

Background: Next-generation sequencing is emerging as a viable alternative to chromosome microarray analysis for the diagnosis of chromosome disease syndromes. One next-generation sequencing methodology, copy number variation sequencing, has been shown to deliver high reliability, accuracy, and reproducibility for detection of fetal copy number variations in prenatal samples. However, its clinical utility as a first-tier diagnostic method has yet to be demonstrated in a large cohort of pregnant women referred for fetal chromosome testing.Objective: We sought to evaluate copy number variation sequencing as a first-tier diagnostic method for detection of fetal chromosome anomalies in a general population of pregnant women with high-risk prenatal indications.Study Design: This was a prospective analysis of 3429 pregnant women referred for amniocentesis and fetal chromosome testing for different risk indications, including advanced maternal age, high-risk maternal serum screening, and positivity for an ultrasound soft marker. Amniocentesis was performed by standard procedures. Amniocyte DNA was analyzed by copy number variation sequencing with a chromosome resolution of 0.1 Mb. Fetal chromosome anomalies including whole chromosome aneuploidy and segmental imbalances were independently confirmed by gold standard cytogenetic and molecular methods and their pathogenicity determined following guidelines of the American College of Medical Genetics for sequence variants.Results: Clear interpretable copy number variation sequencing results were obtained for all 3429 amniocentesis samples. Copy number variation sequencing identified 3293 samples (96%) with a normal molecular karyotype and 136 samples (4%) with an altered molecular karyotype. A total of 146 fetal chromosome anomalies were detected, comprising 46 whole chromosome aneuploidies (pathogenic), 29 submicroscopic microdeletions/microduplications with known or suspected associations with chromosome disease syndromes (pathogenic), 22 other microdeletions/microduplications (likely pathogenic), and 49 variants of uncertain significance. Overall, the cumulative frequency of pathogenic/likely pathogenic and variants of uncertain significance chromosome anomalies in the patient cohort was 2.83% and 1.43%, respectively. In the 3 high-risk advanced maternal age, high-risk maternal serum screening, and ultrasound soft marker groups, the most common whole chromosome aneuploidy detected was trisomy 21, followed by sex chromosome aneuploidies, trisomy 18, and trisomy 13. Across all clinical indications, there was a similar incidence of submicroscopic copy number variations, with approximately equal proportions of pathogenic/likely pathogenic and variants of uncertain significance copy number variations. If karyotyping had been used as an alternate cytogenetics detection method, copy number variation sequencing would have returned a 1% higher yield of pathogenic or likely pathogenic copy number variations.Conclusion: In a large prospective clinical study, copy number variation sequencing delivered high reliability and accuracy for identifying clinically significant fetal anomalies in prenatal samples. Based on key performance criteria, copy number variation sequencing appears to be a well-suited methodology for first-tier diagnosis of pregnant women in the general population at risk of having a suspected fetal chromosome abnormality. [ABSTRACT FROM AUTHOR]

A correction to the article "A pregnancy with discordant fetal and placental chromosome 18 aneuploidies revealed by invasive and noninvasive prenatal diagnosis," published in a previous issue of the journal is presented.

Background Noninvasive prenatal testing (NIPT) by massively parallel sequencing (MPS) of the circulating cell free fetal (cff) DNA during the second trimester of pregnancy is now a frontline test for detecting common fetal chromosomal abnormalities. However, the availability of an earlier test result in the first trimester would enable better clinical management of high-risk pregnancies. The aim of the study was to determine the feasibility of early gestational NIPT. Methods Plasma DNA libraries were subjected to MPS and chromosomal read counts normalized to reference. Chromosomal aneuploidy was determined by z -scores (− 3 < z < 3, normal range). The cff DNA fraction in 96 male pregnancies was calculated by the relative proportion of Y chromosomal reads. Results NIPT results were obtained in the first (8–12 weeks) and second (15–18 weeks) trimester for 182 high-risk women. NIPT identified T21, T13 and 45,X in 3 pregnancies that were confirmed by karyotyping, but missed a T15 pregnancy that eventually miscarried. In the remaining 178 pregnancies, results for first and second trimester NIPT were normal. The median fetal fraction in the first trimester was 7.6 ± 4.18% and 15% of samples were identified with a cff fraction below 4%. Different trends of cff DNA fraction change were observed between the first and second trimester, with 59% of pregnancies showing an increase, 17% showing no change and 24% showing a decrease. Conclusions Although NIPT was highly reliable and accurate at an earlier gestational age, clinical implementation should proceed with caution due to a small, but significant, number of pregnancies associated with a low cff DNA fraction. [ABSTRACT FROM AUTHOR]

