In this study, we identified the origins of 27 sSMCs, of which, eight sSMCs are being reported for the first time (Table 1). Of the 27 defined sSMC origins, 12 were derived from the Y chromosome and two from the X chromosome. The infertile patients showed azoospermia, and their original Y sSMCs were detected. Azoospermia factor (AZF), which is located on the long arm of Y (Yq11.23), regulates spermatogenesis . These patients had deletions of AZF-a region (the Sertoli cell-only syndrome), AZF-b region (sperm-maturation-arrest syndrome), or all AZF regions resulting in azoospermia. Thus, artificial insemination with donor sperm or adoption was suggested for clinical management. The pediatric patients carrying sSMCs from min(Y) or chromosome X or complex sSMCs from min(X) and min(Y) had similar characteristics to Turner syndrome; however, they had different phenotypes depending on their sSMC origins. The short arm of X harbors the short stature-homeobox gene (SHOX on Xp22.33) and lymphogenic gene (forkhead box P3, FOXP3 on Xp11.23), which are associated with stature and immunodeficiency or polyendocrinopathy . Patient W09834 with min(X) had a loss of FOXP3 and an immunological problem. A similar sSMC derived from r(X)(::p11.21→q13.1::) was reported in craniofrontonasal syndrome (CFNS) . The methyl-CpG binding protein-2 gene (MECP2 on Xq28) is located on the long arm of X. This gene correlates with RETT syndrome and the premature ovarian failure gene POF (POF1: Xq21→qter, POF2: Xq13.3→Xq21.1) . As the min(X) from patient W09834 (:p11.2→q13.2:) and r(X) from patient 92568 (::p11.23→q21.1::) did not contain SHOX and MECP2, both patients had growth retardation and a high risk of RETT syndrome. As they had the part of POFs, so being attention to ovarian function. Patient 96932 had a complex sSMC from min(X) and min(Y), resulting in a high risk of type II germ cell tumors [11, 12]. All the pediatric patients were recommended for individualized treatment according to their genotype-related phenotypes.
Our sSMC patients with the 47,XN,+mar karyotype typically had special duplication syndrome, and six sSMCs were identified from inv dul(15). The region 15(q11.2→q13.3) is a known hot breakpoint. This region harbors the GABAAR genes, the paternal gene SNRPN, and the maternal gene UBE3A, which regulate central neural system development and function . It was rare that two neocentric sSMCs derived from inv dup(18) had the same duplication fragment. There may be a hot breakpoint located at 18(p11.21). In region 18p, approximately 67 genes can contribute to the phenotypes, including AFG3L2, MC2R, and TGIF1, which are associated with developmental disorders [5, 6]. So, when taking care of patient 61259, pay attention to artificial feeding, avoiding infections, and evaluating affected organs and systems. The region of 20(p12.3→q11.22) comprises more than 2 hundred genes. Duplication of JAG1, BTBD3, and FLRT3, or ASXL1 induces Alagille syndrome, neurological dysfunction or chromatin remodeling [14, 15]. Patient 70963 with the genotype min(20)(:p12.3→q11.22:) showed moderate symptoms due to 60% mosaic.
The identification of sSMCs is vital in prenatal diagnosis. Of the 75 sSMC cases from this study, 23 were from fetuses with intrauterine growth retardation or abnormal ultrasonic structure, and seven fetal sSMC cases were found to have Y, 18, 9, 11, or 22 chromosomal origins. However, most sSMCs failed to define the original chromosome. Three fetal sSMCs from the Y chromosome needed careful evaluation. If the sSMCs correlated with androgyneity or AZF deletion, it was better to complete the pregnancy. However, if a fetus had an inv dup(18) genotype, termination of the pregnancy was suggested because of the i(18p) syndromes. Fetus 172990 had a duplicated region 9(p24.3→p13.1) that correlated with 9p duplication syndrome, which contains a potential autism spectrum disorder (ASD) and a normal IQ individual region [16, 17]. The sSMC of fetus 160246 was de novo and arose from a maternal balanced translocation t(11;22)(q23;q12), leading to three copies of 11(q23.3→q25). The sSMC derived from the inv dup(22) chromosome was also de novo. The fetus carrying this sSMC had similar regions to the 22q11.2 duplication syndrome (22DupS), which usually produces birth defects, such as congenital heart disease, hearing loss, hypophrenia, or high risk of psychosis (including autism) [18, 19]. A similar sSMC arising from inv dup(22)(q11.1 ~ 11.2) was reported with mild clinical signs .
Most sSMCs in fetuses are de novo, but a few are inherited from their parents. Thus, prenatal diagnosis and genetic counseling are critical. In our department, parents are asked to fill out a form to collect genetic information. Amniotic fluid is then submitted for both karyotyping and STR analysis. If an sSMC is diagnosed, further testing (e.g., NGS) is suggested, and the karyotypes of the parents are requested. If the parents are sSMC or translocation carriers, the fetus should take further testing. Preimplantation genetic screening (PGS) and preimplantation genetic diagnosis (PGD) would help reduce the chances of miscarriage.
Although several sequencing-related techniques were used in our study, there were still 30 sSMCs for which pathogenic information could not be generated. It is possible that the sequencing primers did not cover the sSMC regions in the MLPA or STR (AZF) methods. Also, inverted duplicated chromosomes (acrocentric chromosomes), isochromosomes, or minute chromosomes (centromere-nearby regions) might not have been detected by NGS due to the highly repeated sequences at the centromere regions, which will be improved in read depth, inducing read pair, split pair, or assembly-based analysis of NGS. Thus, a set of efficient techniques should be developed for further sSMC identification.