Analysis of complex chromosomal rearrangements using a combination of current molecular cytogenetic techniques

Clinical outcomes of complex chromosomal rearrangement carriers and couples both harbouring chromosomal rearrangements who undergo preimplantation genetic testing

RESEARCH QUESTION

What are the clinical outcomes for carriers of complex chromosomal rearrangements (CCR) and couples with both partners harbouring chromosomal rearrangements who undergo preimplantation genetic testing (PGT)?

DESIGN

This case series included eight couples with atypical chromosomal rearrangements (five CCR carriers and three couples with both partners harbouring chromosomal rearrangements) who underwent blastocyst trophectoderm biopsy as well as PGT. The clinical outcomes of the transfers were recorded.

RESULTS

PGT was performed on eight carriers of atypical chromosomal rearrangements. A total of 223 oocytes (157 from CCR carriers and 66 from couples where both partners harboured chromosomal rearrangements) were retrieved from the eight participants. Thirty-three (14.8%) blastocysts were obtained, of which 5 (15.1%) were euploid, 2 (6.1%) were mosaic and the remaining 26 (78.8%) were aneuploid. For CCR carriers, there were 3, 0 and 21 euploid, mosaic and aneuploid blastocysts, respectively, and for couples where both partners harboured chromosomal rearrangements there were 2, 2 and 5. Four euploid embryos and one mosaic embryo were successfully transferred, but none of them produced a pregnancy.

CONCLUSIONS

Carriers of atypical chromosomal rearrangements had a high probability of creating aneuploid embryos, and therefore PGT showed a low usefulness for CCR carriers. Thus, spermatozoa/egg donation IVF was advocated. Couples with both partners harbouring chromosomal rearrangements had a reasonable rate of transferable embryos and may benefit from PGT.

Prenatal diagnosis of chromothripsis causing complex chromosomal rearrangement involving chromosomes 5, 7 and 11 leading to TWIST1 deletion and Saethre-Chotzen syndrome

OBJECTIVE

Prenatal detection of complex chromosomal rearrangements (CCR) is extremely rare, but is of great clinical importance, since CCR can be causative of different congenital disorders. We present an exceptionally rare case of prenatally diagnosed Saethre-Chotzen syndrome (SCS) rising as a consequence of chromothripsis involving chromosomes 5, 7 and 11 and deletion of TWIST1 gene.

CASE REPORT

Brachycephaly, hypertelorism, flat face, micrognathia, relative macroglossia and small posterior fossa were noted on ultrasound examination at 28th gestational week. Fetal karyotyping revealed de novo translocation 46,XY,t(7;11)(p15.5;q21)dn. Chromosomal microarray showed presence of three microdeletions on chromosome 7 (7p21.1p15.3 including TWIST1, 7p12.1p11.2 and 7q21.11), and one on chromosome 5p12p11.

CONCLUSION

Use of advanced molecular diagnostic techniques in combination with cytogenetic methods allows for precise characterization of CCRs and detection of molecular mechanisms of their origin. Phenomenon of chromothripsis can be causative of rare genetic syndromes such as SCS.

Fusion Genes in Myeloid Malignancies

Fusion genes arise from gross chromosomal rearrangements and have been closely linked to oncogenesis. In myeloid malignancies, fusion genes play an integral role in the establishment of diagnosis and prognostication. In the clinical management of patients with acute myeloid leukemia, fusion genes are deeply incorporated in risk stratification criteria to guide the choice of therapy. As a result of their intrinsic ability to define specific disease entities, oncogenic fusion genes also have immense potential to be developed as therapeutic targets and disease biomarkers. In the current era of genomic medicine, breakthroughs in innovation of sequencing techniques have led to a rise in the detection of novel fusion genes, and the concept of standard-of-care diagnostics continues to evolve in this field. In this review, we outline the molecular basis, mechanisms of action and clinical impact of fusion genes. We also discuss the pros and cons of available methodologies that can be used to detect fusion genes. To contextualize the challenges encountered in clinical practice pertaining to the diagnostic workup and management of myeloid malignancies with fusion genes, we share our experience and insights in the form of three clinical case studies.

Characterization of cryptic complex chromosome rearrangements in balanced chromosomal rearrangement carriers and their PGT-SR clinical outcome assessments

Several reports have presented that balanced chromosomal rearrangements (BCRs) carriers with normal phenotypes may be carriers of complex rearrangements. However, the incidence and PGT clinical outcomes of cryptic complex chromosome rearrangements (CCCRs) in individuals with BCRs is remain unknown. We recruited a cohort of 1,264 individuals with BCR carriers from 2016 to 2021 at the Reproductive and Genetic Hospital of CITIC Xiangya. Peripheral blood was collected for karyotyping and genomic DNA extraction and the PGT-SR clinical outcomes of CCCRs carriers were analyzed and compared with those of BCR carriers. Our findings revealed that 3.6% (45/1,264) of BCR carriers had CCCRs, involving 3-25 breakpoints on 1-3 chromosomes. Furthermore, when mate-pair sequencing was employed, 63.3% (19/30) of CCCR carriers were found to have chromosome rearrangements that were different from those identified by the MicroSeq technique. And the transferable embryo rate of CCCR carriers with 3 chromosomes was significantly lower than that of CCCR carriers with only 1-2 chromosomes. In this research, we revealed that some of the BCR carriers were actually CCCR carriers, and the prognosis of PGT in CCCR carriers with one or two chromosomes is better than that of CCCR carriers with three chromosomes.

Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.

Identification of a familial complex chromosomal rearrangement by optical genome mapping

BACKGROUND

Complex chromosomal rearrangements (CCRs) are rare chromosomal structural variations, containing a variety of rearrangements such as translocation, inversion and/or insertion. With the development of cytogenetic and molecular genetic techniques, some chromosomal rearrangements that were initially considered to be simple reciprocal translocations in the past might eventually involve more complex chromosomal rearrangements.

CASE PRESENTATION

In this case, a pregnant woman, who had a spontaneous abortion last year, had abnormal prenatal test results again in the second pregnancy. Applying a combination of genetic methods including karyotype analysis, chromosomal microarray analysis, fluorescence in situ hybridization and optical genome mapping confirmed that the pregnant woman was a carrier of a CCR involving three chromosomes and four breakpoints, and the CCR was paternal-origin. Her first and second pregnancy abnormalities were caused by chromosomal microdeletions and microduplications due to the malsegregations of the derivative chromosomes.

CONCLUSIONS

We presented a rare familial CCR involving three chromosomes and four breakpoints. This study provided precise and detailed information for the subsequent reproductive decision-making and genetic counselling of the patient.