CING studies ABT with the help of VarSome Clinical

Saphetor caught up with Constantia Aristidou from The Cyprus Institute of Neurology & Genetics (CING), that highlighted the breadth and scope of VarSome Clinical in their recently published paper; Exploring the Genetic Causality of Discordant Phenotypes in Familial Apparently Balanced Translocation Cases Using Whole Exome Sequencing.

The Cyprus Institute of Neurology & Genetics (CING) is a private, non-profit, bi-communal, medical, research and academic center. In their latest paper, in order to study Apparently Balanced Translocations (ABTs), they performed Whole Exome Sequencing (WES) with the support of VarSome Clinical. 

Constantia Aristidou, one of the paper’s main authors, is an Associate Scientist at CING. In this blog post, she tells us more about their research.

Can you explain what familial apparently balanced translocations are and what effect they can have?

CA: Apparently balanced translocations (ABTs) involve the exchange of segments between chromosomes without visible gain or loss of genetic material. Consequently, the great majority of ABT carriers are phenotypically normal. However, in ~27% of non-inherited cases (de novo), there is an association with congenital anomalies, intellectual disability and other abnormal developmental phenotypes [1]. Direct gene disruption, cryptic imbalances and long-range position effect have been demonstrated to underlie such phenotypic abnormalities in de novo ABT carriers [2,3]. In contrast, familial ABTs are those that have been inherited from a healthy or an affected parent. In balanced offspring of phenotypically normal familial ABT carriers, the phenotypic risk is considered very low. However, there are many reported cases of affected offspring that inherited identical ABTs from healthy parents. In such families with discordant phenotypes, the common familial ABT appears coincidental and unrelated to phenotype presentation, after excluding any cryptic complexity in the affected offspring [4]. Instead, patient-specific causal gene variants, occurring independently from the common translocations, often explain differential phenotypes in such ABT families [5].

Now that this study supports your previous findings, what impact can WES have in the clinic when examining these types of cases?

CA: In our recent publication, a follow-up investigation was performed in four families with discordant phenotypes and identical ABTs [4,5]. Whole exome sequencing (WES) was implemented as a diagnostic tool to identify the underlying genetic etiology of the patients’ phenotypes. Our study identified novel candidate variants potentially explaining phenotypic differences, and occurring independently from the common familial translocations, in three out of four families [5]. WES can be therefore recommended as a valuable tool to successfully resolve familial ABT cases where cryptic complexity has been excluded.

Can you tell us how your in-house pipeline and VarSome Clinical work together and how that leads to validation via Sanger sequencing?

CA: In our research project, we performed WES data analysis using an in-house bioinformatics exome analysis pipeline, which is based on the GATK best practices, alongside a reanalysis using VarSome Clinical. While both approaches could identify the same candidate variants, the automation offered by VarSome Clinical for variant annotation and classification, as well as dynamic and algorithmic filtering, has enabled time-efficient analysis of WES data without requiring specialized bioinformatic skills. All rare (MAF <0.01) candidate variants disrupting clinically-relevant genes, matching the patients’ phenotypic description and suspected mode of inheritance, and having high levels of evidence for pathogenicity were validated with Sanger sequencing before reporting back to the referring physician.

What motivated you to work on familial ABTs?

CA: The Department of Cytogenetics and Genomics of The Cyprus Institute of Neurology and Genetics performs diagnostic services, research and education in chromosomal abnormalities and genomic disorders. It serves as a referral center for preimplantation, prenatal and postnatal diagnosis of chromosomal disorders as well as other genetic diseases and syndromes, including intellectual disability, multiple congenital anomalies and infertility. One of the main research activities of the Department is accurate breakpoint mapping in de novo and familial apparently balanced translocations using next-generation sequencing. This included a number of referred familial ABT cases with discordant phenotypes that remained unresolved after initial karyotype and array-CGH analyses. 

Currently, there is very limited literature regarding the genetic causality of familial ABTs in cases where one member is clinically affected, and the other(s) is/are phenotypically normal. This leads to several diagnostic dilemmas about prenatal diagnosis and phenotypic risk. We performed further investigations using whole-genome mate-pair sequencing (WG-MPS) for accurate breakpoint mapping to shed some light on the underlying mechanisms in this group of familial ABT cases. This study revealed that the common translocations were identical between affected and non-affected individuals within the same family, while cryptic chromosomal complexity was excluded in the patients [4]. Instead, patient-specific causal variants, occurring independently from the common familial translocation, could explain the differential phenotypes [5]. Investigation of additional ABT families with discordant phenotypes will further support our findings and help to accurately describe the underlying genetic mechanisms, thus providing more precise phenotypic risk estimations and better genetic counseling.

Constantia Aristidou, Associate Scientist, CING

Dr Constantia Aristidou holds a BSc in Biochemistry and an MSc in Toxicology, both completed at the University of Surrey, UK. She then continued her doctoral studies by pursuing a PhD degree in Medical Genetics at the Postgraduate School of The Cyprus Institute of Neurology and Genetics (CING), under the supervision of Prof. Carolina Sismani.

Her PhD research project at the Department of Cytogenetics and Genomics, focused on accurately mapping the breakpoints in apparently balanced translocation carriers using WG-MPS. As part of her PhD, she also participated in an Erasmus+ Traineeship program in collaboration with the University of Copenhagen, Denmark where she received training on the WG-MPS technique and data analysis, including derivative chromosome reconstruction of complex chromothripsis cases. In 2018, she joined the High Throughput Arrays team of the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford, UK. Since 2020, she is an Associate Scientist at the Department of Clinical Genetics and Genomics of CING; her research interests include the elucidation of the genetic basis of rare diseases including rare intellectual disability, congenital malformations, and neurodevelopmental disorders. Currently, she is also an Associate Faculty of the Postgraduate School of CING. 

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1. Halgren, C.; Nielsen, N.M.; Nazaryan-Petersen, L.; Silahtaroglu, A.; […] Talkowski, M.E.; Bak, M.; Tommerup, N.; Bache, I. Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes. Am. J. Hum. Genet. 2018, 102, 1090-1103.
2. Aristidou, C.; Theodosiou, A.; Bak, M.; Mehrjouy, M.M.; […] Tommerup, N.; Sismani, C. Position effect, cryptic complexity, and direct gene disruption as disease mechanisms in de novo apparently balanced translocation cases. PLoS One 2018, 13, e0205298-e0205298.
3. Sismani, C.; Kitsiou-Tzeli, S.; Ioannides, M.; Christodoulou, C.; […] Kosmaidou-Aravidou, Z.; Patsalis, P.C. Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype. Mol. Cytogenet. 2008, 1, 15.
4. Aristidou, C.; Koufaris, C.; Theodosiou, A.; Bak, M.; […] Tommerup, N.; Sismani, C. Accurate breakpoint mapping in apparently balanced translocation families with discordant phenotypes using whole genome mate-pair sequencing. PLoS One 2017, 12, e0169935-e0169935.
5. Aristidou, C.; Theodosiou, A.; Alexandrou, A.; Papaevripidou, I.; […] Tanteles, G.A.; Sismani, C. Exploring the Genetic Causality of Discordant Phenotypes in Familial Apparently Balanced Translocation Cases Using Whole Exome Sequencing. Genes 2022, 14, 82.