Breakpoint Mapping Research Articles

The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling.

Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy-number-variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. Here, we report on the use of OGM in a prenatal diagnosis setting. Detailed breakpoint mapping was used to determine the relative orientations of triplicated and duplicated segments in two unrelated foetuses harbouring chromosomal aberrations: a de novo 15q23q24.2 triplication and a paternally inherited 13q14.2 duplication that overlapped partially with the RB1 gene. OGM enabled us to suggest a plausible mechanism for the triplication and confirmed that the RB1 duplication was direct oriented and in tandem. This enabled us to predict the pathogenic consequences, refine the prognosis and adapt the follow-up and familial screening appropriately. Along with an increase in diagnostic rates, OGM can rapidly highlight genotype-phenotype correlations, improve genetic counselling and significantly influence prenatal management.

A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing

Lynch Syndrome (LS) is a hereditary cancer syndrome caused by pathogenic germline variants in one of the four mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. It is characterized by a significantly increased risk of multiple cancer types, particularly colorectal and endometrial cancer, with autosomal dominant inheritance. Access to precise and sensitive methods for genetic testing is important, as early detection and prevention of cancer is possible when the variant is known. We present here two unrelated Norwegian families with family histories strongly suggestive of LS, where immunohistochemical and microsatellite instability analyses indicated presence of a pathogenic variant in MSH2, but targeted exon sequencing and multiplex ligation-dependent probe amplification (MLPA) were negative. Using Bionano optical genome mapping, we detected a 39 kb insertion in the MSH2 gene. Precise mapping of the insertion breakpoints and inserted sequence was performed by low-coverage whole-genome sequencing with an Oxford Nanopore MinION. The same variant was present in both families, and later found in other families from the same region of Norway, indicative of a founder event. To our knowledge, this is the first diagnosis of LS caused by a structural variant using these technologies. We suggest that structural variant detection be performed when LS is suspected but not confirmed with first-tier standard genetic testing.

The Precise Breakpoint Mapping in Paracentric Inversion 10q22.2q23.3 by Comprehensive Cytogenomic Analysis, Multicolor Banding, and Single-Copy Chromosome Sequencing.

Detection and precise genomic mapping of balanced chromosomal abnormalities in patients with impaired fertility or a clinical phenotype represent a challenge for current cytogenomics owing to difficulties with precise breakpoint localization in the regions enriched for DNA repeats and high genomic variation in such regions. Here, we present a comprehensive cytogenomic approach to breakpoint mapping in a rare paracentric inversion on 10q (in a patient with oligoasthenoteratozoospermia and necrozoospermia) that does not affect other phenotype traits. Multicolor banding, chromosomal microarray analysis, chromosome microdissection with reverse painting, and single-copy sequencing of the rearranged chromosome were performed to determine the length and position of the inverted region as well as to rule out a genetic imbalance at the breakpoints. As a result, a paracentric 19.251 Mbp inversion at 10q22.2q23.3 was described. The most probable location of the breakpoints was predicted using the hg38 assembly. The problems of genetic counseling associated with enrichment for repeats and high DNA variability of usual breakpoint regions were discussed. Possible approaches for cytogenomic assessment of couples with balanced chromosome rearrangements and problems like reproductive failures were considered and suggested as useful part of effective genetic counseling.

