Protective chromosome 1q32 haplotypes mitigate risk for age-related macular degeneration associated with the CFH-CFHR5 and ARMS2/HTRA1 loci

Background Single-variant associations with age-related macular degeneration (AMD), one of the most prevalent causes of irreversible vision loss worldwide, have been studied extensively. However, because of a lack of refinement of these associations, there remains considerable ambiguity regarding what constitutes genetic risk and/or protection for this disease, and how genetic combinations affect this risk. In this study, we consider the two most common and strongly AMD-associated loci, the CFH-CFHR5 region on chromosome 1q32 (Chr1 locus) and ARMS2/HTRA1 gene on chromosome 10q26 (Chr10 locus). Results By refining associations within the CFH-CFHR5 locus, we show that all genetic protection against the development of AMD in this region is described by the combination of the amino acid-altering variant CFH I62V (rs800292) and genetic deletion of CFHR3/1. Haplotypes based on CFH I62V, a CFHR3/1 deletion tagging SNP and the risk variant CFH Y402H are associated with either risk, protection or neutrality for AMD and capture more than 99% of control- and case-associated chromosomes. We find that genetic combinations of CFH-CFHR5 haplotypes (diplotypes) strongly influence AMD susceptibility and that individuals with risk/protective diplotypes are substantially protected against the development of disease. Finally, we demonstrate that AMD risk in the ARMS2/HTRA1 locus is also mitigated by combinations of CFH-CFHR5 haplotypes, with Chr10 risk variants essentially neutralized by protective CFH-CFHR5 haplotypes. Conclusions Our study highlights the importance of considering protective CFH-CFHR5 haplotypes when assessing genetic susceptibility for AMD. It establishes a framework that describes the full spectrum of AMD susceptibility using an optimal set of single-nucleotide polymorphisms with known functional consequences. It also indicates that protective or preventive complement-directed therapies targeting AMD driven by CFH-CFHR5 risk haplotypes may also be effective when AMD is driven by ARMS2/HTRA1 risk variants.

JAK2 Negative Erythrocytosis Associated with JAK2 GGCC_46/1 Haplotype, Calr rs1049481_G, and Normal Erythropoietin Level: Is This a New Entity?

