Unbalanced Chromosomal Rearrangements Research Articles

Repeated pregnancy losses with multiple aneuploidies and major genomic imbalance: A case report

Rationale: If one of the partners is having balanced autosomal translocation, it is usually observed that the offspring inherit either normal chromosomes, balanced translocation identical to one of the parent or unbalanced chromosomal rearrangements of the same parental chromosome having translocation. Concern: A unique case presented with history of 8 miscarriages for genetic counseling. The last abortus material evaluation showed monosomy of chromosome X (Turner syndrome) in all the analyzed cells. There was a history of infertility and also repeated second trimester abortions on the paternal side. On the maternal side, there was a history of intellectual disability. Diagnose: History of repeated abnormal pregnancy outcomes. Wife’s karyotype is normal; however, husband shows translocation between chromosome 4 and 22. Intervention: Peripheral blood sample around 3 mL was collected for karyotype. Embryo biopsy was done and DNA was extracted and processed for whole exome sequencing. Outcomes: Wife’s karyotype is normal and husband has translocation between chromosome 4 and 22. Surprisingly, the entire pregnancy outcome including embryo screening has different, complete or partial aneuploidies of chromosomes other than chromosome 4 and 22. Main lesson: Though the translocation in one of the parent is balanced, we have to think beyond traditional ways for evaluating a couple with repeated pregnancy loss as we cannot predict the errors at cell division. Option of in vitro fertilization and preimplantation genetic diagnosis in couples having balanced translocations should be discussed so that early intervention can prevent the agony of pregnancy loss.

Genomic Characterization of Partial Tandem Duplication Involving the KMT2A Gene in Adult Acute Myeloid Leukemia.

Gene rearrangements affecting KMT2A are frequent in acute myeloid leukemia (AML) and are often associated with a poor prognosis. KMT2A gene fusions are often detected by chromosome banding analysis and confirmed by fluorescence in situ hybridization. However, small intragenic insertions, termed KMT2A partial tandem duplication (KMT2A-PTD), are particularly challenging to detect using standard molecular and cytogenetic approaches. We have validated the use of a custom hybrid-capture-based next-generation sequencing (NGS) panel for comprehensive profiling of AML patients seen at our institution. This NGS panel targets the entire consensus coding DNA sequence of KMT2A. To deduce the presence of a KMT2A-PTD, we used the relative ratio of KMT2A exons coverage. We sought to corroborate the KMT2A-PTD NGS results using (1) multiplex-ligation probe amplification (MLPA) and (2) optical genome mapping (OGM). We analyzed 932 AML cases and identified 41 individuals harboring a KMT2A-PTD. MLPA, NGS, and OGM confirmed the presence of a KMT2A-PTD in 22 of the cases analyzed where orthogonal testing was possible. The two false-positive KMT2A-PTD calls by NGS could be explained by the presence of cryptic structural variants impacting KMT2A and interfering with KMT2A-PTD analysis. OGM revealed the nature of these previously undetected gene rearrangements in KMT2A, while MLPA yielded inconclusive results. MLPA analysis for KMT2A-PTD is limited to exon 4, whereas NGS and OGM resolved KMT2A-PTD sizes and copy number levels. KMT2A-PTDs are complex gene rearrangements that cannot be fully ascertained using a single genomic platform. MLPA, NGS panels, and OGM are complementary technologies applied in standard-of-care testing for AML patients. MLPA and NGS panels are designed for targeted copy number analysis; however, our results showed that integration of concurrent genomic alterations is needed for accurate KMT2A-PTD identification. Unbalanced chromosomal rearrangements overlapping with KMT2A can interfere with the diagnostic sensitivity and specificity of copy-number-based KMT2A-PTD detection methodologies.

Long read sequencing on its way to the routine diagnostics of genetic diseases.

The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.

Analysis of chromosomal structural variations in patients with recurrent spontaneous abortion using optical genome mapping.