IKZF1 DELETIONS IN B-ALL: FROM GENETIC BASIS TO DIAGNOSTIC ENHANCEMENT

Because IKZF1 deletions are associated with an increased risk of relapse in patients with B-cell precursor acute lymphoblastic leukemia (B-ALL), the development of methods for rapid and accurate detection of this alteration has a great clinical impact. Although multiplex ligation-dependent probe amplification (MLPA) has been widely used for the evaluation of IKZF1 deletions, multiplex (M)-PCR is a valuable tool for the validation of those IKZF1 deletions. However, this method is still limited to detect recurrent intragenic deletions (Δ2-3, Δ2-7, Δ2-8, Δ4-7, Δ4-8). Therefore, here we evaluate the breakpoint map of IKZF1 deletions with a special focus on non-recurrent deletions to update methodologies for the diagnosis of this genetic alteration. Moreover, we explore the genetic features underlying those IKZF1 deletions to infer its molecular pathogenesis. This study included four international cohorts of pediatric and adult patients with B-ALL. IKZF1 deletions were identified by MLPA (P335 and P202 assays) and M-PCR. Non-recurrent deletions were verified by next-generation sequencing using the Illumina DNA Prep with Enrichment assay. We also revised previously published data regarding IKZF1 deletions in B-ALL for compiling breakpoint sequence information of these deletions. Sequence data from our cohorts and literature were used in further analyses. After identifying the breakpoint clusters, we performed an agnostic motif search using MEME and annotated the presence of filler DNA or microhomologies at the junctions of IKZF1 deletions. A total of 1,472 B-ALL samples were screened, and IKZF1 deletions were found in 16% of these patients. Although non-recurrent deletions were associated with 1% of the total cohort, it represents 8% of all IKZF1 deletions. The analysis of breakpoint sequences at DNA level revealed that non-recurrent IKZF1 deletions comprises miscellaneous alterations, but the majority of them encompases Δ1 and Δ1-3. Considering that IKZF1 exon 1 deletions are more difficult to reliably detect by MLPA due to the high GC content (>50%) of this region, we mapped several exon 1 deletions at DNA level and identified one commonly deleted region which is ideal for designing MLPA probes. Next, we searched for motifs, additional nucleotides/microhomologies associated with IKZF1 deletion sequences. We verified an enrichment of the 5’-CACACAGTG-3’sequence within 21 out of 24 breakpoint clusters of IKZF1 deletion (E-value: 2.9e-008). Additionally, the filler DNA within the junctions of IKZF1 deletions presented a higher GC nucleotide content at these clusters as compared to the deletions outside of them (71% vs. 56%). This study provides the genetic landscape of IKZF1 deletions in B-ALL. Although rare types of deletion may be identified at the routine diagnosis, they should be considered after using adapted MLPA protocols, including additional probes within the common deleted region nearby IKZF1 exon 1. We also verified the occurrence of the heptamer sequence and an enrichment of GC nucleotides exclusively within breakpoint clusters, suggesting that RAG recombination and TdT activity may promote most IKZF1 deletions, although rare types of alterations may be associated with another molecular mechanism of leukemogenesis.

ACCURATE BREAKPOINT MAPPING USING OPTICAL GENOME MAPPING (OGM) HAS THE POTENTIAL TO INCREASE THE ACCURACY OF PREIMPLANTATION GENETIC TESTING FOR STRUCTURAL CHROMOSOMAL REARRANGEMENTS (PGT-SR)

PGT-SR is a genetic test performed on trophectoderm (TE) biopsy from IVF embryos to detect chromosomal structural rearrangements normally caused by balanced translocations and inversions. The feasibility and accuracy of PGT-SR is affected by the breakpoint defined by conventional cytogenetic methods. OGM enables direct high-resolution breakpoint mapping on balanced carriers of translocations. In this study, we applied OGM on the couple who underwent IVF with multiple embryos showing the loss or gain on the same segments, which didn’t match with partner’s previous karyotyping results.

13. Remember breakpoint two: Enhancer swapping, a frequent deleterious consequence of balanced chromosomal rearrangements

HiC proximity-based sequencing has revealed that genomes are organized into megabase-sized topological associating domains (TADs) as units for cis-regulatory interactions. In a joint analysis across consortia studies led by the International Breakpoint Mapping Consortium (IBMC) and the Developmental Genome Anatomy Project (DGAP), we have used systematic mapping of 1,420 breakpoints from simple two-way balanced constitutional chromosomal rearrangements (BCRs) from both affected and healthy carriers to establish a first morbid map of this 3D-genome organization.

