Background

The clinical phenotype of 1q43-q44 deletion or duplication is highly variable, due to the size of the segment and the number of genes involved. The phenotypic features of patients with 1q43-44 deletion include moderate to severe mental retardation, development retardation, microcephaly, corpus callosum dysplasia, epilepsy and dysmorphic features. In individuals with 1q43-q44 duplication, the most recognizable features are macrocephaly, mental retardation, epilepsy and mild malformation. Interstitial deletions of the long arm of chromosome 1 involving only the 1q43-q44 region have been reported in more than 80 patients, with most of these patients arising de novo [1,2,3,4,5,6,7]. A few individuals exhibiting pure 1q43-q44 interstitial duplication have been reported [8,9,10,11,12,13,14,15]. However, both pure 1q43-q44 deletion and duplication occurring in a family have not been reported.

Several cytogenetic and molecular techniques have been applied to detect the deletion or duplication of pathogenic copies, such as G-banding, fluorescence in situ hybridization (FISH) and chromosomal microarrays (CMAs). However, these techniques present individual limitations and can often be technically challenging. Recent studies have shown that whole-genome sequencing (WGS) with a carefully designed data analysis pipeline is a more powerful tool for detecting chromosomal abnormalities due to its higher resolution and the ability to detect balanced translocations and small imbalances that cannot be detected with CMAs [16].

Insertional translocations are complex chromosomal rearrangements that require at least three breakpoints in the involved chromosome, with an incidence of 1:80,000 in live births [17]. Insertional translocations can be divided into simple intrachromosomal or interchromosomal insertional translocations and complex chromosomal insertional translocations [18]. Nowakowska et al. [19] found that 2.1% of de novo copy number variations (CNVs) are actually inherited from a parental balanced insertional translocation. However, this percentage may represent an underestimate because not all parental data may be collected in these studies, and due to technical limitations, some small imbalances have not yet to be discovered. However, WGS can identify nearly all cryptic chromosomal abnormalities or complex rearrangements present in the genome, in addition to characterizing translocation breakpoints at the nucleotide level.

Herein, we present a rare family in which two siblings presented with congenital anomalies. These two individuals harboured an approximately 6.0-Mb deletion or duplication of 1q43-q44 inherited from their mother, a carrier of a cryptic balanced insertional translocation. We further precisely identified the corresponding breakpoints via WGS and Sanger sequencing. This is the first report of the detection of an insertional translocation associated with 1q43-q44 deletion and duplication using WGS.

Case presentation

The proband (III-3, Fig. 1a) is the third child of a non-consanguineous, healthy couple. She is a 6-year-old Chinese girl with profound developmental delay, microcephaly, agenesis of the corpus callosum, epilepsy, language delayed and hearing impairment. She was born at full term after an uncomplicated spontaneous vaginal delivery with a normal birth weight (3400 g). She experienced seizures four times at 3 months of age, with spontaneous remission occurring after more than 10 s. At 7 months of age, she began turning over but could not grasp and sit without support. Intellectual evaluation with the Gesell Development Schedule (GDS) showed that her developmental quotient at 7 months of age was equivalent to that of a 10-week-old infant, indicating significant growth retardation [20]. The detailed data are shown in Additional file 1: Table S1. Brain magnetic resonance imaging (MRI) indicated absence of the corpus callosum and enlargement of the posterior horn of all three ventricles bilaterally. The results of brainstem auditory evoked potential (BAEP) analysis indicated bilateral hearing impairment. At 6 years of age, the proband presented with microcephaly (47.2 cm, <− 2 SD) and began learning to walk but could not speak (Fig. 1b).

Fig. 1
figure 1

a Three-generation pedigree of the family with the proband (III-3) indicated by an arrow. Affected individuals are indicated with black, horizontal or vertical lines in the symbols, including III-3: monosomy 1q43-q44 and III-4: trisomy 1q43-q4; carriers of the cryptic insertion (II-5, III-2) are indicated with dots in the symbols. G-banding analysis was not performed for the elder brother (III-1) due to a lack of sample. b and c Facial profiles of the proband and younger brother at 6 years and 3 months, respectively. The proband presented with microcephaly, and the younger brother presented with macrocephaly. d G-banding analysis of the proband (III-3) at a band resolution of ∼400 showed no visual abnormal karyotype. e The results of SNP-array analysis. The proband (III-3) harbuored an interstitial 1q43-q44 deletion (upper), and the younger brother (III-4) carried an interstitial 1q43-q44 duplication (down). The deletion and duplication regions are indicated by red arrows. f The FISH results for the mother (II-5) with WCP1/14 (left) and WCP1/CEP14 (right) probes. Chromosome 1 is shown in green, and the chromosome 14 is shown in red (left); WCP1 and CEP14 are shown in green and red, respectively (right). The inserted segment is indicated by the white arrows

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The elder brother (III-1, Fig. 1a) presented similar features to the proband, such as developmental delay, cerebral palsy and intracranial haemorrhage after birth, and died at 5 years of age. The elder sister (III-2, Fig. 1a) has a normal phenotype. The younger brother (III-4, Fig. 1a) is the fourth child. At 34 weeks of gestation, an MRI scan of the foetal head and ultrasonography revealed no obvious abnormalities. He was born at term via caesarean section after an uneventful pregnancy and exhibited a normal birth weight (3000 g). At the age of 3 months, he presented macrocephaly (Fig. 1c) and his head circumference was 44.5 cm (> + 2 SD). His developmental quotient was equivalent to that of an 11-week-old infant, with testing demonstrating a borderline full-scale developmental quotient (85), and he exhibited developmental delay in gross motor functions (Additional file 1: Table S1).