Background and aims: Certain chromosomal structural variations (SVs) in biological parents can lead to recurrent spontaneous abortions (RSAs). Unequal crossing over during meiosis can result in the unbalanced rearrangement of gamete chromosomes such as duplication or deletion. Unfortunately, routine techniques such as karyotyping, fluorescence in situ hybridization (FISH), chromosomal microarray analysis (CMA), and copy number variation sequencing (CNV-seq) cannot detect all types of SVs. In this study, we show that optical genome mapping (OGM) quickly and accurately detects SVs for RSA patients with a high resolution and provides more information about the breakpoint regions at gene level. Methods: Seven couples who had suffered RSA with unbalanced chromosomal rearrangements of aborted embryos were recruited, and ultra-high molecular weight (UHMW) DNA was isolated from their peripheral blood. The consensus genome map was created by de novo assembly on the Bionano Solve data analysis software. SVs and breakpoints were identified via alignments of the reference genome GRCh38/hg38. The exact breakpoint sequences were verified using either Oxford Nanopore sequencing or Sanger sequencing. Results: Various SVs in the recruited couples were successfully detected by OGM. Also, additional complex chromosomal rearrangement (CCRs) and four cryptic balanced reciprocal translocations (BRTs) were revealed, further refining the underlying genetic causes of RSA. Two of the disrupted genes identified in this study, FOXK2 [46,XY,t(7; 17)(q31.3; q25)] and PLXDC2 [46,XX,t(10; 16)(p12.31; q23.1)], had been previously shown to be associated with male fertility and embryo transit. Conclusion: OGM accurately detects chromosomal SVs, especially cryptic BRTs and CCRs. It is a useful complement to routine human genetic diagnostics, such as karyotyping, and detects cryptic BRTs and CCRs more accurately than routine genetic diagnostics.

Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage

Naturally occurring balanced, unbalanced, and complex chromosomal rearrangements have been reported to cause pathogenic genomic or genetic variants leading to infertility and recurrent miscarriage. Therefore, balanced chromosomal rearrangements were used as genomic signposts for identification of candidate genes or genomic loci associated with male infertility due to defects of spermatogenesis, or with recurrent miscarriage. In three male probands, structural chromosomal variants and copy number variants were identified at nucleotide resolution by long-insert genome sequencing approaches and Sanger sequencing. The pathogenic potential of these and affected candidate genes was assessed based on convergent genomic and genotype-phenotype correlation data. Identification of balanced chromosomal rearrangement breakpoints and interpretation in the context of their genomic background of structural and copy number variants led us to conclude that the infertility due to oligoasthenozoospermia and oligozoospermia is most likely associated with a position effect on YIPF5 and SPATC1L, respectively. In a third proband with intellectual disability and recurrent miscarriage, disruption of CAMK2B causing autosomal dominant, intellectual developmental disorder 54 and increased meiotic segregation during gametogenesis of a der(22) are responsible for the reported phenotype. Our data further support the existence of loci at 5q23 and 21q22.3 for these spermatogenesis defects and highlight the importance of the naturally occurring balanced chromosomal rearrangements for assessment of the pathogenic mechanisms. Furthermore, we show comorbidities due to the same balanced chromosomal rearrangement caused by different pathogenic mechanisms.

Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding

BackgroundThe frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock production. Since artificial insemination is practiced in almost all intensive pig production systems, the use of elite boars carrying cytogenetic defects that have an impact on fertility can lead to major economic losses. To avoid keeping subfertile boars in artificial insemination centres and spreading chromosomal defects within populations, cytogenetic screening of boars is crucial. Different techniques are used for this purpose, but several issues are frequently encountered, i.e. environmental factors can influence the quality of results, the lack of genomic information outputted by these techniques, and the need for prior cytogenetic skills. The aim of this study was to develop a new pig karyotyping method based on fluorescent banding patterns.ResultsThe use of 207,847 specific oligonucleotides generated 96 fluorescent bands that are distributed across the 18 autosomes and the sex chromosomes. Tested alongside conventional G-banding, this oligo-banding method allowed us to identify four chromosomal translocations and a rare unbalanced chromosomal rearrangement that was not detected by conventional banding. In addition, this method allowed us to investigate chromosomal imbalance in spermatozoa.ConclusionsThe use of oligo-banding was found to be appropriate for detecting chromosomal aberrations in a Canadian pig nucleus and its convenient design and use make it an interesting tool for livestock karyotyping and cytogenetic studies.