The Use of Next-generation Sequencing in the Diagnosis of Rare Inherited Anaemias: A Joint BSH/EHA Good Practice Paper.

The Use of Next-generation Sequencing in the Diagnosis of Rare Inherited Anaemias: A Joint BSH/EHA Good Practice Paper.

Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts

Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.

Multicolor Spectral Karyotyping Identifies New Recurring Breakpoints and Translocations in Multiple Myeloma

Karyotypic information on multiple myeloma (MM) is less extensive than that on other myeloid or lymphoid malignancies due to low mitotic activity of plasma cells. An add(14)(q32) marker chromosome has been reported to be the most frequent recurring abnormality in clonally abnormal cases; in approximately one third of the latter cases, this marker has been identified as a der(14)t(11;14)(q13;q32) chromosome. To map chromosomal breakpoints, characterize the add(14)(q32) marker chromosomes, and to identify other recurring translocations in MM, we used spectral karyotyping (SKY) to analyze a panel of nine bone marrow (BM) biopsy samples from eight patients and 10 tumor cell lines derived from MM patients. SKY involves hybridization of 24 fluorescently labeled chromosome painting probes to metaphase spreads in such a manner that simultaneous visualization of each of the chromosomes in a different color is accomplished. By this method, it was possible to define all chromosomal rearrangements and identify all of the clonal marker chromosomes in tumor cells. By detailed mapping of breakpoints of rearrangement, it was also possible to identify several novel recurring sites of breakage that map to the chromosomal bands 3q27, 17q24-25, and 20q11. The partner chromosomes in translocations that generated the add (14)(q32) marker chromosomes were identified in all cases in which they were detected by G-banding (one biopsy and six cell lines). In addition, two new translocations involving band 14q32, ie, t(12;14)(q24;q32) and t(14;20)(q32;q11) have also been identified. These studies demonstrate the power of SKY in resolving the full spectrum of chromosome abnormalities in tumors.© 1998 by The American Society of Hematology.

How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson.

This historical perspective reviews how work of Eric H. Davidson was a catalyst and exemplar for explaining haematopoietic cell fate determination through gene regulation. Researchers studying blood and immune cells pioneered many of the early mechanistic investigations of mammalian gene regulatory processes. These efforts included the characterization of complex gene regulatory sequences exemplified by the globin and T-cell/B-cell receptor gene loci, as well as the identification of many key regulatory transcription factors through the fine mapping of chromosome translocation breakpoints in leukaemia patients. As the repertoire of known regulators expanded, assembly into gene regulatory network models became increasingly important, not only to account for the truism that regulatory genes do not function in isolation but also to devise new ways of extracting biologically meaningful insights from even more complex information. Here we explore how Eric H. Davidson's pioneering studies of gene regulatory network control in nonvertebrate model organisms have had an important and lasting impact on research into blood and immune cell development. The intellectual framework developed by Davidson continues to contribute to haematopoietic research, and his insistence on demonstrating logic and causality still challenges the frontier of research today.

The genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and implications for assisted reproduction.

