Apparently balanced chromosome rearrangements (ABCRs), including translocation, inversion, and insertion, involve exchange of genomic regions between non-homologous chromosomes without the gain or loss of genetic material. Simple ABCR is a two-breakage rearrangement, whereas complex chromosomal rearrangement (CCR) indicates chromosome abnormalities with three or more breakpoints. CCRs are rare in the population and only around 380 cases have been reported till date [1, 2]. Although most ABCRs are associated with a normal phenotype, they show high reproductive risks including infertility, recurrent spontaneous miscarriage, offspring with developmental defects and so on [3–5].
Reproductive risk increases with an increase in the number of breakpoints, and the particular characteristics of the rearrangement are associated with a peculiar mis-segregation mode in meiosis. For example, in reciprocal translocation, small translocated segments are prone to adjacent-1 segregation, small centric segments are apt for adjacent-2 segregation, and a small quadrivalent is usually associated with 3:1 disjunction. Indeed, some translocation carriers have more than 50% risk of bearing an abnormal child, whereas others have less than 1% risk. Therefore, it is crucial to accurately diagnose the karyotype for ABCR carriers with normal phenotype to determine the reproductive risk and choose an appropriate mode of bearing to avoid birth defects; these methods would include spontaneous pregnancy combined with prenatal diagnosis, preimplantation genetic testing, and use of donor sperm or egg.
Accurate cytogenetic diagnosis depends on the resolution of the testing techniques used. Previously, identification of ABCRs and further breakpoint confirmation were mainly based on high-quality G-banding of the metaphase chromosomes. However, due to the limited resolution of conventional cytogenetic technologies, only large structural rearrangements (> 5 Mb) could be identified. As a result, submicroscopic structural rearrangements could still be missed, even if high-resolution banding technology were used. Molecular testing techniques including FISH, CMA, and WGS, have greatly improved the ability to identify ABCRs [6–10]. Recent studies have shown that WGS can detect extremely complex balance rearrangements, including genome structural variations at the molecular level, which cannot be detected by conventional G banding techniques [11].
In this study, we analyzed the structural features of two cases of CCR using low pass whole-genome mate-pair sequencing in order to perform risk evaluation of ABCR carriers, and to examine complex genome structure variations in ABCRs detected by conventional cytogenetic technology.
Case presentation
Family 1: A couple (I-1 and I-2 in Fig. 1A), with the husband aged 32 years and the wife aged 27 years, visited our hospital for genetic counseling and birth guidance. They had conceived two natural pregnancies, which were terminated due to an abnormal fetus image during routine prenatal check-up. In the first pregnancy, B-ultrasonography at week 13 of pregnancy showed fetal growth retardation, equivalent to the size of a 12 W fetus, NT thickening, and a small amount of regurgitation in the reverse tricuspid valve of the venous catheter. In the second pregnancy, four-dimensional B-ultrasonography revealed a thickened fetal neck skin fold, lymphatic hydrocystoma of the neck, wide eye distance, short nasal bone, and hydramnios. Chromosome microarray (CMA) testing using SNP 750༫for amniotic fluid cells (AFC) showed that the fetus had an unbalanced chromosome rearrangement between chromosomes 10 and 19, i.e. arr(hg19)10q26.13q26.3(124,,625,736 − 135,426,386) × 1 (10.8 Mb deletion) and arr(hg19)19q13.41-q13.43(53,487,026–58,956,816) × 3 (5.5 Mb duplication), respectively. The pregnancy was subsequently terminated. Karyotype analysis showed a normal karyotype in the wife, whereas the husband was a complex translocation carrier with the karyotype 46,XY,t(6;10;19)(p22;q26;q13)(Fig. 1B). The husband had normal semen parameters.
Family 2: This couple (II-3 and II-4 in Fig. 2A), with both the husband and wife aged 36 years, visited our hospital to conceive a healthy baby. They had four natural pregnancies after marriage. The first and the third pregnancies were naturally miscarried in the first trimester due to unknown reasons. At the second pregnancy, they delivered a healthy daughter with a normal chromosome karyotype. At the fourth pregnancy, they gave birth to a boy with anal atresia, congenital heart disease, and penile scrotal transposition; his karyotype analysis at birth showed an unbalanced translocation 46,XY, der(11)t(6;11)(q13;p11.2)mat. He only survived for more than 100 days after birth. The male partner (II-3) in this couple had a normal karyotype, whereas the female partner carried a de novo translocation between chromosome 6 and chromosome 11; her karyotype was interpreted as 46,XX,t(6;11)(q13;p11.2)dn. The parents (I-1 and I-2) of the female partner both had a normal karyotype.