P-719 Evaluation of genetic risk of apparently balanced chromosomal rearrangement carriers by breakpoint characterization

Abstract Study question What are breakpoint characteristics of ABCR carriers? What are the genetic risks of ABCR carriers caused by chromosome rearrangements? Summary answer We analyzed the characteristics of ABCR's breakpoints and found that heterogeneous deletion of some AD disease-related genes may not result in clinical phenotype. What is known already ABCRs are common chromosomal abnormalities. People with ABCRs generally lack any visible abnormal features; however, during childbirth, the abnormal pairing and missegregation of homologous chromosomes can lead to the production of unbalanced gametes, resulting in spontaneous abortion or the birth of children with chromosomal disorders. Prenatal diagnosis or preimplantation diagnosis can effectively prevent the birth of children with unbalanced chromosome rearrangements, but no substantial data has been collected to report on the characteristics and potential genetic risks of the chromosome breakage caused by the rearrangement. Study design, size, duration This is a retrospective study of 2441 breakpoints in 1219 ABCR carriers who underwent Preimplantation Genetic Testing (PGT) at the Reproductive and Genetic Hospital of Citic-Xiangya from August 1, 2016 to December 31, 2021. Participants/materials, setting, methods All patients in this study sought PGT treatment due to primary or secondary infertility caused by ABCRs. To characterize the chromosome breakpoints, the MicroSeq technique, which involves chromosome microdissection and next generation sequencing, was employed. Additionally, gap-junction PCR and Sanger sequencing were utilized to further validate some of the breakpoints. Main results and the role of chance In this study, we retrospectively analyzed 2441 chromosome rearrangement breakpoint MicroSeq localization data from 1219 ABCR carriers, including 2364 breakpoint regions in 1182 reciprocal translocations, 68 breakpoint regions in 34 inversions, and 9 breakpoint regions in 3 insertional translocations. We not only identified 8q24.13, 11q11.23, and 22q11.21 as previously reported hotspots of chromosomal balanced rearrangement breaks, but also identified the 10 Mb region of 12q24.13-q24.3 as a possible rare region of balanced rearrangement breaks. the average range of breakpoints identified by MicroSeq technology was only within 3.8 Kb, which clarified 95.82% (2339/2441) of balanced chromosomal rearrangements as to whether they broke genes or not. We identified 960 genes that were interrupted, of which 53 genes with autosomal dominant mode of inheritance (AD) were interrupted. Clinical phenotypic evaluation of these patients carrying interrupted AD genes identified that some of the AD genetic interruptions may not have a clinical phenotype. Limitations, reasons for caution MicroSeq cannot precisely pinpoint breakpoints to the gene or single base level. Moreover, carriers of ABCRs were not comprehensively assessed for other clinical characteristics, and the alteration in function of the known Haploinsufficiency gene could not be confirmed. Additionally, the position effect of the breakpoints has not been evaluated. Wider implications of the findings This investigation offers a reference for evaluating the pathogenicity and genetic risks of protein-truncation mutations in some AD genes. Trial registration number Not applicable

Role of chromosomal imbalances in the pathogenesis of DSD: A retrospective analysis of 115 prenatal samples