To elucidate the genetic cause of intellectual deficiency and/or congenital malformations in two parental reciprocal translocation carriers and provide appropriate strategies of assisted reproductive therapy (ART). Two similar couples having a child with global developmental delay/intellectual disability symptoms attended the Reproductive and Genetic Hospital of CITIC-Xiangya (Changsha, China) in 2017 and 2019, respectively, in order to determine the cause(s) of the conditions affecting their child and to seek ART to have a healthy baby. Both of the healthy couples were not of consanguineous marriage, denied exposure to toxicants, and had no adverse life history. This study was approved by the Institutional Ethics Committee of the Reproductive & Genetic Hospital of CITIC-Xiangya, and written informed consent was obtained from the parents. Genetic diagnoses were performed by karyotype analysis, breakpoint mapping analysis of chromosomal translocation(s), single-nucleotide polymorphism (SNP) microarray analysis, and whole-exome sequencing (WES) for the two children and different appropriate reproductive strategies were performed in the two families. Karyotype analysis revealed that both patients carried parental reciprocal translocations [46,XY,t(7;16)(p13;q24)pat and 46,XY,t(13;17)(q12.3;p11.2)pat, respectively]. Follow-up breakpoint mapping analysis showed no interruption of associated genes, and SNP microarray analysis identified no significant copy number variations (CNVs) in the two patients. Moreover, WES results revealed that patients 1 and 2 harbored candidate compound heterozygous mutations of MCOLN1 [c.195G>C (p.K65N) and c.1061G>A (p.W354*)] and MCPH1 [c.877A>G (p.S293G) and c.1869_1870delAT (p.C624*)], respectively, that were inherited from their parents and not previously reported. Furthermore, the parents of patient 1 obtained 10 embryos during ART cycle, and an embryo of normal karyotype and non-carrier of observed MCOLN1 mutations according to preimplantation genetic testing for structural rearrangement and monogenic defect was successfully transferred, resulting in the birth of a healthy boy. The parents of patient 2 chose to undergo ART with donor sperm to reduce the risk of recurrence. Systematic genetic diagnosis of two carriers of inherited chromosomal translocations accompanied by clinical phenotypes revealed their cause of disease, which was critical for genetic counseling and further ART for these families.

Whole Genome Low-Coverage Sequencing Concurrently Detecting Copy Number Variations and Their Underlying Complex Chromosomal Rearrangements by Systematic Breakpoint Mapping in Intellectual Deficiency/Developmental Delay Patients.

Simple copy number variations (CNVs) detected by chromosomal microarray (CMA) can result from complex structural changes. Therefore, it is necessary to characterize potential structural changes that cause pathogenic CNVs. We applied whole-genome low-coverage sequencing (WGLCS) to concurrently detect pathogenic CNVs and their associated chromosomal rearrangements in 15 patients. All the patients had an average of 2–3 pathogenic CNVs involving 1–2 chromosomes. WGLCS identified all the 34 pathogenic CNVs found by microarray. By identifying chimeric read pairs, WGLCS mapped 70 breakpoints in these patients, of which 47 were finely mapped at the nucleotide level and confirmed by subsequent PCR amplification and Sanger sequencing of the junction fragments. In 15 patients, structural rearrangements were defined at molecular level in 13 patients. In 13 patients, WGLCS reveal no additional results in two patients. In another 11 patients, WGLCS revealed new breakpoints or finely mapped the genes disrupted by breakpoints or 1–6 bp microhomology and/or short insertion (4–70 bp) in the breakpoints junctions. However, structural changes in the other two patients still remained unclear after WGLCS was performed. The structural alteration identified in the 13 patients could be divided into the following categories: (1) interstitial inverted duplication with concomitant terminal deletion (inv dup del) (P1,P4,P9,P11); (2) the product of pericentric inversion (P5); (3) ring chromosome (P8); (4) interstitial duplication and/or triplication (P6, P7); and (5) +der(22)t(11;22) (P2,P15); (6) complex structural rearrangements (P3,P12,P14). WGLCS displayed the ability to discover CNVs and define breakpoints and its disrupted genes and its surrounding sequences in one experiment at base-pair-resolution, which help us to learn more about the mechanisms of formation of observed genomic rearrangements, and in which DNA replicative/repair mechanism might contribute to the formation of complex rearrangements in 11 patients. Clear karyotype at molecular level could help provide an accurate evaluation of recurrent risk and guide prenatal diagnosis or reproductive planning.

