Approaches to determine clinical significance of genetic variants

Relation Between Genetic Factors and Frailty in Older Adults

OBJECTIVES

Frailty is a geriatric syndrome that identifies individuals at higher risk of disability, institutionalization, and death. We previously reported that frailty is related to oxidative stress and cognitive impairment-related biomarkers. The aim of this study was to determine whether frailty is associated with genetic variants.

DESIGN

Longitudinal population-based cohort of 2488 community-dwelling people from Toledo, Spain, aged 65 years or older.

SETTING AND PARTICIPANTS

We obtained blood samples from 78 individuals with frailty and 74 nonfrail individuals who were nonfrail (according to Fried criteria) from the Toledo Study of Healthy Ageing and extracted DNA using the Chemagic DNA blood kit.

MEASURES

Sample genotyping was carried out by means of Axiom Exome 319 Genotyping Array (Thermo Fisher Scientific), which contains 295,988 markers [single-nucleotide polymorphisms (SNPs) and rare variants], and transferred to the GeneTitan Instrument (Affymetrix).

RESULTS

We found 15 SNPs (P < .001), 18 genes (P < .005), and 4 pathways (P < .05) related to cytokine-cytokine receptor interaction, natural killer cell-mediated cytotoxicity, regulation of autophagy, and renin-angiotensin system as the most strongly associated with frailty.

CONCLUSIONS/IMPLICATIONS

The specific genetic features related to energy metabolism, biological processes regulation, cognition, and inflammation highlighted by this preliminary analysis offer useful insights for finding biologically meaningful biomarkers of frailty that allow early diagnosis and treatment. Further research is needed to confirm our novel findings in a larger population. Indeed, the EU-funded FRAILOMICS research effort will address this question.

[Identification of single nucleotide polymorphisms related to frailty]

INTRODUCTION

The search for biomarkers that can lead to the early diagnosis and thus, early treatment of frailty, has become one of the main challenges facing the geriatric scientific community. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) related to frailty.

MATERIAL AND METHODS

The study was conducted on 152 subjects from the Toledo Study for Healthy Aging (65 to 95 years of age), and classified as frail (n=78), and non-frail (n=74), according to Fried's criteria. After blood collection, DNA was isolated and amplified for the analysis of SNPs using Axiom^TM Genotyping technology (Affymetrix). Statistical analyses were performed using the Plink program and library SNPassoc.

RESULTS

The results of the study showed 15 SNPs with a P<.001. Those SNPs involved in processes related to frailty, such as energy metabolism, regulation of biological processes, cell motility and integrity, and cognition are highlighted.

CONCLUSIONS

These results suggest that the genetic variations identified in frail individuals that are involved in biological processes related to frailty may be considered as biomarkers for the early detection of frailty.

Bioinformatic processing to identify single nucleotide polymorphism that potentially affect Ape1 function

Inactivation of DNA damage response mechanisms is associated with several disease syndromes, including cancer, aging and neurodegeneration. A major corrective pathway for alkylation or oxidative DNA damage is base excision repair (BER). As part of an effort to identify variation in DNA repair genes, we used the expressed sequence tag (EST) database to identify amino acid variation in Ape1, an essential gene in the BER repair pathway. Nucleotide substitutions were considered valid only if the amino acid changes were observed in at least two independent EST sequencing runs (i.e. two independent EST reports). In total eighty amino acid variants were identified for the Ape1 gene. Using software tools SIFT and PolyPhen, which predict impacts of amino acid substitutions on protein structure and function, twenty-six variants were predicted by both algorithms to be deleterious to protein function. Majority of these intolerant mutations such as V206C and F240S, lie within the core of the protein and may affect the stability and folding of Ape1, or in the case of N212H, N212K, and Y171N, are close to the enzyme's active site and could drastically affect its function. A few of the intolerant mutations, i.e., G178V and E217R, are surface residues and are far from the active site, and as such, the predicted effect on Ape1 stability or function is not evident. These variants are reagents for further protein function studies and molecular epidemiology studies of cancer susceptibility.