Objective: High rates of chromosomal mosaicism in human IVF embryos question the accuracy of preimplantation genetic diagnosis, and, with the majority of embryo transfers still resulting in no pregnancy, chromosomal mosaicism is likely to be a contributing factor to human IVF failure. The aim of this study was to investigate the origin and nature of chromosome 21 (Ch21) cell division errors in human IVF embryos. Design: Perform single cell Ch21 allelic profiling on human IVF embryos. Setting: Academic research environment. Patient(s): Women of advanced maternal age (>35 yrs) (n = 65) undergoing infertility treatment; and amniocytes/chorionic cells from trisomy 21 pregnancies (n = 28). Intervention(s): Cells were analyzed by single cell allelic profiling, Main Outcome Measure(s): The origin and nature of cell division errors. Result(s): The vast majority of Ch21 mosaic embryos (∼80%) originated from diploid conceptions. In contrast, all fetal trisomy 21 originated from aneuploid conceptions. Increasing maternal age was significantly associated with aneuploid conceptions, meiotic cell division error, and adverse pregnancy outcome (P&#60;.05). The mean daily FSH dose that produced embryos with normal Ch21 cell division was significantly lower than the mean daily FSH dose that produced embryos with mitotic Ch21 cell division errors (P&#60;.01) and embryos with meiotic cell division errors (P&#60;.05). Conclusion(s): Chromosomal mosaicism of Ch21 in human IVF embryos predominantly originate from diploid conceptions. Further understanding of chromosomal mosaicism with respect to IVF parameters, such as daily FSH dose, may eventually lead to improvements in IVF outcomes. [Copyright &y& Elsevier]

Objective: To apply long-read, third-generation sequencing as a part of a general workup strategy for performing structural rearrangement (PGT-SR) and monogenic disease (PGT-M) embryo testing.Design: Prospective study.Setting: In vitro fertilization unit.Patient(s): Couples presenting for PGT-SR (n = 15) and PGT-M (n = 2).Intervention(s): Blastocyst biopsy with molecular testing for translocation breakpoints or mutations (targets).Main Outcome Measure(s): Detailed, parental-phased, single-nucleotide polymorphism (SNP) profiles around targets for selection of informative polymorphic markers to simplify and facilitate clinical preimplantation genetic testing (PGT) designs that enable discrimination between carrier and noncarrier embryos.Result(s): High definition of chromosome breakpoints together with closely phased polymorphic markers was achieved for all 15 couples presenting for PGT-SR. Similarly, for the two couples presenting for PGT-M, tightly linked informative markers around the mutations were also simply identified. Three couples with translocations t(1;17)(q21;p13), t(3;13)(p25;q21.2), and t(12;13)(q23;q22) proceeded with PGT-SR, requesting preferential identification of noncarrier embryos for transfer. Following selection of a set of informative SNPs linked to breakpoints, we successfully performed PGT-SR tests, resulting in ongoing pregnancies with a noncarrier fetus for all couples. Similarly, with the use of tests based on informative SNPs linked to the parental mutations, one couple proceeded with PGT-M for maple syrup urine disease, resulting in an ongoing pregnancy with a disease-free fetus.Conclusion(s): For couples contemplating clinical PGT, variant haplophasing around the target reduces the workup process by enabling rapid selection of closely linked informative markers for patient-specific test design. [ABSTRACT FROM AUTHOR]

Objective: To develop and validate a new strategy to distinguish between balanced/euploid carrier and noncarrier embryos in preimplantation genetic diagnosis (PGD) cycles for reciprocal translocations and to successfully achieve a live birth after selective transfer of a noncarrier embryo.Design: Retrospective and prospective study.Setting: In vitro fertilization (IVF) units.Patient(s): Eleven patients undergoing mate pair sequencing for identification of translocation breakpoints, followed by clinical PGD cycles.Intervention(s): Embryo biopsy with 24-chromosome testing to determine carrier status of balanced/euploid embryos.Main Outcome Measure(s): Definition of translocation breakpoints and polymerase chain reaction (PCR) diagnostic primers, correct diagnosis of euploid embryos for carrier status, and a live birth with a normal karyotype after transfer of a noncarrier embryo.Result(s): In 9 of 11 patients (82%), translocation breakpoints were successfully identified. In four patients with a term PGD pregnancy established with a balanced/euploid embryo of unknown carrier status, the correct carrier status was retrospectively determined, matching with the cytogenetic karyotype of the resulting newborns. In a prospective PGD cycle undertaken by a patient with a 46,XY,t(7;14)(q22;q24.3) translocation, the four balanced/euploid embryos identified comprised three carriers and one noncarrier. Transfer of the noncarrier embryo resulted in birth of a healthy girl who was subsequently confirmed with a normal 46,XX karyotype.Conclusion(s): The combination of mate pair sequencing and PCR breakpoint analysis of balanced reciprocal translocation derivatives is a novel, reliable, and accurate strategy for distinguishing between carrier and noncarrier balanced/euploid embryos. The method has potential application in clinical PGD cycles for patients with reciprocal translocations or other structural rearrangements. [ABSTRACT FROM AUTHOR]