Structural variation of the malaria-associated human glycophorin A-B-E region

BackgroundApproximately 5% of the human genome shows common structural variation, which is enriched for genes involved in the immune response and cell-cell interactions. A well-established region of extensive structural variation is the glycophorin gene cluster, comprising three tandemly-repeated regions about 120 kb in length and carrying the highly homologous genes GYPA, GYPB and GYPE. Glycophorin A (encoded by GYPA) and glycophorin B (encoded by GYPB) are glycoproteins present at high levels on the surface of erythrocytes, and they have been suggested to act as decoy receptors for viral pathogens. They are receptors for the invasion of the protist parasite Plasmodium falciparum, a causative agent of malaria. A particular complex structural variant, called DUP4, creates a GYPB-GYPA fusion gene known to confer resistance to malaria. Many other structural variants exist across the glycophorin gene cluster, and they remain poorly characterised.ResultsHere, we analyse sequences from 3234 diploid genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection of these variants using fibre-FISH and breakpoint mapping at the sequence level. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. We show that almost all variants can be explained by non-allelic homologous recombination and by comparing the structural variant breakpoints with recombination hotspot maps, confirm the importance of a particular meiotic recombination hotspot on structural variant formation in this region.ConclusionsWe identify and validate large structural variants in the human glycophorin A-B-E gene cluster which may be associated with different clinical aspects of malaria.

Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation

Balanced chromosomal rearrangements are usually associated with a normal phenotype, although in some individuals, phenotypic alterations are observed. In these patients, molecular characterization of the breakpoints can reveal the pathogenic mechanism, providing the annotation of disease-associated loci and a better genotype-phenotype correlation. In this study, we describe a patient with a balanced reciprocal translocation between 4q27 and 7p22 associated with neurodevelopmental delay. We performed cytogenetic evaluation, next-generation sequencing of microdissected derivative chromosomes, and Sanger sequencing of the junction points to define the translocation's breakpoints at base pair resolution. We found that the PCDH10 and TNRC18 genes were disrupted by the breakpoints at chromosomes 4 and 7, respectively, with the formation of chimeric genes at the junction points. Gene expression studies in the patient's peripheral blood showed reduced expression of TNRC18, a gene with unknown function and clinical significance. PCDH10 plays a role in the development of the nervous system and might be involved with the patient's neurodevelopmental delay. In this study, the full molecular characterization of the junction points was shown as an efficient tool for fine breakpoint mapping in balanced translocations in order to unmask gene disruptions and investigate the potential pathogenic role of the disrupted genes.

Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype.

De novo balanced chromosomal aberrations (BCAs), such as reciprocal translocations and inversions, are genomic aberrations that, in approximately 25% of cases, affect the human phenotype. Delineation of the exact structure of BCAs may provide a precise diagnosis and/or point to new disease loci. We report on six patients with de novo balanced chromosomal translocations (BCTs) and one patient with a de novo inversion, in whom we mapped breakpoints to a resolution of 1 bp, using shallow whole-genome mate pair sequencing. In all seven cases, a disruption of at least one gene was found. In two patients, the phenotypic impact of the disrupted genes is well known (NFIA, ATP7A). In five patients, the aberration damaged genes: PARD3, EPHA6, KLF13, STK24, UBR3, MLLT10 and TLE3, whose influence on the human phenotype is poorly understood. In particular, our results suggest novel candidate genes for retinal degeneration with anophthalmia (EPHA6), developmental delay with speech impairment (KLF13), and developmental delay with brain dysembryoplastic neuroepithelial tumor (UBR3). In conclusion, identification of the exact structure of symptomatic BCTs using next generation sequencing is a viable method for both diagnosis and finding novel disease candidate genes in humans.