Materials and methods

G-banding at a band resolution of ∼400 was performed on metaphase peripheral blood lymphocytes obtained from the proband (III-3) and four other family members (II-4, II-5, III-2 and III-4) according to the laboratory’s protocols. DNA was isolated from their peripheral blood lymphocytes using the QIAamp® DNA blood midi kit (QIAGEN, Hilden, Germany). Single-nucleotide polymorphism (SNP) array analysis was performed using Cytoscan 750 K chips (Affymetrix, Santa Clara, CA, USA) as we described in a previous report [1 for a comparison of phenotypic differences. In the present study, the proband exhibiting 1q43-q44 deletion was found to show some characteristic features, such as profound developmental delay, microcephaly, agenesis of the corpus callosum, epilepsy, and unusual hearing impairment. The younger brother carrying this duplicated region presented with macrocephaly and mild developmental delay in gross motor functions. We speculate that some symptoms have not yet emerged in this child because he is very young or that other symptoms might be very mild.

Table 1 Features presented in patients with 1q43-q44 deletion and duplication
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Many patients with 1q43-q44 deletion or duplication including part or all of the regions identified in our patients have been reported. However, the identification of well-detailed genotype-phenotype correlations is hindered by inaccurate map** of the detailed breakpoints, due to the use of karyoty** or FISH analyses, before the era of high-resolution cytogenetics and the fact that those patients exhibit affected 1q43-q44 regions that differ in size and location. We identified a cryptic chromosomal rearrangement in the mother (II-5) via WGS and confirmed it via FISH. Moreover, we accurately mapped the breakpoints with a combination of a carefully designed data analysis pipeline and Sanger sequencing. The combination of these molecular and cytogenetics techniques characterized the breakpoints at the base-pair level and identified two intron-disrupted genes, EFCAB2 and PRKCH, that have observable clinical phenotypes.

In our study, the two patients with 1q43-q44 deletion or duplication presented congenital anomalies, and the proband exhibited a more serious phenotype than her younger brother. Thus, dosage effects or pathogenic variants of some genes within 1q43-q44 likely contribute to their phenotypes. There are 20 known genes that lie within the 6.0-Mb genomic region, 9 of which are indicated to be disease genes in the Online Mendelian Inheritance in Man (OMIM) database according to NCBI Map Viewer (https://www.ncbi.nlm.nih.gov/mapview). The details of these 9 OMIM disease genes and their clinical characteristics and inheritances are shown in Table 2. We analysed the dominant genes for potential dose-effect phenotypes. The AKT3 gene encodes a serine-threonine kinase belonging to the protein kinase B family that is highly expressed in the brain tissue of humans and rodents [24]. The expression of this gene is significantly decreased in the brain and corpus callosum of AKT3-null mice [25], and some studies in humans and mice have demonstrated that AKT3 plays an important role in controlling the sizes of cells and organs [26, 27]. Boland et al. [5] reported a patient with a 46,XY,t(1;13)(q44;q32) translocation who presented postnatal microcephaly and agenesis of the corpus callosum and demonstrated that AKT3 was a candidate gene for these phenotypes. Another study showed that a critical region comprising CEP170, SDCCAG8 and AKT3 was associated with microcephaly [4]. However, among patients with 1q43-q44 duplication, macrocephaly is observed in patients exhibiting AKT3 gene duplication [8]. The ZBTB18 gene encodes a protein that acts as a transcriptional repressor of key pro-neurogenic genes. ** of a new autosomal recessive non-syndromic hearing impairment locus (DFNB45) to chromosome 1q43-q44. Clin Genet. 2008;73(4):395–8." href="/article/10.1186/s13039-018-0371-7#ref-CR34" id="ref-link-section-d51247658e1468">34] found that homozygosity of 1q43-q44 deletion might cause non-syndromic hearing impairment and deemed a region containing CHLM, OPN3 and MAP1LC3C a new autosomal recessive non-syndromic hearing impairment locus. In the present study, the proband also showed bilateral hearing impairment, but it may have been caused by genes of unknown function or other pathogenic factors. The elder brother presented a similar phenotype to that of the proband, and we cannot rule out the possibility that he might have exhibited the same karyotype as the proband. Analysis of families harbouring translocations via WGS and the associated analysis strategy can help us to gain a better understanding of the relationship between phenotype and karyotype, in addition to providing evidence for genetic and reproductive counselling, which may be especially important for the unaffected mother and sister, who are carriers of the insertional translocation.

Table 2 OMIM genes deleted or duplicated in our patients, with related phenotypes and model of inheritance
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Accurate breakpoint map** not only facilitates the elucidation of the relationship between phenotype and karyotype but also offers insights into the possible mechanisms involved in the generation of balanced translocations. In this study, the molecular characterization of the breakpoints showed that they occurred in homologous regions between two non-homologous chromosomes, in addition to demonstrating the presence of small imbalances around the breakpoint site. These findings suggest that the translocation was likely generated through microhomology-mediated repair (MHMR) of double-strand breaks.

Conclusion

In summary, we report a rare family in which two siblings exhibit pure 1q43-q44 deletion or duplication caused by a maternal balanced insertional translocation. Our study demonstrated that WGS is a powerful tool that allows rapid and accurate map** of translocation breakpoints at the nucleotide level and could provide useful information for genetic and reproductive counselling for balanced translocation carriers. In addition, the results may help us to better understand detailed karyotype-phenotype correlations, and investigate the possible mechanisms underlying the generation of translocations.