Differences of sex development (DSDs) are a group of congenital conditions characterized by a discrepancy between chromosomal, gonadal, and genital sex development of an individual, with significant impact on medical, psychological and reproductive life. The genetic heterogeneity of DSDs complicates the diagnosis and almost half of the patients remains undiagnosed. In this context, chromosomal imbalances in syndromic DSD patients may help to identify new genes implicated in DSDs. In this study, we aimed at describing the burden of chromosomal imbalances including submicroscopic ones (copy number variants or CNVs) in a cohort of prenatal syndromic DSD patients, and review their role in DSDs. Our patients carried at least one pathogenic or likely pathogenic chromosomal imbalance/CNV or low-level mosaicism for aneuploidy. Almost half of the cases resulted from an unbalanced chromosomal rearrangement. Chromosome 9p/q, 4p/q, 3q and 11q anomalies were more frequently observed. Review of the literature confirmed the causative role of CNVs in DSDs, either in disruption of known DSD-causing genes (SOX9, NR0B1, NR5A1, AR, ATRX, …) or as a tool to suspect new genes in DSDs (HOXD cluster, ADCY2, EMX2, CAMK1D, …). Recurrent CNVs of regulatory elements without coding sequence content (i.e. duplications/deletions upstream of SOX3 or SOX9) confirm detection of CNVs as a mean to explore our non-coding genome. Thus, CNV detection remains a powerful tool to explore undiagnosed DSDs, either through routine techniques or through emerging technologies such as long-read whole genome sequencing or optical genome mapping.

Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries.

The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.

Higher chromosomal abnormality rate in blastocysts from a subset of patients with pericentric inversion (Inv) 1 variant

The purpose of this study was to evaluate the incidence of unbalanced chromosome rearrangement in blastocyst-stage embryos from carriers of pericentric inversion of chromosome 1 (PEI-1). A total of 98 embryos from 22 PEI-1 carriers were tested for unbalanced rearrangements, originating from inversion carriers, and overall aneuploidy. Logistic regression analysis indicated that the ratio of inverted segment size to chromosome length was a statistically significant risk factor for unbalanced chromosome rearrangement from PEI-1 carriers (p = 0.003). The optimal cut-off values to predict the risk of unbalanced chromosome rearrangement was 36%, with the incidence being 2.0% in the <36% group and 32.7% in the ≥36% group. The unbalanced embryo rate was 24.4% in male carriers compared to 12.3% in female carriers. Inter-chromosomal effect analysis was performed using 98 blastocysts from PEI-1 carriers and 116 blastocysts from age-matched controls. PEI-1 carriers had similar sporadic aneuploidy rates compared to those of age-matched controls at 32.7 vs. 31.9%, respectively. In conclusion, the risk of unbalanced chromosome rearrangement is affected by inverted segment size in PEI-1 carriers.

P619: Rates of unbalanced chromosome rearrangements associated with pericentric and paracentric inversions: Analysis of molecular chromosome results in blastocyst-stage embryos samples*

P619: Rates of unbalanced chromosome rearrangements associated with pericentric and paracentric inversions: Analysis of molecular chromosome results in blastocyst-stage embryos samples*

A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders.

Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.

A Central Role of Telomere Dysfunction in the Formation of a Unique Translocation within the Sub-Telomere Region Resulting in Duplication and Partial Trisomy

Telomeres play a major role in maintaining genome stability and integrity. Putative involvement of telomere dysfunction in the formation of various types of chromosomal aberrations is an area of active research. Here, we report a case of a six-month-old boy with a chromosomal gain encompassing the 11q22.3q25 region identified by SNP array analysis. The size of the duplication is 26.7 Mb and contains 170 genes (OMIM). The duplication results in partial trisomy of the region in question with clinical consequences, including bilateral renal dysplasia, delayed development, and a heart defect. Moreover, the karyotype determined by R-banding and chromosome painting as well as by hybridization with specific sub-telomere probes revealed the presence of an unbalanced t(9;11)(p24;q22.3) translocation with a unique breakpoint involving the sub-telomere region of the short arm of chromosome 9. The karyotypes of the parents were normal. Telomere integrity in circulating lymphocytes from the child and from his parents was assessed using an automated high-throughput method based on fluorescence in situ hybridization (FISH) with telomere- and centromere-specific PNA probes followed by M-FISH multicolor karyotyping. Very short telomeres, as well as an increased frequency of telomere loss and formation of telomere doublets, were detected in the child’s cells. Interestingly, similar telomere profiles were found in the circulating lymphocytes of the father. Moreover, an assessment of clonal telomere aberrations identified chromosomes 9 and 11 with particularly high frequencies of such aberrations. These findings strongly suggest that telomere dysfunction plays a central role in the formation of this specific unbalanced chromosome rearrangement via chromosome end-to-end fusion and breakage–fusion–bridge cycles.