Abstract P6-08-13: Personalized and cost-effective detection of copy number variants by molecular-barcode next-generation sequencing and long-read nanopore sequencing

Abstract Background: Germline copy number variants (CNV) of hereditary breast and ovarian cancer genes are a known class of clinically significant mutations. However, failure to detect CNV is a known limitation of Sanger sequencing and conventional amplicon next-generation sequencing (NGS). Multiplex ligation-dependent probe amplification (MLPA), while robust for CNV detection, is labor-intensive, costly to scale up and has limited breakpoint resolution at exon level only. We evaluated the clinical utility of molecular-barcode NGS and long-read nanopore sequencing in our genetic testing algorithm, specifically on CNV detection and breakpoint characterization of probands and family members. Methods: Both molecular-barcode NGS (BRCA1, BRCA2, TP53, PTEN, PALB2 and CDH1) and MLPA (BRCA1 and BRCA2) were performed in parallel on 200 high-risk breast and/or ovarian cancer probands and 11 CNV positive controls. CNV calling from MLPA and NGS data was performed by Coffalyser.Net and a novel in-house bioinformatics algorithm BAMClipper-SE, respectively. Nanopore amplicon or whole-genome sequencing was attempted to map the exact breakpoint of CNV controls and any newly identified CNV positive probands (up to May 2019). Personalized breakpoint PCR test for specific CNVs was designed and validated on probands and subsequently applied to corresponding family members for carrier testing. Results: Molecular-barcode NGS was 100% sensitive in detecting all BRCA1/2 CNVs from 11 positive controls. A total of 4 BRCA1/2 CNVs were detected by NGS from the 200 probands and matched the corresponding MLPA results. In addition, a PALB2 CNV (exons 4-6 deletion) was also detected by NGS during the parallel comparison. Up to May 2019, a total of 22 probands with detectable CNV in BRCA1, BRCA2, PALB2 or CHEK2 were accrued. Exact CNV breakpoint at nucleotide resolution was identified from 20 probands by nanopore and Sanger sequencing (BRCA1 n=12, BRCA2 n=5, PALB2 n=2 and CHEK2 n=1). High-resolution breakpoint mapping was applicable to inform variant pathogenicity and to enable recurrent CNV identification. Personalized breakpoint PCR designed for the 20 probands were applied to 42 family members, of whom 16 were CNV carriers and 26 were non-carriers. Breakpoint PCR results and any available MLPA results of these family members were 100% concordant. Conclusion: Molecular-barcode NGS allows a streamlined workflow to detect both sequence mutations and CNVs. It proves to be a reliable and cost-effective replacement of BRCA1/2 MLPA in genetic testing algorithm of new probands. Simultaneously the NGS workflow expands CNV detection coverage to additional genes (e.g. PALB2) without costly scale-up of MLPA gene panels. Nanopore sequencing is a practical alternative to MLPA in orthogonal validation of newly detected CNV. The high-resolution breakpoint mapping transforms CNV carrier testing to a personalized, simple and cost-effective breakpoint PCR. Citation Format: Ava Kwong, Chun H Au, Dona N Ho, Elaine YL Wong, Yvonne Chung, Fian BF Law, Cecilia YS Ho, Jiawei Chen, Isabella W Cheuk, Vivian Y Shin, Tsun L Chan, Hextan YS Ngan, Edmond SK Ma. Personalized and cost-effective detection of copy number variants by molecular-barcode next-generation sequencing and long-read nanopore sequencing [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-13.

Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants

BackgroundWe investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.MethodsGenomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.ResultsHigh-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).ConclusionsThese data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

Validating Gene Fusion as the Source of Chimeric RNAs.

While chimeric RNAs may be generated by transcription-mediated mechanisms such as "trans-splicing" and "read-through/splicing" (Zhang et al., Cancer Discov 2:598-607, 2012; Zaphiropoulos, Front Genet 2:92, 2011; Li et al., Cell Cycle 8:218-222, 2009; Jividen and Li, Genes Chromosomes Cancer 53:963-971, 2014; Jia et al., Trends Cancer 2:475-484, 2016), most highly expressed chimeric RNA species identified so far are usually transcribed directly from fusion genes. Fusion genes, formed by joining two parental genes as a result of chromosomal rearrangements, are hallmarks of many types of cancer. Various methods can be deployed for confirming a particular fusion gene as the original source of transcribed chimeric RNA. In this chapter, we discuss commonly used methodologies such as genomic DNA breakpoint mapping and fluorescent in situ hybridization useful for confirming gene fusion events. In addition, we highlight the development of new technologies such as de novo whole-genome optical mapping suitable for global analysis of genomic arrangements. The advantages and disadvantages of each of these technologies are presented and compared.

