Family-based germline sequencing in children with cancer

Oncogene (2019) 38:1367–1380 https://doi.org/10.1038/s41388-018-0520-9 REVIEW ARTICLE Family-based germline sequencing in children with cancer Michaela Kuhlen Arndt Borkhardt 1 ● Julia Taeubner1 Triantafyllia Brozou1 Dagmar Wieczorek2 Reiner Siebert3 ● ● ● ● 1 1234567890();,: 1234567890();,: Received: 19 March 2018 / Revised: 22 August 2018 / Accepted: 4 September 2018 / Published online: 10 October 2018 © The Author(s) 2018. This article is published with open access Abstract The discovery of cancer-predisposing syndromes (CPSs) using next-generation sequencing (NGS) technologies is of increasing importance in pediatric oncology with regard to diagnosis, treatment, surveillance, family counselling and research. Recent studies indicate that a considerable percentage of childhood cancers are associated with CPSs. However, the ratio of CPSs that are caused by inherited vs. de novo mutations (DNMs), the risk of recurrence, and even the total number of genes, which should be considered as a true cancer-predisposing gene, are still unknown. In contrast to sequencing only single index patients, family-based NGS of the germline is a very powerful tool for providing unique insights into inheritance patterns (e.g., DNMs, parental mosaicism) and types of aberrations (e.g., SNV, CNV, indels, SV). Furthermore, functional perturbations of key cancer pathways (e.g., TP53, FA/BRCA) by at least two co-inherited heterozygous digenic mutations from each parent and currently unrecognized rare variants and unmeasured genetic interactions between common and rare variants may be a widespread genetic phenomenon in the germline of affected children. Therefore, family-based trio sequencing has the potential to reveal a striking new landscape of inheritance in childhood cancer and to facilitate the integration and efforts of individualized treatment strategies, including personalized and preventive medicine and cancer surveillance programs. Consequently, cancer genetics is becoming an increasingly common approach in modern oncology, so trio-sequencing should also be routinely integrated into pediatric oncology. Introduction Lifestyle factors such as UV exposure, smoking and alcohol consumption are major contributors to cancer development in adults. As these factors are negligible in children, one can speculate that a substantial (and previously underestimated) number of pediatric cancers must be attributable to inherited mutations in cancer predisposition genes (CPGs), currently unrecognized rare variants, and the combination of inherited * Michaela Kuhlen 1 Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children’s Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany 2 Institute of Human Genetics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany 3 Institute Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany susceptibility and environmental factors such as influences during pregnancy and infection exposure [1]. Recent studies indicate that 8.5% of childhood cancers are associated with cancer predisposition syndromes (CPSs), including 16.7% of non-central nervous system solid tumors, 8.6% of central nervous system tumors and 4.4% of leukemias [2]. In fact, it is probable that the percentage of cancers linked to CPSs in children is even higher. In a recent pan-cancer study by the International Cancer Genome Consortium, likely deleterious variants of 109 known autosomal CPGs were shown to affect 11% of 2642 cancer patients across 39 cancer types. This number increased to 20% of donors when considering germline pathogenic variants in 183 DNA damage-response genes, which do not have a presently established link to cancer risk [3]. However, the exact proportion of children and adolescents with a malignancy that is attributable to an underlying CPS is still unclear. A major reason for this is the fact that most published data on this topic relies on sequencing of only index patients, i.e., the affected children. These data does not take into account the family context, and, therefore, valuable discovery and interpretation information are disregarded. The most well-known mutated genes in childhood cancer are TP53, followed by APC, 1368 BRCA2, NF1, PMS2, RB1, and RUNX1 [2]. According to a recent study, affected families show great interest in genetic testing for an underlying CPSs [4]. Unexpectedly, the predictive value of the family history is still unclear, as related studies report inconsistent results [2, 5]. Additionally, the proportion of de novo vs. inherited germline mutations in CPGs is widely undetermined resulting in considerable uncertainty about recurrence risk in siblings. For example, the prevalence of TP53 mutations has been estimated to be anywhere from 1 in 20,000 up to 1 in 5000, with 7–24% being expected to occur de novo [6]. In contrast, ~50% of the mutations in NF1 originate de novo [7]. The identification of children affected with CPSs could have direct impact on therapeutic cancer management. For instance, Li–Fraumeni syndrome (LFS) patients have an increased risk of radiation-induced secondary malignancies [8]. Next-generation germline sequencing of parent-child trios Genetic variations arise through new mutations; thus, determining the properties and rates of mutations is fundamental to understanding the genetics of human disease. Due to technical limitations, the number of loci studied was limited in past mutation rate analyses. However, advances in sequencing technology rapidly replaced classic molecular diagnostics, and the number of its applications has increased immensely in the past decade. Next-generation sequencing (NGS) provides a powerful tool to identify genomic variations associated with specific diseases, including cancer. With increasing adoption of whole-exome sequencing (WES) and whole-genome sequencing (WGS), the detection of novel, previously uncharacterized sequence variants has increased and will continue to increase dramatically in the near future. Today, using NGS approaches, the occurrence of all types of mutations, including single-nucleotide variants (SNVs), small insertions and deletions (indels) and also large structural variations (SVs) can be analyzed. Compared to WES, WGS is the better technique to detect many types of variants, including indels, non-coding variants, CNVs, repeat expansions, and SVs (such as inversions and translocations) and can also reveal pathogenic mutations in the non-coding part of the genome (promoter regions, introns, enhancer and regulatory regions). However, both methods are hampered by challenges in methodical approaches (e.g., depth, coverage), data analysis and interpretation, storage of vast amounts of data, and relatively high costs. M. Kuhlen et al. Typically, in cancer syndromes only the single patient is sequenced. However, in order to test hereditary CPSs and family members at high-risk, WES of (...truncated)