Identification of unbalanced complex chromosomal rearrangements in IVF-derived embryos during NGS analysis of preimplantation genetic testing: A case report

Identification of unbalanced complex chromosomal rearrangements in IVF-derived embryos during NGS analysis of preimplantation genetic testing: A case report

Efficacy and initial clinical evaluation of optical genome mapping in the diagnosis of structural variations

To investigate the efficacy and value of optical genome mapping (OGM) in detecting chromosomal structural variations. In a clinical study about high-precision analysis of genomic structural variation for complex genetic diseases, a retrospective study was performed on the cases with karyotyping at the department of Obstetrics and Gynecology, and Endocrinology of Peking Union Medical College Hospital from January to December 2021. Ten cases with abnormal karyotype was detected by OGM. Partial cases were verified by fluorescence in situ hybridization (FISH), SNP array or CNV-seq. Results of ten cases, nine were detected with abnormality by OGM, including unbalanced chromosomal rearrangements (n=3), translocation (n=5) and paracentric inversion (n=1), and the results were in concordance with other standard assays. However, one case with breakpoint and reconnected at centromere has not been detected. In conclusion, ten samples were comprehensively analyzed by karyotyping, FISH, SNP array or CNV-seq, and OGM, and results demonstrated that optical genome mapping as a new technology can not only detect unbalanced rearrangements such as copy number variants as well as balanced translocations and inversions, but more importantly, it can refine breakpoints and orientation of duplicated segments or insertions. So it can contribute to the diagnosis of genetic diseases and prevent birth defect. However, the current technology is not yet capable of detecting breakpoints of balanced structural variations lying within unmapped regions.

EP314: Rare unbalanced complex chromosomal rearrangement in a case of infertility: Insight into the 8p23.1 duplication syndrome

Complex chromosomal rearrangements (CCR) are defined as structural abnormalities involving more than 2 chromosomal breaks and subsequent exchange of chromosomal material. These events are rare, with less than 255 cases reported to date involving 3 chromosomes. The majority of CCRs are detected in phenotypically normal individuals, presenting with abnormal sperm parameters in males and reproductive failure in females. In these patients, the rearrangement is usually balanced and inherited from a mother carrying the same translocations.

Detection of aneuploidy using multiplex ligation–dependent probe amplification in fetal tissues from aborted pregnancies

Purpose: About 10-15% of all pregnancies terminate as spontaneous miscarriages. In the first trimester, ≈50% of spontaneous miscarriages are the result of chromosomal aberrations, mostly chromosomal aneuploidies. Cytogenetic analyses are used to confirm aneuploidy in failed pregnancies. Culture failure or poor-quality chromosomes are often problems in those cases. In such situations, methods that are independent of tissue culture are used, and we employed multiplex ligation-dependent probe amplification (MLPA). We determined if MLPA is an appropriate and compatible method compared with classical cytogenetic analyses on fetal tissues.&#x0D; Methods: All fetal samples received from spontaneous abortions were cultured, karyotyped (if possible) and genomic DNA extracted. MLPA analyses were undertaken using subtelomeric probe kits. Additionally, comparative genomic hybridization (CGH) was used to confirm aneuploidy detected by MLPA in cases of failed culture growth.&#x0D; Results: MLPA analyses confirmed an unbalanced chromosome abnormality identified by cytogenetic analyses in all cases in which tissue culture was successful, and provided data in cases of failed culture growth. Several common numeric chromosome aberrations were detected, as well as rare trisomies and other unbalanced chromosome rearrangements.&#x0D; Conclusions: MLPA analyses can provide information about the karyotype of a DNA sample if cytogenetic analyses are not possible because of a lack of viable cells or if only a small amount of genomic DNA is available. Th

Characterization of a Rare Mosaicism in Autosomal Translocation of t(5;21) Using Conventional Cytogenetics and FISH Methods