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.

3. SELECTIVE TRANSFER OF EUPLOID NONCARRIER EMBRYOS WITH THE USE OF LONG-READ SEQUENCING IN PREIMPLANTATION GENETIC TESTING FOR RECIPROCAL TRANSLOCATION

Introduction Balanced reciprocal translocation is one of the most common chromosomal abnormalities in humans. Carriers are usually phenotypically normal but are at an increased risk of infertility, recurrent miscarriage or having affected children. Preimplantation genetic testing for chromosomal structural rearrangement (PGT-SR) offers a way to screen against embryos with unbalanced translocation during in vitro fertilization (IVF) treatment cycles. In this case report, we demonstrated a new approch to discriminate carrier from noncarrier embryos. First, high-resolution breakpoint mapping was performed using long-read sequencing, followed by breakpoint PCR. In the treatment cycle, PGT-SR was performed by NGS and euploid noncarrier embryos were selected using breakpoint PCR. Material & methods a) Long-read sequencing A couple requested PGT-SR because the wife, aged 33 years, was known to be a carrier of balanced translocation [46,XX,t(7:13)(p13;q12.3)]. A sequencing library (1D) was prepared on the genomic DNA of the wife using the SQK-LSK-108 kit (Oxford Nanopore, UK) according to the manufacturers's protocol. 1D sequencing was performed on a MinION flow cell (R9.4, Oxford Nanopore) with a 48-hour protocol on MinKNOW (2.2.12). Local base calling was performed by Albacore 2.3.1. After sequence alignemnt, breakpoints were determined by NanoSV 1.2.0. b) Breakpoint PCR Based on the predicted breakpoints that correlated with cytogenetic report, breakpoint PCR primers were designed and validated using genomic DNA of couple and the sequences flanking the breakpoints were confirmed by Sanger sequencing. c) PGT-SR Whole genomic amplification (WGA, REPLI-g Single Cell kit) was performed followed by PGT-SR by NGS (VeriSeq-PGS, Illumina). Breakpoint PCR primers validated in (b) were used to discriminate carrier from noncarrier embryos. Results Nanopore sequencing obtained an average read length of 7000 bases. The total no. of based aligned to human genome was 16 Giga bases. Breakpoints were accurately predicted on chromosomes 7 and 13. Eighteen oocytes were retrieved and 15 were fertilized. Trophectoderm biopsy was performed on 9 blastocyts. After PGT-SR, there were 2 euploid embryos and 2 mosaic embryos. Four embryos were unbalanced carriers and one embryo with no result due to failure in WGA. Breakpoint PCR was used to discriminate carrier from noncarrier embryos. Both euploid embryos and one mosaic embryo were noncarriers while the other mosaic embryo was a carrier. One euploid noncarrier blastocytst was replaced in FET cycle. The patient is pregnant and has been referred to prenatal clinic for follow up (10-week at the time of abstract submission). Conclusion Long-read sequencing enables accurate high-resolution breakpoint mapping directly on balanced reciprocal translocation carriers. In addition, nanopore sequencing required simple library preparation (90 minutes) and low capital cost, therefore the cost of preclincial test (nanopore sequencing and validation of breakpoint PCR) for the first PGT-SR cycle is approximately US$ 1000. In conclusion, we demonstrated a new method to discriminate carrier from noncarrier embryos with the use of nanopore sequencing and breakpoint PCR. This method allows patients to prioritize the transfer of euploid noncarrier embryos.