Background Tooth agenesis is a common developmental dental anomaly. The aim of the study was to identify the causal genetic mutation in a four-generation Chinese family affected with non-syndromic autosomal dominant tooth agenesis. Methods Genome-wide scanning was performed using the Illumina Linkage-12 array. Genotyping of short tandem repeat markers was used to finely map the causative locus. Haplotype analysis and Sanger sequencing was performed to precisely locate the position and nature of the gene defect. Results Clinical examination of the available 23 family members showed variable tooth agenesis in 10 subjects, ranging from oligodontia to mild hypodontia. Genome-wide scanning and haplotype analyses identified the 4p16.1–p16.3 region with a maximum multi-point LOD score of 3.50, which overlapped with the MSX1 gene. A single heterozygous point mutation IVS1–5 G > A in the MSX1 gene was exclusively detected in the 10 family members affected with tooth agenesis. Sequencing of MSX1 cDNA revealed that the intronic mutation did not affect the normal splicing pattern of the pre-mRNA. However, real-time qPCR analysis of lymphocyte RNA showed that the level of MSX1 mRNA was significantly decreased in individuals heterozygous for the mutation. Conclusions We identified and characterized a novel intronic mutation in the MSX1 gene in a large Chinese pedigree, adding to the small repertoire of MSX1 mutations associated with autosomal dominant tooth agenesis. We hypothesize that the variable degree of tooth agenesis observed in each affected individual may be due to sub-optimal levels of MSX1 expression during critical stages tooth development. [ABSTRACT FROM AUTHOR]

Background Plasma based EGFR mutation analysis is emerging as a viable alternative to tumour tissue genotyping for patients with non-small cell lung carcinoma (NSCLC). The purpose of the study was to determine the degree of concordance between EGFR genotypes derived from matching tissue and blood samples. Methods EGFR activating mutations L858R, exon 19 deletions, G719A/C/S and L861Q as well as resistance mutations T790M and exon 20 insertions were co-analysed in 61 matching tissue and blood biopsies collected from NCSLC patients. Tissue and plasma genotyping was performed by amplification refractory mutation system PCR (ARMS-PCR) and circulating single molecule amplification and re-sequencing technology (cSMART), respectively. Results Of the 61 paired samples, 44 (72.1%) were fully concordant, 2 (3.3%) were partially concordant and 15 (24.6%) were discordant for EGFR genotypes. The discordance was bidirectional with tissue and plasma failing to reveal the equivalent mutation in eight and nine cases, respectively. Benchmarking against ARMS-PCR tissue biopsy results as the gold standard, the sensitivity and concordance rates for plasma mutation detection by cSMART assay were 72.7% and 90.2% (L858R), 72.7% and 86.9% (exon 19 deletions) and 100% and 98.4% (T790M). Conclusions The cSMART assay was highly reliable and accurate for plasma EGFR genotyping. Based on discordance trends, tumour heterogeneity was suspected to be the major factor preventing a concordant diagnosis in matching samples. [ABSTRACT FROM AUTHOR]

Background Calculation of the fetal DNA fraction (FF) is important for reliable and accurate noninvasive prenatal testing (NIPT) for fetal genetic abnormalities. The aim of the study was to develop and validate a novel method for FF determination. Methods FF was calculated using the chromosome Y (ChrY) sequence read assay and by circulating single molecule amplification and re-sequencing technology of 76 autosomal SNPs. Results By Pearson correlation for FF (4.73–22.11%) in 33 male pregnancy samples, the R 2 co-efficient for the 76-SNP versus the ChrY assay was 0.9572 (p < 0.001). In addition, the co-efficient of variation (CV) of FF measurement by the 76-SNP assay was low (0.15–0.35). As a control, the FF measurement for four non-pregnant plasma samples was virtually zero. In prospective longitudinal studies of 14 women with normal pregnancies, FF generally increased with gestational age. However, in eight women (71%) there was a significant decrease in FF between the first trimester (11–13 weeks) and the second trimester (15–19 weeks), and this was attributable to significant maternal weight gain. Conclusions The novel 76-SNP cSMART assay has the precision to accurately measure FF in all pregnancies at a detection threshold of 5%. Based on FF trends in individual pregnancies, our results suggest that the end of the first trimester may be a more optimal window for performing NIPT. [ABSTRACT FROM AUTHOR]