Single nucleotide polymorphisms in DNA repair genes XRCC1 and APEX1 in progression and survival of primary cutaneous melanoma patients

Single nucleotide polymorphisms, besides influencing susceptibility can potentially alter progression and survival in melanoma patients. In this study we evaluated the association of polymorphisms in the base-excision repair genes XRCC1 and APEX1 with overall survival (OS), metastasis-free survival (MFS) and survival following the first metastasis (SFM) in patients with cutaneous melanoma. We genotyped the D148E APEX1, -77 T>C XRCC1, R280H XRCC1, and R399Q XRCC1 polymorphisms in 400 German melanoma patients (Tx, N0, M0) using an allelic discrimination method. The results were correlated with the patient follow-up parameters. The significant association detected between the R399Q XRCC1 polymorphism and MFS was also evaluated in 529 Spanish melanoma patients. In a Kaplan-Meier survival model the AA genotype of the polymorphism showed a median OS of 24.4 years compared to 11.5 years for two other genotypes. Similarly patients with the AA genotype showed median MFS of 20.9 years compared to 5.3 years for two other genotypes. In a multivariate Cox proportional hazard model, the AA genotype was associated with a hazard ratio (HR) of 0.40, 95% (CI 0.21-0.78, p=0.007) for MFS and 0.32 (95% CI 0.11-0.90, p=0.03) for OS in 400 German melanoma patients. The decreased risk of metastasis was confirmed by adding 529 Spanish melanoma patients with a combined HR of 0.40 (95% CI 0.24-0.68, p=0.0006). A significant association with SFM was also found for -77 T>C XRCC1 (HR 1.73, 95% CI 1.02-2.94, p=0.04). Our results show that non-synonymous variants or those located in potential regulatory regions of DNA repair genes probably influence the disease outcome in melanoma patients and have potentially significant implications for patient surveillance and tailored treatment.

Can risk of radiotherapy-induced normal tissue complications be predicted from genetic profiles?

Over the last decade, increasing efforts have been taken to establish associations between various genetic germline alterations and risk of normal tissue complications after radiotherapy. Though the studies have been relatively small and methodologically heterogeneous, preliminary indications have been provided that single nucleotide polymorphisms in the genes TGFB1 and ATM may modulate risk of particularly late toxicity. In addition, rare ATM alterations may enhance complication susceptibility. Nevertheless, we are still far from having an exhaustive understanding of the genetics that may underlie differences in clinical normal tissue radiosensitivity. Recent technical advances and emerging insights to the structure of inter-individual genetic variation open up unprecedented opportunities to dissect the molecular and genetic basis of normal tissue radiosensitivity. However, to fully exploit these new possibilities well-planed large-scale clinical studies are mandatory. Currently, international initiatives are taken to establish the bio banks and databases needed for this task.

Allelic spectrum of the natural variation in CRP

With the recent completion of the International HapMap Project, many tools are in hand for genetic association studies seeking to test the common variant/common disease hypothesis. In contrast, very few tools and resources are in place for genotype–phenotype studies hypothesizing that rare variation has a large impact on the phenotype of interest. To create these tools for rare variant/common disease studies, much interest is being generated towards investing in re-sequencing either large sample sizes of random chromosomes or smaller sample sizes of patients with extreme phenotypes. As a case study for rare variant discovery in random chromosomes, we have re-sequenced ~1,000 chromosomes representing diverse populations for the gene C-reactive protein (CRP). CRP is an important gene in the fields of cardiovascular and inflammation genetics, and its size (~2 kb) makes it particularly amenable medical or deep re-sequencing. With these data, we explore several issues related to the present-day candidate gene association study including the benefits of complete SNP discovery, the effects of tagSNP selection across diverse populations, and completeness of dbSNP for CRP. Also, we show that while deep re-sequencing uncovers potentially medically relevant coding SNPs, these SNPs are fleetingly rare when genotyped in a population-based survey of 7,000 Americans (NHANES III). Collectively, these data suggest that several different types re-sequencing and genotyping approaches may be required to fully understand the complete spectrum of alleles that impact human phenotypes.