Introduction. The JAK2 haplotype known as "GGCC or 46/1 haplotype" consists of a germline combination of single nucleotide polymorphisms (SNPs) that are inherited together and are frequently associated with the onset of myeloproliferative neoplasms (MPNs) positive for both JAK2 V617 and exon 12 mutations. It has been reported a significant association between JAK2 negative erythrocytosis and the simultaneous occurrence of JAK2 haplotype GGCC_46/1 and CALR rs1049481_G allele, mapping in the 3' UTR of the gene. In the present study, we investigated the presence of JAK2 haplotype GGCC_46/1 and CALR rs1049481_G allele in a more extensive series of erythrocytosis patients and evaluated a possible correlation with serum erythropoietin (EPO) level. Methods. Fifty-nine erythrocytosis patients, diagnosed at our Center from 2009 to 2020, negative for canonical JAK2 mutations, and secondary causes, were included in this study. Forty-nine (83%) out of 59 cases met only two major WHO 2016 diagnostic criteria for polycythemia vera (PV); the remaining 10 cases were "JAK2 negative PV", as they also showed the minor criterion with subnormal serum EPO. Genomic DNA from all patients was extracted from peripheral blood granulocytes and analyzed for the presence of both SNPs. The occurrence of the JAK2 haplotype was investigated by analyzing rs10974944 tagging SNP, using distal JAK2 intron 12 primers (forward: 5'-CTGTGCAGTCCAAACCCATG-3' and reverse: 5'-TTCTCTGCTTGCTAGTGGGT-3'). This amplification generated a PCR product of 272 bp, revealing a C/G substitution by Sanger sequencing. PCR investigated the occurrence of the G/T allele in the SNP rs1049481 in the CALR gene with primers CALR-UTR-F 5'-GACAAGGAGGATGATGAGGACAAA-3' and CALR-UTR-R 5'- AAAAATGAAAGTTCTCGAGTCTCACAGA-3' generating a 205 bp product. In silico data from 2504 healthy individuals of the 1000G Project (1000G) were used as a control group. Fisher's exact test was used to compare the differences of both SNPs and the frequency of their alleles between cases and controls, respectively; the c-square test was employed for evaluating the distribution of JAK2 GGCC haplotype in erythrocytosis patients and controls. Results. Thirty-eight (64.4%) and 21 (35.6%) cases resulted in being positive and negative for the JAK2 GGCC haplotype, respectively. The JAK2 GGCC haplotype occurred to be associated with erythrocytosis as a statistically significant difference in frequency was detected as respect to 2504 healthy individuals from the 1000G Project (p=0.0013). This finding was also confirmed considering the Genome Aggregation Database (gnomAD v2.1.1, https://gnomad.broadinstitute.org/)(p=0.0024). The association was also demonstrated in terms of allelic frequency (p=0.0131) and genotype distribution (p=0.0030). Regarding CALR rs1049481 SNP, a significant difference in the CALR rs1049481_G allelic rate was confirmed in our cohort compared to 1000G controls (p=0.0360). Overall, the association between JAK2 GGCC haplotype and CALR rs1049481_G was observed in 28/59 (47.5%) erythrocytosis cases compared to healthy individuals (628/2504, 25%), and this difference resulted in being statistically significant (p=0.0002). Based on the EPO level, erythrocytosis patients were divided into two groups: normal (49 cases) or subnormal (10 cases). Interestingly, the simultaneous presence of JAK2 GGCC haplotype and CALR rs1049481_G was statistically significantly associated with the erythrocytosis group showing normal EPO (p=0.0133). Conclusions. This study suggests that the JAK2 GGCC haplotype and the presence of the CALR rs1049481_G allele were significantly associated with erythrocytosis cases, negative for canonical JAK2 mutations. Our findings are in line with recent literature evidence showing that germline predisposition factors such as SNPs and haplotypes may play a crucial role in MPN pathogenesis. Moreover, this study shows that patients showing two major WHO 2016 diagnostic criteria (erythrocytosis and panmyelosis) without JAK2 mutations and with normal EPO levels can benefit from the search for germline polymorphisms combination in JAK2 and CALR driver genes for a better diagnostic classification. Therefore, the presence of these polymorphisms could represent a novel minor criterion for the diagnosis of "JAK2 negative PV". Disclosures No relevant conflicts of interest to declare.

Polymorphisms in the Angiogenesis-Related Genes EFNB2, MMP2 and JAG1 Are Associated with Survival of Colorectal Cancer Patients

An individual’s inherited genetic variation may contribute to the ‘angiogenic switch’, which is essential for blood supply and tumor growth of microscopic and macroscopic tumors. Polymorphisms in angiogenesis-related genes potentially predispose to colorectal cancer (CRC) or affect the survival of CRC patients. We investigated the association of 392 single nucleotide polymorphisms (SNPs) in 33 angiogenesis-related genes with CRC risk and survival of CRC patients in 1754 CRC cases and 1781 healthy controls within DACHS (Darmkrebs: Chancen der Verhütung durch Screening), a German population-based case-control study. Odds ratios and 95% confidence intervals (CI) were estimated from unconditional logistic regression to test for genetic associations with CRC risk. The Cox proportional hazard model was used to estimate hazard ratios (HR) and 95% CIs for survival. Multiple testing was adjusted for by a false discovery rate. No variant was associated with CRC risk. Variants in EFNB2, MMP2 and JAG1 were significantly associated with overall survival. The association of the EFNB2 tagging SNP rs9520090 (p < 0.0001) was confirmed in two validation datasets (p-values: 0.01 and 0.05). The associations of the tagging SNPs rs6040062 in JAG1 (p-value 0.0003) and rs2241145 in MMP2 (p-value 0.0005) showed the same direction of association with overall survival in the first and second validation sets, respectively, although they did not reach significance (p-values: 0.09 and 0.25, respectively). EFNB2, MMP2 and JAG1 are known for their functional role in angiogenesis and the present study points to novel evidence for the impact of angiogenesis-related genetic variants on the CRC outcome.