Next-generation sequencing is emerging as a reliable and accurate technology for pre-implantation genetic diagnosis (PGD) of aneuploidies and translocations. The aim of this study was to extend the clinical utility of copy number variation sequencing (CNV-Seq) to the detection of small pathogenic copy number variations (CNVs) associated with chromosome disease syndromes. In preliminary validation studies, CNV-Seq was highly sensitive and specific for detecting small CNV in whole-genome amplification products from three replicates of one and five cell samples, with a resolution in the order of 1–2 Mb. Importantly, the chromosome positions of all CNV were correctly mapped with copy numbers similar to those measured in matching genomic DNA samples. In seven clinical PGD cycles where results were obtained for 34 of 35 blastocysts, CNV-Seq identified 18 blastocysts with aneuploidies, one with an aneuploidy and a 4.98 Mb 5q35.2-qter deletion associated with Sotos syndrome, one with a 6.66 Mb 7p22.1-pter deletion associated with 7p terminal deletion syndrome and 14 with no detectable abnormalities that were suitable for transfer. On the basis of these findings, CNV-Seq displays the hallmarks of a comprehensive PGD technology for detection of aneuploidies and CNVs that are known to affect the development and health of patient's embryos. [ABSTRACT FROM AUTHOR]

Background The sensitivity and specificity of noninvasive prenatal testing (NIPT) for detection of sex chromosome aneuploidies (SCAs) compared to common autosomal trisomies are significantly lower. We speculated that in addition to altered maternal X chromosome karyotype, maternal X chromosome copy number variations (CNVs) may also contribute to discordant NIPT SCA results. Methods Clinical NIPT was performed for pregnant women at a single hospital. Copy number variation sequencing (CNV-Seq) was used to identify and quantitate the copy number of maternal X chromosome CNVs for each positive SCA pregnancy. Results Two out of 25 SCA positive NIPT samples had slightly abnormal ChrX/ChrY z-scores and were referred for invasive test confirmation. However, fetal karyotypes were found to be normal. CNV-Seq analysis of the maternal white blood cell DNA archived from the original two NIPT blood samples identified small CNVs spanning the STS gene, which is associated with X-linked ichthyosis. Correcting for the altered plasma levels of X chromosome DNA caused by the two CNVs and, taking into consideration the phenotypic consequences for X-linked disease, both fetuses were diagnosed as normal. Conclusions Maternal DNA sequencing is recommended for all positive NIPT SCA results to avoid unnecessary referral for invasive testing and also to evaluate the risk to the fetus of X-linked disease. [ABSTRACT FROM AUTHOR]

Abstract: Background: Complex chromosomal rearrangements and chromosomal deletion and duplication syndromes are commonly associated with abnormal clinical phenotypes. The 2q31.1 microdeletion syndrome is a rare cytogenetic event that leads to limb and multi-internal organ anomalies. In this study we investigated the genetic basis of the physical and mental symptoms exhibited by a 4-year-old boy with a suspected 2q31.1 deletion. Methods: Cytogenetic and molecular techniques including karyotyping, array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH) and real-time PCR were used to identify the nature and extent of chromosome abnormalities in the patient. Results: A 3.6Mb interstitial microdeletion of 2q31.1 was identified in association with complex balanced genomic structural rearrangements involving chromosomes 2, 3, 6, 15 and 18. The 2q31.1 deletion resulted in the loss of one copy of several known disease genes, including GAD1, DCAF17, SLC25A12 and ITGA6 associated with mental retardation and facial abnormalities and DLX1/DLX2 partially associated with limb abnormalities. Two additional genes, HOXD13 and CHN1, required for normal limb and eye development that map immediately distal to the 2q31.1 deletion had normal copy numbers, although CHN1 was found to express at a lower level in patient's lymphocytes. Conclusions: We speculated that the 2q31.1 deletion and/or translocation may have a positional effect which reduces expression of HOXD13 and CHN1 causing haplo-insufficiency, and in combination with the hemizygous expression of the disease genes at 2q31.1, provides a plausible explanation for the diverse clinical symptoms exhibited by the patient. [Copyright &y& Elsevier]