10p12.31-12.2 variants and risk of childhood acute lymphoblastic leukemia in a Chinese population

Genetic factors for differentiated thyroid cancer in French Polynesia: new candidate loci

Background

Populations of French Polynesia (FP), where France performed atmospheric tests between 1966 and 1974, experience a high incidence of differentiated thyroid cancer (DTC). However, up to now, no sufficiently large study of DTC genetic factors in this population has been performed to reach definitive conclusion. This research aimed to analyze the genetic factors of DTC risk among the native FP populations.

Methods

We analyzed more than 300 000 single nucleotide polymorphisms (SNPs) genotyped in 283 DTC cases and 418 matched controls born in FP, most being younger than 15 years old at the time of the first nuclear tests. We analyzed the genetic profile of our cohort to identify population subgroups. We then completed a genome-wide analysis study on the whole population.

Results

We identified a specific genetic structure in the FP population reflecting admixture from Asian and European populations. We identified three regions associated with increased DTC risk at 6q24.3, 10p12.2, and 17q21.32. The lead SNPs at these loci showed respective p-values of 1.66 × 10^-7, 2.39 × 10^-7, and 7.19 × 10^-7 and corresponding odds ratios of 2.02, 1.89, and 2.37.

Conclusion

Our study results suggest a role of the loci 6q24.3, 10p12.2 and 17q21.32 in DTC risk. However, a whole genome sequencing approach would be better suited to characterize these factors than genotyping with microarray chip designed for the Caucasian population. Moreover, the functional impact of these three new loci needs to be further explored and validated.

Genetic susceptibility in childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading cause of death due to disease in children. The genetic basis of ALL susceptibility has been supported by its association with certain congenital disorders and, more recently, by several genome-wide association studies (GWAS). These GWAS identified common variants in ARID5B, IKZF1, CEBPE, CDKN2A, PIP4K2A, LHPP and ELK3 influencing ALL risk. However, the risk variants of these SNPs were not validated in all populations, suggesting that some of the loci could be population specific. On the other hand, the currently identified risk SNPs in these genes only account for 19% of the additive heritable risk. This estimation indicates that additional susceptibility variants could be discovered. In this review, we will provide an overview of the most important findings carried out in genetic susceptibility of childhood ALL in all GWAS and subsequent studies and we will also point to future directions that could be explored in the near future.

Association Between PIP4K2A Polymorphisms and Acute Lymphoblastic Leukemia Susceptibility

Acute lymphoblastic leukemia (ALL) is one of the most common pediatric cancers in the world. Several single-nucleotide polymorphisms (SNPs) locating at PIP4K2A locus were identified to be associated with ALL susceptibility through genome-wide association studies, however, followed by inconsistent reports in replication studies. In this study, we conducted a meta-analysis to investigate the association status of the top independent SNPs (rs7088318 and rs4748793) with ALL susceptibility by combining the data from 6 independent studies, totally including 3508 cases and 12,446 controls with multiethnic populations. Consistent association with ALL risk of both SNPs were observed (odds ratio [OR] 1.28 and 1.29, 95% confidence interval [CI] 1.20-1.36 and 1.19-1.40, respectively). Considering clinic characteristics, rs7088318 is more related to patients with African ancestry (OR 1.48, 95% CI 1.21-1.80) and hyperdiploid subtype (OR 1.42, 95% CI 1.25-1.61). Moreover, several SNPs (eg, rs45469096) were identified to be in high linage disequilibrium with rs7088318, and affected PIP4K2A expression in lymphocytes probably by altering the binding affinity of some transcriptional factors. In conclusion, we systematically investigated the relationship between SNPs at PIP4K2A locus and ALL susceptibility, and further found potential causal variant candidates, thus better elucidating the role of PIP4K2A gene in leukemogenesis.