Analysis of common and rare VPS13C variants in late-onset Parkinson disease

ObjectiveWe aimed to study the role of coding VPS13C variants in a large cohort of patients with late-onset Parkinson disease (PD) (LOPD).MethodsVPS13C and its untranslated regions were sequenced using targeted next-generation sequencing in 1,567 patients with PD and 1,667 controls from 3 cohorts. Association tests of rare potential homozygous and compound heterozygous variants and burden tests for rare heterozygous variants were performed. Common variants were analyzed using logistic regression adjusted for age and sex in each of the cohorts, followed by a meta-analysis.ResultsNo biallelic carriers of rare VPS13C variants were found among patients, and 2 carriers of compound heterozygous variants were found in 2 controls. There was no statistically significant burden of rare (minor allele frequency [MAF] <1%) or very rare (MAF <0.1%) coding VPS13C variants in PD. A VPS13C haplotype including the p.R153H-p.I398I-p.I1132V-p.Q2376Q variants was nominally associated with a reduced risk for PD (meta-analysis of the tagging SNP p.I1132V [odds ratio = 0.48, 95% confidence interval = 0.28–0.82, p = 0.0052]). This haplotype was not in linkage disequilibrium with the known genome-wide association study top hit.ConclusionsOur results do not support a role for rare heterozygous or biallelic VPS13C variants in LOPD. Additional genetic replication and functional studies are needed to examine the role of the haplotype identified here associated with reduced risk for PD.

Analysis of common and rare VPS13C variants in late onset Parkinson disease

ObjectiveWe aimed to study the role of coding VPS13C variants in a large cohort of late-onset PD (LOPD) patients.MethodsVPS13C and its untranslated regions were sequenced using targeted next-generation sequencing in 1,567 PD patients and 1,667 controls from 3 cohorts. Association tests of rare potential homozygous and compound heterozygous variants and burden tests for rare heterozygous variants were performed. Common variants were analyzed using logistic regression adjusted for age and sex in each of the cohorts, followed by a meta-analysis.ResultsNo bi-allelic carriers of rare VPS13C variants were found among patients and two carriers of compound heterozygous variants were found in two controls. There was no statistically significant burden of rare (MAF<1%) or very rare (MAF<0.1%) coding VPS13C variants in PD. A VPS13C haplotype including the p.R153H-p.I398I-p.I1132V-p.Q2376Q variants was nominally associated with a reduced risk for PD (meta-analysis of the tagging SNP p.I1132V (OR=0.48, 95%CI=0.28-0.82, p=0.0052). This haplotype was not in linkage disequilibrium (LD) with the known genome-wide association study (GWAS) top hit.ConclusionsOur results do not support a role for rare heterozygous or bi-allelic VPS13C variants in LOPD. Additional genetic replication and functional studies are needed to examine the role of the haplotype identified here associated with reduced risk for PD.

A novel SNP-set analytical method without distinguishing common variants or rare variants in genome-wide association study

Single nucleotide polymorphism (SNP)-set analysis in genome-wide association studies (GWASs) has become a hot topic. Most existing SNP-set analystic methods are designed and work well according to the different natures of common or rare variants and associated diseases. But the information that the disease associated variants are common or rare cannot be gained in advance. Therefore, in this research, we proposed a new and powerful weighted function method without distinguishing common or rare variants to select tagging SNP-set. We applied our selection method to sequence kernel association test (SKAT) and compared the power with some existing methods. The simulation results showed that our method has higher power not only than SKAT in un-weighted case, but also than SKAT in other weighted functions. Moreover, the power is improved significantly when the minor allele frequency (MAF) of causal SNP is relatively small.