Background:Mosaicism of a normal cell population and an unbalanced autosomal chromosome rearrangement is rarely seen. If the abnormal cell line contributes to a minor part of soma, the phenotype is expected to be normal. Case Report:We report a 29-year-old woman who had balance chromosomal translocation of 46,XX,t(5;21) with a two-year-old affected girl, characterized by mental retardation, dystrophia, hearing impartment, and dysphagia. Methods and Results:Cytogenetic investigation revealed a low mosaic unbalanced translocation of 46,XX,t(5;21)/ 46,XX, which was confirmed by FISH analysis. Studying 200 metaphases and interphases of peripheral blood sample revealed 70% partial monosomy of 21q22 and partial trisomy of 5q(35.3) and 30% of normal pattern. Conclusion:In rare cases such as this study, parents with balanced translocation with no phenotypes may lead to a mosaic unbalanced translocation with abnormal phenotypes in offspring, which underscores the need for prenatal karyotyping and genetics counseling.

Pericentric inversion (Inv) 9 variant\u2014reproductive risk factor or benign finding?

PurposeTo report the unbalanced chromosome rearrangement rate and overall aneuploidy rate in day 5/6 embryos from a series of patients who underwent in vitro fertilization (IVF) with preimplantation genetic testing for structural rearrangements (PGT-SR) for the pericentric inversion 9 variant, inv(9)(p11q13) or inv(9)(p12q13), with concurrent 24 chromosome preimplantation genetic testing for aneuploidy (PGT-A).MethodsThis was a retrospective cohort analysis. IVF cycles and embryo biopsies were performed by referring clinics. Fifty-two trophectoderm biopsy samples from seven couples were sent to a single lab for PGT-SR for an inversion 9 variant with concurrent 24 chromosome PGT-A using single-nucleotide polymorphism (SNP) microarrays with bioinformatics.ResultsThe unbalanced rearrangement rate for this embryo cohort was 0/52 (0.0%); mean maternal age per embryo was 33.3 years (range 21–39 years). The overall euploid rate was 61.5% and aneuploidy rate was 38.5%.ConclusionsChromosome 9 pericentric inversions did not result in unbalanced structural rearrangements in day 5/6 embryo samples, supporting that this population variant is not associated with increased reproductive risks.

Breakpoint mapping uncovering about 1.32% of apparent balanced reciprocal translocation (ABRT) carriers existing cryptic complex chromosomal structural variations in preimplantation genetic testing (PGT)

To identify precise breakpoints, evaluate the reproduction-related risks and guide the following PGT treatment, high resolution breakpoint mapping was performed in ABRT carriers indicated by G-banding. A single-center, descriptive research. A large sample of 833 cases with ABRT who planned to accept PGT treatment were recruited in this study. For these patients, the approach of the next-generation sequencing following microdissection (MiroSeq) of the junction region in the derivative chromosomes, and linkage analysis of the adjacent single nucleotide polymorphisms (SNPs) were performed to distinguish the carriers from noncarriers in balanced embryos. For some cases with unbalanced chromosome rearrangement in the breakpoint region, SNP-array and fluorescence in situ hybridization (FISH) techniques were further used to determine the accurate karyotype. In the 833 cases with ABRT, we found 11 cases (1.32%) carried cryptic complex chromosomal structural variation, including 3 unbalanced chromosome rearrangements and 8 balanced ones in which 2 cases carried both inversion and translocation. In these 11 cases, 5 cases related to 3 chromosomes with 4 to 21 breakpoints and 6 cases involved 2 chromosomes with 3 to 6 breakpoints. It is noteworthy that there were two cases exhibited rare chromoanagenesis, including chromothripsis and chromoplexy. Fortunately, two couples have been both successfully transplanted a normal embryo and given birth to a healthy child, and the remaining nine cases are undergoing PGT treatment. In this large-scale analysis of ABRT, high resolution breakpoint mapping precisely characterized these breakpoints and uncovered 1.32% of the ABRT carriers existed cryptic complex chromosomal structural rearrangement. These data suggests that high resolution breakpoint mapping used in PGT can improve the accuracy of evaluating the reproduction-related risks and avoid genetic risks for the ABRT carriers.